Starting phenix.real_space_refine on Sat Sep 12 00:04:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s4v_24835/09_2026/7s4v_24835.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s4v_24835/09_2026/7s4v_24835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7s4v_24835/09_2026/7s4v_24835.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s4v_24835/09_2026/7s4v_24835.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s4v_24835/09_2026/7s4v_24835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s4v_24835/09_2026/7s4v_24835.map" model { file = "/net/cci-nas-00/data/ceres_data/7s4v_24835/09_2026/7s4v_24835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s4v_24835/09_2026/7s4v_24835.cif" } resolution = 3.28 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= -0.000 sd= 0.015 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: 5 Type Number sf(0) Gaussians P 141 5.49 5 S 18 5.16 5 C 7249 2.51 5 N 2149 2.21 5 O 2658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12215 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 9167 Classifications: {'peptide': 1122} Link IDs: {'PTRANS': 30, 'TRANS': 1091} Chain breaks: 5 Chain: "B" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2100 Classifications: {'RNAv2': 98} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 52, 'rna3p_pyr': 33} Link IDs: {'rna2p': 13, 'rna3p': 84} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 665 Classifications: {'DNA': 33} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 32} Chain: "D" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 283 Inner-chain residues flagged as termini: ['pdbres=" DC D 30 "'] Classifications: {'DNA': 14} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 13} Time building chain proxies: 2.90, per 1000 atoms: 0.24 Number of scatterers: 12215 At special positions: 0 Unit cell: (88, 143, 129.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 141 15.00 O 2658 8.00 N 2149 7.00 C 7249 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 593.8 milliseconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 7 sheets defined 54.2% alpha, 8.2% beta 22 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 3.673A pdb=" N ARG A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 76 " --> pdb=" O TYR A 72 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 4.059A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 196 Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.928A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.571A pdb=" N PHE A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 246 Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 275 through 280 removed outlier: 4.185A pdb=" N ALA A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.949A pdb=" N LYS A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.548A pdb=" N ALA A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.627A pdb=" N PHE A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 368 through 382 Proline residue: A 378 - end of helix removed outlier: 3.919A pdb=" N LYS A 382 " --> pdb=" O PRO A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 removed outlier: 3.500A pdb=" N ASN A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.645A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.164A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.960A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 445 removed outlier: 3.649A pdb=" N ILE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.552A pdb=" N GLU A 480 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 494 removed outlier: 3.862A 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 removed outlier: 3.906A pdb=" N ASP A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 567 removed outlier: 3.554A pdb=" N LEU A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 removed outlier: 4.053A pdb=" N LYS A 571 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 576 removed outlier: 4.299A pdb=" N ASP A 576 " --> pdb=" O GLU A 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 573 through 576' Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.989A pdb=" N LEU A 621 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 623 " --> pdb=" O ILE A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 643 removed outlier: 4.928A 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 668 removed outlier: 3.814A pdb=" N ILE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 686 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 705 through 712 removed outlier: 3.547A pdb=" N GLN A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.579A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 940 Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.603A pdb=" N SER A 964 " --> pdb=" O SER A 960 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 998 Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.028A pdb=" N VAL A1083 " --> pdb=" O ASP A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1184 Processing helix