Starting phenix.real_space_refine on Fri Jul 3 11:47:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzz_41775/07_2026/8tzz_41775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzz_41775/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tzz_41775/07_2026/8tzz_41775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzz_41775/07_2026/8tzz_41775.map" model { file = "/net/cci-nas-00/data/ceres_data/8tzz_41775/07_2026/8tzz_41775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzz_41775/07_2026/8tzz_41775.cif" } 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-dev-6108/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: 3.96, per 1000 atoms: 0.28 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: 1.27 Conformation dependent library (CDL) restraints added in 787.3 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: 1.84 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: 3.37 Time building geometry restraints manager: 1.65 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=" C PRO A1199 " pdb=" O PRO A1199 " ideal model delta sigma weight residual 1.235 1.192 0.043 1.30e-02 5.92e+03 1.09e+01 ... (remaining 14555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 19582 2.13 - 4.25: 594 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: 2143 0.089 - 0.178: 161 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: 3.820 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.890 Find NCS groups from input model: 0.060 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.250 ------------------------------------------------------------------------------- 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= 0.430 Angle : 0.874 10.629 20271 Z= 0.582 Chirality : 0.051 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 0.00685 / 0.43 (14560) covalent geometry : angle 0.87377 / 0.58 (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 : 0.476 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: 0.5279 (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: 0.8126 (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: 0.1326 time to fit residues: 18.8826 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 : 0.456 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.106801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.079228 restraints weight = 60887.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.081474 restraints weight = 27516.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.082305 restraints weight = 16489.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.082820 restraints weight = 14090.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.083242 restraints weight = 13155.550| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 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 = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1090 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= 0.161 Angle : 0.630 11.663 20271 Z= 0.352 Chirality : 0.045 0.321 2322 Planarity : 0.004 0.052 2066 Dihedral : 20.270 175.028 3432 Min Nonbonded Distance : 1.381 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.83 % Allowed : 3.65 % Favored : 95.51 % 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: -0.15 (0.22), residues: 1331 helix: 0.44 (0.20), residues: 640 sheet: -0.03 (0.47), residues: 126 loop : -0.62 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 221 TYR 0.026 0.002 TYR A1326 PHE 0.028 0.002 PHE A1045 TRP 0.011 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 (14560) covalent geometry : angle 0.63006 / 0.35 (20271) hydrogen bonds : bond 0.06600 / 4.40 ( 602) hydrogen bonds : angle 5.22217 / 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: 10 poor density : 69 time to evaluate : 0.542 Fit side-chains REVERT: A 221 ARG cc_start: 0.7476 (mtt180) cc_final: 0.7232 (ptm160) REVERT: A 919 ARG cc_start: 0.8564 (ttp-170) cc_final: 0.8206 (ttp80) outliers start: 10 outliers final: 4 residues processed: 76 average time/residue: 0.1288 time to fit residues: 14.2366 Evaluate side-chains 63 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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: 5.9990 chunk 74 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 0.3980 chunk 140 optimal weight: 20.0000 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.106830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.080347 restraints weight = 58318.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.081653 restraints weight = 29059.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.082594 restraints weight = 19240.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.083016 restraints weight = 16349.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.083167 restraints weight = 15263.734| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 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 = 0.3251 r_free = 0.3251 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: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14560 Z= 0.134 Angle : 0.544 7.512 20271 Z= 0.308 Chirality : 0.041 0.224 2322 Planarity : 0.004 0.049 2066 Dihedral : 20.042 170.783 3430 Min Nonbonded Distance : 1.324 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.66 % Allowed : 5.81 % Favored : 93.52 % 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 (0.23), residues: 1331 helix: 0.75 (0.20), residues: 639 sheet: 0.28 (0.50), residues: 117 loop : -0.58 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1078 TYR 0.040 0.001 TYR A1201 PHE 0.023 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 0.00269 / 0.13 (14560) covalent geometry : angle 0.54353 / 0.31 (20271) hydrogen bonds : bond 0.05391 / 3.50 ( 602) hydrogen bonds : angle 4.87253 / 3.52 ( 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 82 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.320 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 0.1043 time to fit residues: 12.3265 Evaluate side-chains 65 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 769 THR 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: 0.9990 chunk 1 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 123 optimal weight: 7.9990 chunk 76 optimal weight: 0.0970 chunk 135 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 126 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 863 ASN ** A1262 HIS ** 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 = 0.3684 r_free = 0.3684 target = 0.108155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.081965 restraints weight = 53866.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.083196 restraints weight = 27687.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.084190 restraints weight = 18730.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.084535 restraints weight = 15157.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.084702 restraints weight = 14320.537| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 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 = 0.3270 r_free = 0.3270 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: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1689 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= 0.120 Angle : 0.516 7.072 20271 Z= 0.294 Chirality : 0.040 0.247 2322 Planarity : 0.004 0.049 2066 Dihedral : 19.845 167.270 3430 Min Nonbonded Distance : 1.280 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.58 % Allowed : 7.23 % Favored : 92.19 % 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: 0.23 (0.23), residues: 1331 helix: 0.78 (0.20), residues: 657 sheet: 0.30 (0.49), residues: 117 loop : -0.54 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 221 TYR 0.016 0.001 TYR A1326 PHE 0.021 0.001 PHE A 606 TRP 0.006 0.001 TRP A1136 HIS 0.024 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (14560) covalent geometry : angle 0.51635 / 0.29 (20271) hydrogen bonds : bond 0.04830 / 3.10 ( 602) hydrogen bonds : angle 4.69892 / 3.39 ( 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 72 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.304 Fit side-chains REVERT: A 781 MET cc_start: 0.8075 (tmm) cc_final: 0.7862 (tmm) outliers start: 7 outliers final: 4 residues processed: 69 average time/residue: 0.1240 time to fit residues: 12.5297 Evaluate side-chains 63 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 769 THR 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: 2.9990 chunk 21 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3645 r_free = 0.3645 target = 0.105389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.079007 restraints weight = 45718.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.080322 restraints weight = 25617.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.081585 restraints weight = 16608.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.081589 restraints weight = 13675.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.082099 restraints weight = 13446.357| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 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 = 0.3229 r_free = 0.3229 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: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14560 Z= 0.199 Angle : 0.567 8.817 20271 Z= 0.316 Chirality : 0.042 0.246 2322 Planarity : 0.004 0.051 2066 Dihedral : 19.790 167.481 3430 Min Nonbonded Distance : 1.159 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.66 % Allowed : 8.22 % 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: 0.16 (0.23), residues: 1331 helix: 0.71 (0.20), residues: 657 sheet: 0.25 (0.48), residues: 123 loop : -0.56 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1078 TYR 0.012 0.002 TYR A1010 PHE 0.029 0.002 PHE A 606 TRP 0.007 0.001 TRP A 883 HIS 0.008 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (14560) covalent geometry : angle 0.56690 / 0.32 (20271) hydrogen bonds : bond 0.05081 / 3.30 ( 602) hydrogen bonds : angle 4.70323 / 3.40 ( 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 71 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.417 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 67 average time/residue: 0.1270 time to fit residues: 12.5798 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 : 0.294 ------------------------------------------------------------------------------- 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: 0.0040 chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 142 optimal weight: 20.0000 chunk 110 optimal weight: 0.9990 chunk 104 optimal weight: 0.0870 chunk 122 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 overall best weight: 0.9574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN ** A1262 HIS ** 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 = 0.3669 r_free = 0.3669 target = 0.107145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.080697 restraints weight = 51010.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.082491 restraints weight = 26558.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.083107 restraints weight = 17308.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.083492 restraints weight = 14049.