Starting phenix.real_space_refine on Thu Aug 6 06:32:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzz_41775/08_2026/8tzz_41775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzz_41775/08_2026/8tzz_41775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tzz_41775/08_2026/8tzz_41775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzz_41775/08_2026/8tzz_41775.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tzz_41775/08_2026/8tzz_41775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzz_41775/08_2026/8tzz_41775.map" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 144 5.49 5 Mg 5 5.21 5 S 22 5.16 5 C 8375 2.51 5 N 2458 2.21 5 O 3008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 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: 14012 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 10962 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1336, 10951 Classifications: {'peptide': 1336} Link IDs: {'PTRANS': 35, 'TRANS': 1300} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 1336, 10951 Classifications: {'peptide': 1336} Link IDs: {'PTRANS': 35, 'TRANS': 1300} Chain breaks: 3 bond proxies already assigned to first conformer: 11134 Chain: "B" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2103 Classifications: {'RNA': 98} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 53, 'rna3p_pyr': 34} Link IDs: {'rna2p': 10, 'rna3p': 87} Chain: "C" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "c" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 341 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "D" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "c" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 783 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 783 " occ=0.50 Time building chain proxies: 4.77, per 1000 atoms: 0.34 Number of scatterers: 14012 At special positions: 0 Unit cell: (87.465, 129.115, 120.785, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 144 15.00 Mg 5 11.99 O 3008 8.00 N 2458 7.00 C 8375 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: 1.11 Conformation dependent library (CDL) restraints added in 568.0 milliseconds 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2548 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 8 sheets defined 55.5% alpha, 7.9% beta 49 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.055A pdb=" N LYS A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (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 144 Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 175 through 179 removed outlier: 3.613A pdb=" N ASN A 178 " --> pdb=" O ASN A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.953A pdb=" N GLN A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 238 through 244 removed outlier: 3.847A pdb=" N ALA A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 290 through 306 removed outlier: 4.414A pdb=" N LYS A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN A 295 " --> pdb=" O LEU A 291 " (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 383 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: 3.524A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.038A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.863A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) 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 removed outlier: 3.593A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 553 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.589A 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 637 Processing helix chain 'A' and resid 638 through 643 removed outlier: 4.965A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 652 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 698 Processing helix chain 'A' and resid 703 through 711 Processing helix chain 'A' and resid 719 through 727 Processing helix chain 'A' and resid 732 through 751 removed outlier: 4.059A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 779 through 792 removed outlier: 3.751A pdb=" N GLY A 787 " --> pdb=" O AARG A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 804 through 807 Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 829 through 834 removed outlier: 5.608A pdb=" N SER A 834 " --> pdb=" O ASN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 860 through 866 Processing helix chain 'A' and resid 872 through 889 removed outlier: 5.191A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.412A 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 902 through 906 removed outlier: 3.797A pdb=" N GLY A 906 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 Processing helix chain 'A' and resid 917 through 940 removed outlier: 4.143A pdb=" N LEU A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 922 " --> pdb=" O LYS A 918 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 981 through 1001 Processing helix chain 'A' and resid 1002 through 1005 removed outlier: 3.682A pdb=" N GLU A1005 " --> pdb=" O PRO A1002 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1002 through 1005' Processing helix chain 'A' and resid 1033 through 1042 removed outlier: 3.604A pdb=" N ILE A1042 " --> pdb=" O PHE A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1046 removed