chain 'A' and resid 1229 through 1240 removed outlier: 3.627A pdb=" N SER A1240 " --> pdb=" O LEU A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1251 Processing helix chain 'A' and resid 1252 through 1262 removed outlier: 3.533A pdb=" N GLN A1256 " --> pdb=" O ASN A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1280 removed outlier: 4.380A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1296 Processing helix chain 'A' and resid 1301 through 1310 Processing helix chain 'A' and resid 1311 through 1316 removed outlier: 3.766A pdb=" N THR A1314 " --> pdb=" O HIS A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1343 removed outlier: 3.940A pdb=" N VAL A1342 " --> pdb=" O THR A1339 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1339 through 1343' 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 956 through 957 removed outlier: 6.144A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A1095 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.114A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A1210 " --> pdb=" O LEU A1206 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 530 through 531 Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1162 removed outlier: 3.648A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1162 removed outlier: 3.648A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1325 removed outlier: 3.592A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 3.07 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3053 1.33 - 1.45: 3123 1.45 - 1.58: 6250 1.58 - 1.70: 282 1.70 - 1.82: 34 Bond restraints: 12742 Sorted by residual: bond pdb=" C3' DC D 2 " pdb=" C2' DC D 2 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.13e+00 bond pdb=" C3' DC C 12 " pdb=" C2' DC C 12 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.70e+00 bond pdb=" C1' DC C 20 " pdb=" N1 DC C 20 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.00e+00 bond pdb=" C3' DT C 5 " pdb=" C2' DT C 5 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.06e+00 bond pdb=" C3' DT C 29 " pdb=" C2' DT C 29 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.82e+00 ... (remaining 12737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 17153 1.73 - 3.45: 585 3.45 - 5.18: 81 5.18 - 6.90: 7 6.90 - 8.63: 2 Bond angle restraints: 17828 Sorted by residual: angle pdb=" O4' DT C 14 " pdb=" C4' DT C 14 " pdb=" C3' DT C 14 " ideal model delta sigma weight residual 106.00 103.17 2.83 6.00e-01 2.78e+00 2.23e+01 angle pdb=" O4' DG D 33 " pdb=" C4' DG D 33 " pdb=" C3' DG D 33 " ideal model delta sigma weight residual 106.00 103.24 2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" N3 DT C 16 " pdb=" C4 DT C 16 " pdb=" O4 DT C 16 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT C 25 " pdb=" C4 DT C 25 " pdb=" O4 DT C 25 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT D 37 " pdb=" C4 DT D 37 " pdb=" O4 DT D 37 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 ... (remaining 17823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.01: 6972 35.01 - 70.03: 404 70.03 - 105.04: 23 105.04 - 140.06: 1 140.06 - 175.07: 6 Dihedral angle restraints: 7406 sinusoidal: 4107 harmonic: 3299 Sorted by residual: dihedral pdb=" C4' U B 63 " pdb=" C3' U B 63 " pdb=" C2' U B 63 " pdb=" C1' U B 63 " ideal model delta sinusoidal sigma weight residual 36.34 -36.69 73.04 1 3.10e+00 1.04e-01 7.08e+02 dihedral pdb=" C4' G B 43 " pdb=" C3' G B 43 " pdb=" C2' G B 43 " pdb=" C1' G B 43 " ideal model delta sinusoidal sigma weight residual 36.34 -36.45 72.79 1 3.10e+00 1.04e-01 7.03e+02 dihedral pdb=" C4' A B 8 " pdb=" C3' A B 8 " pdb=" C2' A B 8 " pdb=" C1' A B 8 " ideal model delta sinusoidal sigma weight residual 36.34 -36.40 72.75 1 3.10e+00 1.04e-01 7.03e+02 ... (remaining 7403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1650 0.057 - 0.114: 268 0.114 - 0.171: 17 0.171 - 0.228: 30 0.228 - 0.285: 96 Chirality restraints: 2061 Sorted by residual: chirality pdb=" C2' C B 55 " pdb=" C3' C B 55 " pdb=" O2' C B 55 " pdb=" C1' C B 55 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C2' A B 8 " pdb=" C3' A B 8 " pdb=" O2' A B 8 " pdb=" C1' A B 8 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C2' U B 63 " pdb=" C3' U B 63 " pdb=" O2' U B 63 " pdb=" C1' U B 63 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 2058 not shown) Planarity restraints: 1745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 343 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO A 344 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B 69 " 0.031 2.00e-02 2.50e+03 1.43e-02 5.65e+00 pdb=" N9 A B 69 " -0.035 2.00e-02 2.50e+03 pdb=" C8 A B 69 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A B 69 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A B 69 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A B 69 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 69 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A B 69 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A B 69 