Starting phenix.real_space_refine on Fri May 16 04:08:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzz_41775/05_2025/8tzz_41775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzz_41775/05_2025/8tzz_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_41775/05_2025/8tzz_41775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzz_41775/05_2025/8tzz_41775.map" model { file = "/net/cci-nas-00/data/ceres_data/8tzz_41775/05_2025/8tzz_41775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzz_41775/05_2025/8tzz_41775.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.02, per 1000 atoms: 0.93 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: 3.37 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 5.21 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: 7.01 Time building geometry restraints manager: 3.98 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=" 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 bond pdb=" CA ALA A1217 " pdb=" CB ALA A1217 " ideal model delta sigma weight residual 1.533 1.483 0.050 1.63e-02 3.76e+03 9.33e+00 ... (remaining 14555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 19629 2.13 - 4.25: 548 4.25 - 6.38: 76 6.38 - 8.50: 13 8.50 - 10.63: 5 Bond angle restraints: 20271 Sorted by residual: 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=" O3' DG C 17 " pdb=" C3' DG C 17 " pdb=" C2' DG C 17 " ideal model delta sigma weight residual 111.50 103.83 7.67 1.50e+00 4.44e-01 2.61e+01 angle pdb=" CG MET A 383 " pdb=" SD MET A 383 " pdb=" CE MET A 383 " ideal model delta sigma weight residual 100.90 90.65 10.25 2.20e+00 2.07e-01 2.17e+01 angle pdb=" N TYR A1326 " pdb=" CA TYR A1326 " pdb=" C TYR A1326 " ideal model delta sigma weight residual 110.17 103.51 6.66 1.51e+00 4.39e-01 1.95e+01 angle pdb=" N GLN A 190 " pdb=" CA GLN A 190 " pdb=" CB GLN A 190 " ideal model delta sigma weight residual 110.28 116.83 -6.55 1.55e+00 4.16e-01 1.79e+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 - 0.087: 2152 0.087 - 0.173: 153 0.173 - 0.260: 13 0.260 - 0.347: 3 0.347 - 0.434: 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 2.35 -2.78 -0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" C3' DG C 17 " pdb=" C4' DG C 17 " pdb=" O3' DG C 17 " pdb=" C2' DG C 17 " both_signs ideal model delta sigma weight residual False -2.66 -2.97 0.31 2.00e-01 2.50e+01 2.44e+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 ... (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: 7.350 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 43.240 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 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= 0.323 Angle : 0.857 10.629 20271 Z= 0.494 Chirality : 0.050 0.434 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.002 TRP A1136 HIS 0.009 0.002 HIS A 328 PHE 0.018 0.002 PHE A 643 TYR 0.026 0.003 TYR A1326 ARG 0.018 0.001 ARG A1078 Details of bonding type rmsd hydrogen bonds : bond 0.17116 ( 602) hydrogen bonds : angle 7.72888 ( 1629) covalent geometry : bond 0.00676 (14560) covalent geometry : angle 0.85674 (20271) *********************** 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 : 1.403 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: 0.6200 (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) outliers start: 8 outliers final: 1 residues processed: 99 average time/residue: 0.3048 time to fit residues: 43.0381 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 : 1.317 ------------------------------------------------------------------------------- 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 122 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 HIS ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.106781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.080336 restraints weight = 58735.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.081751 restraints weight = 28677.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.082567 restraints weight = 19907.747| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 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) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14560 Z= 0.150 Angle : 0.597 7.306 20271 Z= 0.320 Chirality : 0.041 0.201 2322 Planarity : 0.004 0.051 2066 Dihedral : 20.076 167.975 3432 Min Nonbonded Distance : 1.358 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.66 % Allowed : 3.90 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.22), residues: 1331 helix: 0.53 (0.20), residues: 643 sheet: 0.01 (0.48), residues: 122 loop : -0.63 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1136 HIS 0.004 0.001 HIS A 328 PHE 0.026 0.001 PHE A1045 TYR 0.023 0.001 TYR A1326 ARG 0.006 0.001 ARG A 864 Details of bonding type rmsd hydrogen bonds : bond 0.05311 ( 602) hydrogen bonds : angle 5.01297 ( 1629) covalent geometry : bond 0.00318 (14560) covalent geometry : angle 0.59713 (20271) *********************** 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 82 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 1.329 Fit side-chains REVERT: A 919 ARG cc_start: 0.8483 (ttp-170) cc_final: 0.8191 (ttp80) outliers start: 8 outliers final: 4 residues processed: 80 average time/residue: 0.3148 time to fit residues: 36.9927 Evaluate side-chains 67 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 107 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.105976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.079600 restraints weight = 53237.