outlier: 3.526A pdb=" N PHE A1046 " --> pdb=" O MET A1043 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1043 through 1046' 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 removed outlier: 3.721A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1240 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1310 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 4.026A pdb=" N THR A1316 " --> pdb=" O LEU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.672A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 959 removed outlier: 7.313A pdb=" N TYR A 5 " --> pdb=" O ASN A 758 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N VAL A 760 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N LEU A 9 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.685A pdb=" N GLU A1357 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA4, first strand: chain 'A' and resid 836 through 840 Processing sheet with id=AA5, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 4.233A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 5.369A pdb=" N LYS A1156 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU A1150 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LYS A1158 " --> pdb=" O LYS A1148 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS A1148 " --> pdb=" O LYS A1158 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL A1160 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL A1146 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU A1162 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU A1144 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A1164 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER A1142 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1324 through 1325 487 hydrogen bonds defined for protein. 1411 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 115 hydrogen bonds 218 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2075 1.31 - 1.44: 4532 1.44 - 1.56: 7627 1.56 - 1.69: 284 1.69 - 1.81: 42 Bond restraints: 14560 Sorted by residual: bond pdb=" CA SER A1216 " pdb=" CB SER A1216 " ideal model delta sigma weight residual 1.530 1.457 0.073 1.69e-02 3.50e+03 1.87e+01 bond pdb=" C PRO A1137 " pdb=" O PRO A1137 " ideal model delta sigma weight residual 1.233 1.186 0.047 1.12e-02 7.97e+03 1.76e+01 bond pdb=" N LEU A1214 " pdb=" CA LEU A1214 " ideal model delta sigma weight residual 1.456 1.502 -0.046 1.22e-02 6.72e+03 1.40e+01 bond pdb=" C3' DG C 8 " pdb=" O3' DG C 8 " ideal model delta sigma weight residual 1.435 1.480 -0.045 1.30e-02 5.92e+03 1.21e+01 bond pdb=" O3' DA D 40 " pdb=" P DG D 41 " ideal model delta sigma weight residual 1.607 1.647 -0.040 1.20e-02 6.94e+03 1.14e+01 ... (remaining 14555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 19365 2.13 - 4.25: 811 4.25 - 6.38: 77 6.38 - 8.50: 13 8.50 - 10.63: 5 Bond angle restraints: 20271 Sorted by residual: angle pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sigma weight residual 118.80 124.96 -6.16 1.10e+00 8.26e-01 3.14e+01 angle pdb=" N ALA A1217 " pdb=" CA ALA A1217 " pdb=" C ALA A1217 " ideal model delta sigma weight residual 113.02 105.12 7.90 1.49e+00 4.50e-01 2.81e+01 angle pdb=" O4' DT c 25 " pdb=" C4' DT c 25 " pdb=" C3' DT c 25 " ideal model delta sigma weight residual 106.00 103.03 2.97 6.00e-01 2.78e+00 2.44e+01 angle pdb=" O2 C B 70 " pdb=" C2 C B 70 " pdb=" N3 C B 70 " ideal model delta sigma weight residual 121.90 118.52 3.38 7.00e-01 2.04e+00 2.34e+01 angle pdb=" O4' DC c 26 " pdb=" C4' DC c 26 " pdb=" C3' DC c 26 " ideal model delta sigma weight residual 106.00 103.14 2.86 6.00e-01 2.78e+00 2.27e+01 ... (remaining 20266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.57: 8312 33.57 - 67.14: 478 67.14 - 100.70: 40 100.70 - 134.27: 1 134.27 - 167.84: 5 Dihedral angle restraints: 8836 sinusoidal: 4901 harmonic: 3935 Sorted by residual: dihedral pdb=" O4' U B 59 " pdb=" C1' U B 59 " pdb=" N1 U B 59 " pdb=" C2 U B 59 " ideal model delta sinusoidal sigma weight residual 200.00 32.16 167.84 1 1.50e+01 4.44e-03 8.44e+01 dihedral pdb=" O4' C B 70 " pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sinusoidal sigma weight residual 200.00 33.20 166.80 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" CA TYR A1326 " pdb=" C TYR A1326 " pdb=" N PHE A1327 " pdb=" CA PHE A1327 " ideal model delta harmonic sigma weight residual 180.00 -153.09 -26.91 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 8833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2054 0.089 - 0.178: 250 0.178 - 0.266: 16 0.266 - 0.355: 1 0.355 - 0.444: 1 Chirality restraints: 2322 Sorted by residual: chirality pdb=" P DT c 23 " pdb=" OP1 DT c 23 " pdb=" OP2 DT c 23 " pdb=" O5' DT c 23 " both_signs ideal model delta sigma weight residual True 2.34 -2.78 -0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CA LYS A1222 " pdb=" N LYS A1222 " pdb=" C LYS A1222 " pdb=" CB LYS A1222 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA ILE A1331 " pdb=" N ILE A1331 " pdb=" C ILE A1331 " pdb=" CB ILE A1331 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 2319 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 730 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO A 731 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 