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.083483 restraints weight = 13317.869| |-----------------------------------------------------------------------------| 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: 0.8377 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14560 Z= 0.133 Angle : 0.514 8.834 20271 Z= 0.291 Chirality : 0.040 0.258 2322 Planarity : 0.003 0.047 2066 Dihedral : 19.699 166.414 3430 Min Nonbonded Distance : 1.145 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.58 % Allowed : 8.97 % 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: 0.34 (0.23), residues: 1331 helix: 0.86 (0.20), residues: 656 sheet: 0.30 (0.50), residues: 118 loop : -0.46 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1078 TYR 0.011 0.001 TYR A1010 PHE 0.024 0.001 PHE A 606 TRP 0.009 0.001 TRP A 883 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (14560) covalent geometry : angle 0.51389 / 0.29 (20271) hydrogen bonds : bond 0.04711 / 3.03 ( 602) hydrogen bonds : angle 4.58610 / 3.32 ( 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 66 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.453 Fit side-chains REVERT: A 161 MET cc_start: 0.8303 (mmt) cc_final: 0.8053 (mmt) outliers start: 7 outliers final: 6 residues processed: 63 average time/residue: 0.1252 time to fit residues: 11.7540 Evaluate side-chains 64 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 1038 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 142 optimal weight: 20.0000 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 121 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.105815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.079354 restraints weight = 48005.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.081009 restraints weight = 25404.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.081777 restraints weight = 16883.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.082027 restraints weight = 13954.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.082032 restraints weight = 13195.972| |-----------------------------------------------------------------------------| 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: 3 (3 function evaluations) r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14560 Z= 0.164 Angle : 0.530 8.012 20271 Z= 0.298 Chirality : 0.040 0.260 2322 Planarity : 0.004 0.052 2066 Dihedral : 19.650 166.590 3430 Min Nonbonded Distance : 1.109 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.66 % Allowed : 9.05 % Favored : 90.28 % 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: 0.31 (0.23), residues: 1331 helix: 0.86 (0.20), residues: 657 sheet: 0.09 (0.49), residues: 123 loop : -0.47 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1078 TYR 0.011 0.001 TYR A1010 PHE 0.023 0.001 PHE A 606 TRP 0.006 0.001 TRP A 883 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (14560) covalent geometry : angle 0.53046 / 0.30 (20271) hydrogen bonds : bond 0.04762 / 3.07 ( 602) hydrogen bonds : angle 4.56783 / 3.32 ( 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 67 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.630 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 63 average time/residue: 0.1186 time to fit residues: 11.3569 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 : 0.385 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 78 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 62 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.106592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.080476 restraints weight = 39152.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.081903 restraints weight = 22552.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.083041 restraints weight = 15418.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.083068 restraints weight = 13409.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.083170 restraints weight = 12773.736| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 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 = 0.3255 r_free = 0.3255 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: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2024 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= 0.136 Angle : 0.504 7.740 20271 Z= 0.286 Chirality : 0.040 0.267 2322 Planarity : 0.003 0.047 2066 Dihedral : 19.581 165.657 3430 Min Nonbonded Distance : 1.142 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.66 % Allowed : 9.22 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.23), residues: 1331 helix: 0.96 (0.20), residues: 656 sheet: 0.12 (0.49), residues: 123 loop : -0.38 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1078 TYR 0.011 0.001 TYR A1010 PHE 0.020 0.001 PHE A 606 TRP 0.007 0.001 TRP A 883 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (14560) covalent geometry : angle 0.50357 / 0.29 (20271) hydrogen bonds : bond 0.04531 / 2.91 ( 602) hydrogen bonds : angle 4.49282 / 3.26 ( 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 65 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.319 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 62 average time/residue: 0.1185 time to fit residues: 11.0812 Evaluate side-chains 63 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 341 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 134 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.105378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.078588 restraints weight = 67275.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.080520 restraints weight = 32933.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.081564 restraints weight = 19016.