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.081025 restraints weight = 26466.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.081913 restraints weight = 18323.243| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 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 = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14560 Z= 0.159 Angle : 0.559 6.623 20271 Z= 0.298 Chirality : 0.039 0.227 2322 Planarity : 0.004 0.091 2066 Dihedral : 19.796 167.285 3430 Min Nonbonded Distance : 1.186 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.58 % Allowed : 5.98 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.23), residues: 1331 helix: 0.68 (0.20), residues: 647 sheet: 0.28 (0.51), residues: 112 loop : -0.58 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 PHE 0.023 0.001 PHE A1045 TYR 0.020 0.001 TYR A1201 ARG 0.006 0.001 ARG A 864 Details of bonding type rmsd hydrogen bonds : bond 0.04634 ( 602) hydrogen bonds : angle 4.74544 ( 1629) covalent geometry : bond 0.00351 (14560) covalent geometry : angle 0.55860 (20271) *********************** 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 76 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 1.265 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 73 average time/residue: 0.2905 time to fit residues: 31.1640 Evaluate side-chains 67 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 1.404 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 54 optimal weight: 0.3980 chunk 22 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 134 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3632 r_free = 0.3632 target = 0.104681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.078091 restraints weight = 61185.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.079619 restraints weight = 29649.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.080373 restraints weight = 19187.446| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14560 Z= 0.205 Angle : 0.587 7.020 20271 Z= 0.311 Chirality : 0.041 0.212 2322 Planarity : 0.004 0.050 2066 Dihedral : 19.739 167.548 3430 Min Nonbonded Distance : 1.062 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.75 % Allowed : 6.73 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.23), residues: 1331 helix: 0.68 (0.20), residues: 653 sheet: -0.07 (0.46), residues: 130 loop : -0.58 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1136 HIS 0.008 0.001 HIS A1262 PHE 0.022 0.002 PHE A1045 TYR 0.025 0.002 TYR A1201 ARG 0.005 0.001 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 602) hydrogen bonds : angle 4.73583 ( 1629) covalent geometry : bond 0.00458 (14560) covalent geometry : angle 0.58721 (20271) *********************** 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 74 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 1.306 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 70 average time/residue: 0.3037 time to fit residues: 30.9485 Evaluate side-chains 68 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 733 ILE 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 109 optimal weight: 0.0870 chunk 118 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.0030 overall best weight: 0.5168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.107982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.081931 restraints weight = 41423.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.084017 restraints weight = 22637.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.085054 restraints weight = 14475.932| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 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 = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14560 Z= 0.110 Angle : 0.498 6.425 20271 Z= 0.269 Chirality : 0.037 0.210 2322 Planarity : 0.003 0.046 2066 Dihedral : 19.455 165.500 3430 Min Nonbonded Distance : 1.201 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.66 % Allowed : 7.64 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.23), residues: 1331 helix: 1.03 (0.21), residues: 646 sheet: 0.21 (0.49), residues: 123 loop : -0.37 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1136 HIS 0.006 0.001 HIS A 840 PHE 0.020 0.001 PHE A1045 TYR 0.018 0.001 TYR A1201 ARG 0.007 0.000 ARG A1303 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 602) hydrogen bonds : angle 4.50327 ( 1629) covalent geometry : bond 0.00233 (14560) covalent geometry : angle 0.49820 (20271) *********************** 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 76 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 1.312 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 73 average time/residue: 0.2980 time to fit residues: 31.9307 Evaluate side-chains 63 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 1038 PHE Chi-restraints excluded: chain A residue 1339 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 54 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 42 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.102685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.076631 restraints weight = 36734.