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A B 69 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A B 69 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 502 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO A 503 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 503 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 503 " -0.025 5.00e-02 4.00e+02 ... (remaining 1742 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1082 2.74 - 3.28: 11247 3.28 - 3.82: 19240 3.82 - 4.36: 23326 4.36 - 4.90: 37704 Nonbonded interactions: 92599 Sorted by model distance: nonbonded pdb=" OH TYR A 515 " pdb=" OP1 C B 5 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR A 5 " pdb=" O HIS A 754 " model vdw 2.253 3.040 nonbonded pdb=" N2 G B 73 " pdb=" OP2 A B 76 " model vdw 2.271 3.120 nonbonded pdb=" OG SER A 541 " pdb=" OE2 GLU A 543 " model vdw 2.291 3.040 nonbonded pdb=" O GLY A 533 " pdb=" NH1 ARG A 535 " model vdw 2.309 3.120 ... (remaining 92594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.770 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 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 : 0.003 0.071 12742 Z= 0.234 Angle : 0.693 8.627 17828 Z= 0.407 Chirality : 0.070 0.285 2061 Planarity : 0.004 0.067 1745 Dihedral : 19.238 175.071 5266 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.24), residues: 1110 helix: -0.28 (0.23), residues: 518 sheet: -0.79 (0.55), residues: 101 loop : -1.71 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 951 TYR 0.013 0.001 TYR A 325 PHE 0.010 0.001 PHE A 97 TRP 0.005 0.001 TRP A 476 HIS 0.004 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.23 (12742) covalent geometry : angle 0.69261 / 0.41 (17828) hydrogen bonds : bond 0.19746 / 13.78 ( 430) hydrogen bonds : angle 7.12044 / 4.90 ( 1211) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 540 LEU cc_start: 0.6211 (tp) cc_final: 0.5895 (mp) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1431 time to fit residues: 15.9409 Evaluate side-chains 42 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 GLN A 721 HIS A1256 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.101093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.072191 restraints weight = 31299.609| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.45 r_work: 0.2972 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12742 Z= 0.249 Angle : 1.031 17.326 17828 Z= 0.455 Chirality : 0.090 1.161 2061 Planarity : 0.004 0.044 1745 Dihedral : 18.957 173.522 2888 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.40 % Allowed : 7.95 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.24), residues: 1110 helix: -0.05 (0.22), residues: 536 sheet: -0.72 (0.50), residues: 118 loop : -1.63 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 221 TYR 0.017 0.002 TYR A 325 PHE 0.016 0.002 PHE A 491 TRP 0.012 0.001 TRP A 476 HIS 0.007 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.25 (12742) covalent geometry : angle 1.03051 / 0.45 (17828) hydrogen bonds : bond 0.06907 / 4.51 ( 430) hydrogen bonds : angle 4.94514 / 3.44 ( 1211) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.385 Fit side-chains REVERT: A 540 LEU cc_start: 0.6929 (tp) cc_final: 0.6563 (mp) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.1264 time to fit residues: 8.0910 Evaluate side-chains 39 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 651 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 15 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 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 = 0.3814 r_free = 0.3814 target = 0.101525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.072091 restraints weight = 31703.589| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.40 r_work: 0.3003 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12742 Z= 0.158 Angle : 0.742 12.526 17828 Z= 0.346 Chirality : 0.062 0.771 2061 Planarity : 0.003 0.045 1745 Dihedral : 19.014 172.885 2888 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.99 % Allowed : 10.14 % Favored : 88.87 % 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: -0.85 (0.25), residues: 1110 helix: 0.42 (0.23), residues: 533 sheet: -0.69 (0.50), residues: 118 loop : -1.67 (0.25), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 221 TYR 0.014 0.001 TYR A 325 PHE 0.011 0.001 PHE A 97 TRP 0.009 0.001 TRP A 476 HIS 0.004 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (12742) covalent geometry : angle 0.74222 / 0.35 (17828) hydrogen bonds : bond 0.05399 / 3.50 ( 430) hydrogen bonds : angle 4.46191 / 3.12 ( 1211) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.408 Fit side-chains REVERT: A 321 MET cc_start: 0.8522 (mmt) cc_final: 0.8095 (mmm) REVERT: A 441 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8479 (mp0) REVERT: A 540 LEU cc_start: 0.7018 (tp) cc_final: 0.6671 (mp) REVERT: A 586 ARG cc_start: 0.7688 (ptt90) cc_final: 0.7382 (ptt90) REVERT: A 629 ARG cc_start: 0.7043 (mmm160) cc_final: 0.6767 (mmt180) REVERT: A 631 MET cc_start: 0.8296 (mmm) cc_final: 0.8044 (mmm) outliers start: 10 outliers final: 6 residues processed: 50 average time/residue: 0.1205 time to fit residues: 8.7625 Evaluate side-chains 41 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 1146 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN ** A 595 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 = 0.3717 r_free = 0.3717 target = 0.098077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.063643 restraints weight = 31474.171| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.64 r_work: 0.2886 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12742 Z= 0.231 Angle : 0.790 12.308 17828 Z= 0.369 Chirality : 0.061 0.560 2061 Planarity : 0.004 0.047 1745 Dihedral : 19.045 172.394 2888 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.99 % Allowed : 12.72 % Favored : 86.28 % 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: -0.99 (0.24), residues: 1110 helix: 0.34 (0.22), residues: 541 sheet: -0.97 (0.53), residues: 107 loop : -1.76 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 70 TYR 0.018 0.002 TYR A 325 PHE 0.020 0.002 PHE A 491 TRP 0.013 0.002 TRP A 476 HIS 0.009 0.002 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 (12742) covalent geometry : angle 0.79049 / 0.37 (17828) hydrogen bonds : bond 0.06561 / 4.24 ( 430) hydrogen bonds : angle 4.44897 / 3.09 ( 1211) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.444 Fit side-chains REVERT: A 90 MET cc_start: 0.9007 (tpp) cc_final: 0.8738 (tpp) REVERT: A 321 MET cc_start: 0.8621 (mmt) cc_final: 0.8248 (mmm) REVERT: A 531 THR cc_start: 0.5385 (OUTLIER) cc_final: 0.5049 (p) outliers start: 10 outliers final: 8 residues processed: 43 average time/residue: 0.1064 time to fit residues: 7.3093 Evaluate side-chains 41 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 64 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.0770 chunk 34 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 86 optimal weight: 0.0770 chunk 72 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 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 = 0.3722 r_free = 0.3722 target = 0.098431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.068615 restraints weight = 31341.850| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.37 r_work: 0.2890 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12742 Z= 0.135 Angle : 0.676 10.644 17828 Z= 0.318 Chirality : 0.055 0.460 2061 Planarity : 0.003 0.045 1745 Dihedral : 19.140 172.038 2888 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.49 % Allowed : 13.22 % Favored : 85.29 % 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: -0.71 (0.24), residues: 1110 helix: 0.58 (0.23), residues: 537 sheet: -0.86 (0.49), residues: 118 loop : -1.62 (0.25), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 951 TYR 0.013 0.001 TYR A 325 PHE 0.009 0.001 PHE A 97 TRP 0.009 0.001 TRP A 476 HIS 0.003 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (12742) covalent geometry : angle 0.67573 / 0.32 (17828) hydrogen bonds : bond 0.04972 / 3.20 ( 430) hydrogen bonds : angle 4.23367 / 2.97 ( 1211) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 441 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8551 (mp0) REVERT: A 531 THR cc_start: 0.5567 (OUTLIER) cc_final: 0.5156 (p) REVERT: A 629 ARG cc_start: 0.7413 (mmm-85) cc_final: 0.7129 (mmt180) outliers start: 15 outliers final: 6 residues processed: 46 average time/residue: 0.1013 time to fit residues: 7.4567 Evaluate side-chains 41 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.0980 chunk 86 optimal weight: 0.0370 chunk 21 optimal weight: 6.9990 chunk 83 optimal weight: 0.0670 chunk 103 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 980 ASN A1177 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.099531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.069162 restraints weight = 31317.562| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.53 r_work: 0.2889 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12742 Z= 0.130 Angle : 0.653 9.592 17828 Z= 0.306 Chirality : 0.053 0.355 2061 Planarity : 0.003 0.045 1745 Dihedral : 19.101 171.841 2888 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.29 % Allowed : 14.21 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.25), residues: 1110 helix: 0.74 (0.23), residues: 537 sheet: -0.85 (0.49), residues: 118 loop : -1.52 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 951 TYR 0.012 0.001 TYR A 325 PHE 0.009 0.001 PHE A 491 TRP 0.008 0.001 TRP A 476 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (12742) covalent geometry : angle 0.65340 / 0.31 (17828) hydrogen bonds : bond 0.04636 / 3.00 ( 430) hydrogen bonds : angle 4.13240 / 2.91 ( 1211) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 441 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8544 (mp0) REVERT: A 534 MET cc_start: 0.2764 (ppp) cc_final: 0.0344 (ppp) REVERT: A 629 ARG cc_start: 0.7375 (mmm-85) cc_final: 0.7092 (mmt180) REVERT: A 631 MET cc_start: 0.8550 (mmm) cc_final: 