731 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 731 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1228 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO A1229 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A1229 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A1229 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 549 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C VAL A 549 " 0.035 2.00e-02 2.50e+03 pdb=" O VAL A 549 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP A 550 " -0.012 2.00e-02 2.50e+03 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 3 2.13 - 2.82: 4064 2.82 - 3.51: 19523 3.51 - 4.21: 35299 4.21 - 4.90: 57477 Nonbonded interactions: 116366 Sorted by model distance: nonbonded pdb="MG MG A1401 " pdb="MG MG A1402 " model vdw 1.432 1.300 nonbonded pdb=" OP2 DT c 23 " pdb="MG MG c 101 " model vdw 1.995 2.170 nonbonded pdb=" OP2 A B 65 " pdb="MG MG B 101 " model vdw 2.013 2.170 nonbonded pdb=" O3' DG C 22 " pdb="MG MG c 101 " model vdw 2.137 2.170 nonbonded pdb=" OG SER A 860 " pdb=" NH1 ARG A 864 " model vdw 2.138 3.120 ... (remaining 116361 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.080 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 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 0.073 14560 Z= 0.441 Angle : 0.922 10.629 20271 Z= 0.625 Chirality : 0.058 0.444 2322 Planarity : 0.004 0.064 2066 Dihedral : 18.892 167.840 6288 Min Nonbonded Distance : 1.432 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.66 % Allowed : 0.25 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.22), residues: 1331 helix: 0.01 (0.20), residues: 633 sheet: -0.54 (0.47), residues: 128 loop : -0.67 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A1078 TYR 0.026 0.003 TYR A1326 PHE 0.018 0.002 PHE A 643 TRP 0.011 0.002 TRP A1136 HIS 0.009 0.002 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.44 (14560) covalent geometry : angle 0.92171 / 0.63 (20271) hydrogen bonds : bond 0.17116 / 11.68 ( 602) hydrogen bonds : angle 7.72888 / 5.50 ( 1629) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.313 Fit side-chains REVERT: A 221 ARG cc_start: 0.7705 (mtt180) cc_final: 0.7358 (ttt-90) REVERT: A 311 GLU cc_start: 0.5489 (mp0) cc_final: 0.5280 (mp0) REVERT: A 383 MET cc_start: 0.6979 (ttt) cc_final: 0.6146 (ttt) REVERT: A 919 ARG cc_start: 0.8498 (ttp-170) cc_final: 0.8127 (ttp80) REVERT: A 1006 SER cc_start: 0.8563 (t) cc_final: 0.8224 (m) REVERT: A 1303 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7576 (ttp80) outliers start: 8 outliers final: 1 residues processed: 99 average time/residue: 0.1269 time to fit residues: 17.9661 Evaluate side-chains 63 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1332 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN A 595 HIS ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.106140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.079050 restraints weight = 61233.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.080875 restraints weight = 30220.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.081833 restraints weight = 19559.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.081841 restraints weight = 15732.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.082185 restraints weight = 14751.492| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14560 Z= 0.158 Angle : 0.641 11.681 20271 Z= 0.354 Chirality : 0.045 0.319 2322 Planarity : 0.004 0.052 2066 Dihedral : 20.172 173.516 3432 Min Nonbonded Distance : 1.384 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.91 % Allowed : 3.49 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.22), residues: 1331 helix: 0.43 (0.20), residues: 640 sheet: -0.04 (0.47), residues: 126 loop : -0.63 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1078 TYR 0.025 0.002 TYR A1326 PHE 0.028 0.002 PHE A1045 TRP 0.010 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (14560) covalent geometry : angle 0.64147 / 0.35 (20271) hydrogen bonds : bond 0.06660 / 4.42 ( 602) hydrogen bonds : angle 5.22373 / 3.77 ( 1629) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.408 Fit side-chains REVERT: A 919 ARG cc_start: 0.8456 (ttp-170) cc_final: 0.8130 (ttp80) outliers start: 11 outliers final: 4 residues processed: 75 average time/residue: 0.1097 time to fit residues: 12.0395 Evaluate side-chains 65 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 738 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 0.0060 chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 140 optimal weight: 20.0000 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 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 = 0.3658 r_free = 0.3658 target = 0.106325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.079732 restraints weight = 58277.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.081271 restraints weight = 28711.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.082349 restraints weight = 18807.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.082738 restraints weight = 15753.