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.077781 restraints weight = 22645.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.078709 restraints weight = 16191.646| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 14560 Z= 0.321 Angle : 0.685 7.782 20271 Z= 0.355 Chirality : 0.044 0.217 2322 Planarity : 0.005 0.073 2066 Dihedral : 19.737 168.589 3430 Min Nonbonded Distance : 1.059 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.16 % Allowed : 8.80 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.23), residues: 1331 helix: 0.58 (0.20), residues: 651 sheet: -0.17 (0.47), residues: 130 loop : -0.66 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.009 0.002 HIS A 723 PHE 0.021 0.002 PHE A1045 TYR 0.029 0.002 TYR A1201 ARG 0.015 0.001 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.05227 ( 602) hydrogen bonds : angle 4.88554 ( 1629) covalent geometry : bond 0.00723 (14560) covalent geometry : angle 0.68451 (20271) *********************** 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 68 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 1.423 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 61 average time/residue: 0.3076 time to fit residues: 27.8514 Evaluate side-chains 64 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 893 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 99 optimal weight: 0.0670 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.106677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.080223 restraints weight = 50558.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.082397 restraints weight = 26302.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.082965 restraints weight = 16509.591| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 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 = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14560 Z= 0.122 Angle : 0.517 7.966 20271 Z= 0.275 Chirality : 0.038 0.211 2322 Planarity : 0.003 0.046 2066 Dihedral : 19.451 166.322 3430 Min Nonbonded Distance : 1.172 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.66 % Allowed : 9.30 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.23), residues: 1331 helix: 0.93 (0.20), residues: 650 sheet: 0.09 (0.49), residues: 125 loop : -0.41 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1136 HIS 0.004 0.001 HIS A 328 PHE 0.018 0.001 PHE A1045 TYR 0.019 0.001 TYR A1201 ARG 0.008 0.000 ARG A1078 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 602) hydrogen bonds : angle 4.51638 ( 1629) covalent geometry : bond 0.00267 (14560) covalent geometry : angle 0.51740 (20271) *********************** 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 : 1.282 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 62 average time/residue: 0.3185 time to fit residues: 28.4110 Evaluate side-chains 60 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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 651 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 893 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 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3650 r_free = 0.3650 target = 0.106158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.079597 restraints weight = 53343.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.081502 restraints weight = 28438.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.082135 restraints weight = 17959.315| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 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 = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2289 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= 0.143 Angle : 0.526 8.128 20271 Z= 0.279 Chirality : 0.038 0.214 2322 Planarity : 0.003 0.046 2066 Dihedral : 19.433 166.029 3430 Min Nonbonded Distance : 1.096 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.66 % Allowed : 9.39 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.23), residues: 1331 helix: 0.97 (0.20), residues: 655 sheet: 0.05 (0.49), residues: 125 loop : -0.45 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1074 HIS 0.005 0.001 HIS A 328 PHE 0.019 0.001 PHE A1045 TYR 0.023 0.001 TYR A1201 ARG 0.009 0.000 ARG A1078 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 602) hydrogen bonds : angle 4.45372 ( 1629) covalent geometry : bond 0.00317 (14560) covalent geometry : angle 0.52581 (20271) *********************** 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 64 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 1.491 Fit side-chains REVERT: A 1038 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.7290 (t80) outliers start: 8 outliers final: 7 residues processed: 60 average time/residue: 0.3087 time to fit residues: 27.6800 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 : 1.478 ------------------------------------------------------------------------------- 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 893 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 29 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 14 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 128 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3676 r_free = 0.3676 target = 0.107870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.081381 restraints weight = 48075.