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.081901 restraints weight = 15749.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.082113 restraints weight = 14381.099| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 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 = 0.3231 r_free = 0.3231 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: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14560 Z= 0.199 Angle : 0.552 7.489 20271 Z= 0.308 Chirality : 0.041 0.263 2322 Planarity : 0.004 0.050 2066 Dihedral : 19.594 166.352 3430 Min Nonbonded Distance : 1.085 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.75 % Allowed : 9.47 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.23), residues: 1331 helix: 0.85 (0.20), residues: 656 sheet: -0.03 (0.48), residues: 125 loop : -0.48 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1078 TYR 0.012 0.001 TYR A1010 PHE 0.019 0.002 PHE A 606 TRP 0.006 0.001 TRP A 883 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (14560) covalent geometry : angle 0.55179 / 0.31 (20271) hydrogen bonds : bond 0.04748 / 3.08 ( 602) hydrogen bonds : angle 4.55064 / 3.31 ( 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 66 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.336 Fit side-chains REVERT: A 311 GLU cc_start: 0.5177 (mp0) cc_final: 0.4855 (mp0) outliers start: 9 outliers final: 8 residues processed: 63 average time/residue: 0.1164 time to fit residues: 11.1860 Evaluate side-chains 63 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 341 GLN 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 84 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 88 optimal weight: 0.0980 chunk 124 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 chunk 109 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 chunk 3 optimal weight: 0.0970 chunk 74 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.107720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.081150 restraints weight = 48310.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.083449 restraints weight = 25905.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.084140 restraints weight = 16079.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.084168 restraints weight = 13609.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.084297 restraints weight = 12966.509| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 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 = 0.3271 r_free = 0.3271 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: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14560 Z= 0.110 Angle : 0.503 8.037 20271 Z= 0.286 Chirality : 0.039 0.273 2322 Planarity : 0.004 0.055 2066 Dihedral : 19.548 165.055 3430 Min Nonbonded Distance : 1.179 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.66 % Allowed : 9.63 % Favored : 89.70 % 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: 0.54 (0.23), residues: 1331 helix: 1.06 (0.21), residues: 650 sheet: 0.09 (0.49), residues: 123 loop : -0.31 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1078 TYR 0.013 0.001 TYR A 155 PHE 0.018 0.001 PHE A 606 TRP 0.011 0.001 TRP A 883 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.11 (14560) covalent geometry : angle 0.50345 / 0.29 (20271) hydrogen bonds : bond 0.04367 / 2.80 ( 602) hydrogen bonds : angle 4.45275 / 3.23 ( 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 67 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.465 Fit side-chains REVERT: A 311 GLU cc_start: 0.5187 (mp0) cc_final: 0.4888 (mp0) outliers start: 8 outliers final: 6 residues processed: 63 average time/residue: 0.1298 time to fit residues: 12.3228 Evaluate side-chains 61 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 383 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 70 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 0.0870 chunk 56 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 125 optimal weight: 0.1980 chunk 103 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 overall best weight: 0.4960 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.107823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.081458 restraints weight = 68094.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.082846 restraints weight = 35000.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.084250 restraints weight = 20017.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.084615 restraints weight = 15146.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.084736 restraints weight = 14249.197| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 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 = 0.3285 r_free = 0.3285 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: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14560 Z= 0.112 Angle : 0.493 9.029 20271 Z= 0.279 Chirality : 0.039 0.272 2322 Planarity : 0.003 0.056 2066 Dihedral : 19.464 164.670 3430 Min Nonbonded Distance : 1.166 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.50 % Allowed : 10.05 % Favored : 89.45 % 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: 0.54 (0.23), residues: 1331 helix: 1.07 (0.20), residues: 655 sheet: 0.12 (0.50), residues: 123 loop : -0.35 (0.27), residues: 553 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 0.009 0.001 TRP A 883 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (14560) covalent geometry : angle 0.49299 / 0.28 (20271) hydrogen bonds : bond 0.04272 / 2.73 ( 602) hydrogen bonds : angle 4.38144 / 3.19 ( 1629) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2009.21 seconds wall clock time: 35 minutes 43.53 seconds (2143.53 seconds total)