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.082938 restraints weight = 14486.761| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14560 Z= 0.144 Angle : 0.557 7.328 20271 Z= 0.313 Chirality : 0.042 0.251 2322 Planarity : 0.004 0.097 2066 Dihedral : 19.956 170.202 3430 Min Nonbonded Distance : 1.313 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.58 % Allowed : 5.73 % Favored : 93.69 % 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: 0.05 (0.23), residues: 1331 helix: 0.62 (0.20), residues: 646 sheet: 0.26 (0.50), residues: 117 loop : -0.60 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1078 TYR 0.040 0.001 TYR A1201 PHE 0.022 0.001 PHE A1045 TRP 0.006 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (14560) covalent geometry : angle 0.55720 / 0.31 (20271) hydrogen bonds : bond 0.05528 / 3.59 ( 602) hydrogen bonds : angle 4.92126 / 3.55 ( 1629) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.318 Fit side-chains REVERT: A 221 ARG cc_start: 0.6567 (ptm160) cc_final: 0.6354 (ptm160) outliers start: 7 outliers final: 5 residues processed: 78 average time/residue: 0.1176 time to fit residues: 13.4426 Evaluate side-chains 65 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1038 PHE Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 77 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 76 optimal weight: 0.0020 chunk 135 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN A 863 ASN ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.107058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.080733 restraints weight = 53966.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.082069 restraints weight = 27519.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.083076 restraints weight = 18298.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.083390 restraints weight = 14742.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.083511 restraints weight = 14029.112| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14560 Z= 0.130 Angle : 0.527 6.765 20271 Z= 0.298 Chirality : 0.041 0.275 2322 Planarity : 0.004 0.054 2066 Dihedral : 19.754 166.091 3430 Min Nonbonded Distance : 1.241 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.75 % Allowed : 7.31 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.23), residues: 1331 helix: 0.74 (0.20), residues: 646 sheet: 0.30 (0.49), residues: 117 loop : -0.54 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1078 TYR 0.016 0.001 TYR A1265 PHE 0.022 0.001 PHE A1045 TRP 0.006 0.001 TRP A1136 HIS 0.012 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (14560) covalent geometry : angle 0.52727 / 0.30 (20271) hydrogen bonds : bond 0.04905 / 3.14 ( 602) hydrogen bonds : angle 4.72448 / 3.41 ( 1629) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.472 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 73 average time/residue: 0.1173 time to fit residues: 12.4152 Evaluate side-chains 67 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1038 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 125 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 0.3980 chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.106109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.079743 restraints weight = 45681.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.081559 restraints weight = 25419.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.082276 restraints weight = 16688.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.082432 restraints weight = 13798.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.082593 restraints weight = 13222.560| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14560 Z= 0.159 Angle : 0.542 11.069 20271 Z= 0.302 Chirality : 0.041 0.276 2322 Planarity : 0.004 0.048 2066 Dihedral : 19.679 165.606 3430 Min Nonbonded Distance : 1.165 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.75 % Allowed : 8.14 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.23), residues: 1331 helix: 0.75 (0.20), residues: 650 sheet: 0.36 (0.50), residues: 117 loop : -0.60 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1078 TYR 0.013 0.001 TYR A1010 PHE 0.031 0.002 PHE A 606 TRP 0.007 0.001 TRP A 883 HIS 0.006 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (14560) covalent geometry : angle 0.54158 / 0.30 (20271) hydrogen bonds : bond 0.04898 / 3.15 ( 602) hydrogen bonds : angle 4.67969 / 3.38 ( 1629) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.352 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 66 average time/residue: 0.1217 time to fit residues: 11.6853 Evaluate side-chains 65 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1038 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 96 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 0.1980 chunk 39 optimal weight: 4.9990 chunk 10 optimal weight: 0.0980 chunk 142 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.104817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.078349 restraints weight = 51360.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.079863 restraints weight = 25924.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.080732 restraints weight = 17517.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.080906 restraints weight = 15049.