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.083283 restraints weight = 25177.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.084581 restraints weight = 16142.065| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 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 = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2512 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 : 0.494 8.389 20271 Z= 0.263 Chirality : 0.037 0.212 2322 Planarity : 0.003 0.043 2066 Dihedral : 19.303 164.760 3430 Min Nonbonded Distance : 1.171 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.75 % Allowed : 9.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.23), residues: 1331 helix: 1.24 (0.21), residues: 647 sheet: 0.23 (0.51), residues: 119 loop : -0.32 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.005 0.001 HIS A 328 PHE 0.018 0.001 PHE A1045 TYR 0.020 0.001 TYR A1201 ARG 0.009 0.000 ARG A1078 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 602) hydrogen bonds : angle 4.33365 ( 1629) covalent geometry : bond 0.00235 (14560) covalent geometry : angle 0.49405 (20271) *********************** 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 69 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 1.291 Fit side-chains REVERT: A 161 MET cc_start: 0.8238 (mmt) cc_final: 0.7885 (mmt) REVERT: A 1038 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.6839 (t80) outliers start: 9 outliers final: 5 residues processed: 64 average time/residue: 0.2803 time to fit residues: 27.2155 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 : 1.263 ------------------------------------------------------------------------------- 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 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 78 optimal weight: 1.9990 chunk 37 optimal weight: 0.0570 chunk 123 optimal weight: 7.9990 chunk 75 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 70 optimal weight: 0.0000 chunk 48 optimal weight: 0.8980 chunk 117 optimal weight: 0.0770 chunk 107 optimal weight: 0.0980 chunk 20 optimal weight: 0.0010 overall best weight: 0.0466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 933 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.110149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.084004 restraints weight = 53892.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.086128 restraints weight = 26983.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.086953 restraints weight = 16836.620| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2887 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= 0.099 Angle : 0.485 8.560 20271 Z= 0.258 Chirality : 0.036 0.210 2322 Planarity : 0.003 0.043 2066 Dihedral : 19.146 161.551 3430 Min Nonbonded Distance : 1.235 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.50 % Allowed : 10.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.24), residues: 1331 helix: 1.35 (0.21), residues: 659 sheet: 0.44 (0.53), residues: 114 loop : -0.25 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 18 HIS 0.005 0.001 HIS A 328 PHE 0.017 0.001 PHE A1045 TYR 0.020 0.001 TYR A1010 ARG 0.006 0.000 ARG A1303 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 602) hydrogen bonds : angle 4.23534 ( 1629) covalent geometry : bond 0.00203 (14560) covalent geometry : angle 0.48488 (20271) ********************** 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 76 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 1.262 Fit side-chains REVERT: A 1038 PHE cc_start: 0.7224 (OUTLIER) cc_final: 0.6487 (t80) outliers start: 6 outliers final: 4 residues processed: 72 average time/residue: 0.2673 time to fit residues: 29.3030 Evaluate side-chains 64 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 141 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 933 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.105553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.078889 restraints weight = 51469.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.080915 restraints weight = 27541.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.081631 restraints weight = 16910.407| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 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 = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14560 Z= 0.208 Angle : 0.582 8.009 20271 Z= 0.304 Chirality : 0.040 0.212 2322 Planarity : 0.004 0.048 2066 Dihedral : 19.349 165.753 3430 Min Nonbonded Distance : 1.058 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.58 % Allowed : 10.63 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1331 helix: 1.14 (0.20), residues: 660 sheet: 0.14 (0.51), residues: 119 loop : -0.39 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 464 HIS 0.008 0.001 HIS A 328 PHE 0.023 0.002 PHE A 606 TYR 0.031 0.002 TYR A1201 ARG 0.010 0.001 ARG A1078 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 602) hydrogen bonds : angle 4.41567 ( 1629) covalent geometry : bond 0.00468 (14560) covalent geometry : angle 0.58247 (20271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3967.12 seconds wall clock time: 70 minutes 51.84 seconds (4251.84 seconds total)