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.081122 restraints weight = 14399.602| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14560 Z= 0.212 Angle : 0.586 6.642 20271 Z= 0.322 Chirality : 0.043 0.280 2322 Planarity : 0.004 0.050 2066 Dihedral : 19.664 165.972 3430 Min Nonbonded Distance : 1.074 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.66 % Allowed : 8.80 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.23), residues: 1331 helix: 0.65 (0.20), residues: 656 sheet: -0.06 (0.47), residues: 125 loop : -0.53 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 139 TYR 0.013 0.002 TYR A 136 PHE 0.023 0.002 PHE A 606 TRP 0.005 0.001 TRP A1074 HIS 0.007 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 (14560) covalent geometry : angle 0.58633 / 0.32 (20271) hydrogen bonds : bond 0.05116 / 3.32 ( 602) hydrogen bonds : angle 4.73071 / 3.43 ( 1629) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.307 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 63 average time/residue: 0.1148 time to fit residues: 10.6615 Evaluate side-chains 65 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1038 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 142 optimal weight: 20.0000 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 124 optimal weight: 0.2980 chunk 121 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.106302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.079540 restraints weight = 48199.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.081157 restraints weight = 25949.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.082140 restraints weight = 16492.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.082363 restraints weight = 13777.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.082524 restraints weight = 13087.202| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14560 Z= 0.134 Angle : 0.514 6.371 20271 Z= 0.291 Chirality : 0.040 0.287 2322 Planarity : 0.004 0.084 2066 Dihedral : 19.581 164.778 3430 Min Nonbonded Distance : 1.148 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.66 % Allowed : 9.14 % Favored : 90.20 % 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: 0.32 (0.23), residues: 1331 helix: 0.85 (0.20), residues: 651 sheet: 0.09 (0.49), residues: 123 loop : -0.41 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1078 TYR 0.011 0.001 TYR A 155 PHE 0.023 0.001 PHE A 606 TRP 0.006 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (14560) covalent geometry : angle 0.51405 / 0.29 (20271) hydrogen bonds : bond 0.04707 / 3.03 ( 602) hydrogen bonds : angle 4.60266 / 3.34 ( 1629) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.385 Fit side-chains REVERT: A 822 MET cc_start: 0.8060 (mmm) cc_final: 0.7072 (mmm) outliers start: 8 outliers final: 6 residues processed: 60 average time/residue: 0.1035 time to fit residues: 9.3996 Evaluate side-chains 63 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1038 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 78 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 140 optimal weight: 20.0000 chunk 73 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.107459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.081645 restraints weight = 39198.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.083501 restraints weight = 22570.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.084755 restraints weight = 14606.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.084754 restraints weight = 12213.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.084862 restraints weight = 12015.207| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14560 Z= 0.118 Angle : 0.491 5.964 20271 Z= 0.278 Chirality : 0.039 0.295 2322 Planarity : 0.004 0.081 2066 Dihedral : 19.451 163.637 3430 Min Nonbonded Distance : 1.151 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.42 % Allowed : 9.14 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1331 helix: 0.99 (0.20), residues: 654 sheet: 0.11 (0.49), residues: 123 loop : -0.33 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1078 TYR 0.011 0.001 TYR A1010 PHE 0.019 0.001 PHE A 606 TRP 0.007 0.001 TRP A 883 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (14560) covalent geometry : angle 0.49065 / 0.28 (20271) hydrogen bonds : bond 0.04396 / 2.81 ( 602) hydrogen bonds : angle 4.47450 / 3.25 ( 1629) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.426 Fit side-chains REVERT: A 822 MET cc_start: 0.8086 (mmm) cc_final: 0.7173 (mmm) outliers start: 5 outliers final: 5 residues processed: 68 average time/residue: 0.1238 time to fit residues: 12.3847 Evaluate side-chains 58 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 1038 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 74 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.106248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.079540 restraints weight = 67176.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.081126 restraints weight = 32634.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.082054 restraints weight = 19575.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.082516 restraints weight = 16530.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.082701 restraints weight = 15203.211| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14560 Z= 0.154 Angle : 0.528 8.231 20271 Z= 0.292 Chirality : 0.040 0.293 2322 Planarity : 0.004 0.107 2066 Dihedral : 19.451 163.971 3430 Min Nonbonded Distance : 1.101 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.83 % Allowed : 9.97 % Favored : 89.20 % 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: 0.41 (0.23), residues: 1331 helix: 0.95 (0.20), residues: 653 sheet: -0.01 (0.49), residues: 125 loop : -0.37 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 925 TYR 0.013 0.001 TYR A1010 PHE 0.018 0.001 PHE A1045 TRP 0.005 0.001 TRP A1074 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (14560) covalent geometry : angle 0.52778 / 0.29 (20271) hydrogen bonds : bond 0.04538 / 2.92 ( 602) hydrogen bonds : angle 4.50268 / 3.27 ( 1629) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.363 Fit side-chains REVERT: A 311 GLU cc_start: 0.5251 (mp0) cc_final: 0.4921 (mp0) REVERT: A 822 MET cc_start: 0.8034 (mmm) cc_final: 0.7122 (mmm) REVERT: A 879 MET cc_start: 0.7024 (mmt) cc_final: 0.6278 (mmp) outliers start: 10 outliers final: 8 residues processed: 63 average time/residue: 0.1061 time to fit residues: 10.2300 Evaluate side-chains 62 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1013 TYR Chi-restraints excluded: chain A residue 1038 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 84 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 88 optimal weight: 0.0870 chunk 124 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 3 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 108 optimal weight: 0.8980 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 190 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 = 0.3670 r_free = 0.3670 target = 0.107397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.080997 restraints weight = 48217.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.082282 restraints weight = 25822.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.083236 restraints weight = 17289.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.083456 restraints weight = 14331.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.083726 restraints weight = 13664.179| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14560 Z= 0.114 Angle : 0.502 7.609 20271 Z= 0.282 Chirality : 0.039 0.298 2322 Planarity : 0.003 0.054 2066 Dihedral : 19.414 163.038 3430 Min Nonbonded Distance : 1.151 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.66 % Allowed : 10.13 % Favored : 89.20 % 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: 0.53 (0.23), residues: 1331 helix: 1.05 (0.20), residues: 653 sheet: 0.07 (0.50), residues: 123 loop : -0.32 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1078 TYR 0.014 0.001 TYR A1010 PHE 0.017 0.001 PHE A1045 TRP 0.006 0.001 TRP A 18 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (14560) covalent geometry : angle 0.50209 / 0.28 (20271) hydrogen bonds : bond 0.04358 / 2.78 ( 602) hydrogen bonds : angle 4.44223 / 3.22 ( 1629) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.456 Fit side-chains REVERT: A 311 GLU cc_start: 0.5215 (mp0) cc_final: 0.4892 (mp0) REVERT: A 822 MET cc_start: 0.7990 (mmm) cc_final: 0.7099 (mmm) REVERT: A 879 MET cc_start: 0.7015 (mmt) cc_final: 0.6268 (mmp) outliers start: 8 outliers final: 7 residues processed: 60 average time/residue: 0.1214 time to fit residues: 11.2419 Evaluate side-chains 62 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1038 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 70 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 56 optimal weight: 0.0470 chunk 106 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 103 optimal weight: 0.0370 chunk 87 optimal weight: 0.8980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 190 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 = 0.3685 r_free = 0.3685 target = 0.108430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.081639 restraints weight = 68294.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.083241 restraints weight = 31299.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.084484 restraints weight = 19046.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.084698 restraints weight = 14999.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.084863 restraints weight = 14418.432| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14560 Z= 0.110 Angle : 0.487 7.213 20271 Z= 0.274 Chirality : 0.038 0.299 2322 Planarity : 0.003 0.047 2066 Dihedral : 19.307 161.936 3430 Min Nonbonded Distance : 1.171 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.66 % Allowed : 10.13 % Favored : 89.20 % 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: 0.69 (0.23), residues: 1331 helix: 1.22 (0.21), residues: 647 sheet: 0.14 (0.50), residues: 123 loop : -0.28 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1078 TYR 0.014 0.001 TYR A1010 PHE 0.017 0.001 PHE A1045 TRP 0.007 0.001 TRP A 18 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.11 (14560) covalent geometry : angle 0.48656 / 0.27 (20271) hydrogen bonds : bond 0.04182 / 2.66 ( 602) hydrogen bonds : angle 4.35131 / 3.15 ( 1629) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1791.56 seconds wall clock time: 31 minutes 55.53 seconds (1915.53 seconds total)