0.8262 (mmm) REVERT: A 696 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8003 (mm) outliers start: 13 outliers final: 7 residues processed: 45 average time/residue: 0.1002 time to fit residues: 7.2700 Evaluate side-chains 43 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1177 ASN Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 40 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 98 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.099360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.065319 restraints weight = 31165.187| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.63 r_work: 0.2918 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12742 Z= 0.134 Angle : 0.649 9.521 17828 Z= 0.303 Chirality : 0.052 0.333 2061 Planarity : 0.003 0.043 1745 Dihedral : 19.090 171.944 2888 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.09 % Allowed : 14.41 % Favored : 84.49 % 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: -0.46 (0.25), residues: 1110 helix: 0.81 (0.23), residues: 537 sheet: -0.85 (0.49), residues: 118 loop : -1.50 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 951 TYR 0.013 0.001 TYR A 325 PHE 0.010 0.001 PHE A 491 TRP 0.007 0.001 TRP A 476 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (12742) covalent geometry : angle 0.64890 / 0.30 (17828) hydrogen bonds : bond 0.04647 / 3.02 ( 430) hydrogen bonds : angle 4.08414 / 2.87 ( 1211) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 441 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8486 (mp0) REVERT: A 629 ARG cc_start: 0.7344 (mmm-85) cc_final: 0.7057 (mmt180) REVERT: A 631 MET cc_start: 0.8527 (mmm) cc_final: 0.8190 (mmm) REVERT: A 696 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8053 (mm) outliers start: 11 outliers final: 7 residues processed: 43 average time/residue: 0.1072 time to fit residues: 7.2261 Evaluate side-chains 42 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 6 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 36 optimal weight: 0.0370 chunk 7 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1177 ASN A1308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.099723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.069690 restraints weight = 31206.537| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.43 r_work: 0.2917 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12742 Z= 0.116 Angle : 0.627 9.331 17828 Z= 0.293 Chirality : 0.051 0.329 2061 Planarity : 0.003 0.043 1745 Dihedral : 19.051 172.036 2888 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.19 % Allowed : 14.81 % Favored : 84.00 % 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: -0.36 (0.25), residues: 1110 helix: 0.90 (0.23), residues: 541 sheet: -0.78 (0.50), residues: 118 loop : -1.49 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 535 TYR 0.011 0.001 TYR A 325 PHE 0.008 0.001 PHE A 491 TRP 0.006 0.001 TRP A 476 HIS 0.003 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 (12742) covalent geometry : angle 0.62715 / 0.29 (17828) hydrogen bonds : bond 0.04174 / 2.70 ( 430) hydrogen bonds : angle 3.97916 / 2.81 ( 1211) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 441 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8515 (mp0) REVERT: A 629 ARG cc_start: 0.7328 (mmm-85) cc_final: 0.7035 (mmt180) REVERT: A 696 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8054 (mm) REVERT: A 1307 GLU cc_start: 0.8680 (tp30) cc_final: 0.8450 (tp30) outliers start: 12 outliers final: 7 residues processed: 46 average time/residue: 0.1090 time to fit residues: 8.0354 Evaluate side-chains 44 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 23 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 91 optimal weight: 0.0870 chunk 94 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.099153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.069742 restraints weight = 31104.689| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.40 r_work: 0.2898 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12742 Z= 0.127 Angle : 0.633 9.246 17828 Z= 0.295 Chirality : 0.051 0.341 2061 Planarity : 0.003 0.043 1745 Dihedral : 19.012 172.343 2888 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.29 % Allowed : 14.91 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.25), residues: 1110 helix: 0.96 (0.23), residues: 545 sheet: -0.73 (0.50), residues: 118 loop : -1.50 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 951 TYR 0.012 0.001 TYR A 325 PHE 0.023 0.001 PHE A 432 TRP 0.007 0.001 TRP A 476 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (12742) covalent geometry : angle 0.63282 / 0.30 (17828) hydrogen bonds : bond 0.04432 / 2.86 ( 430) hydrogen bonds : angle 3.97231 / 2.80 ( 1211) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 441 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8560 (mp0) REVERT: A 696 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8055 (mm) REVERT: A 1307 GLU cc_start: 0.8710 (tp30) cc_final: 0.8454 (tp30) outliers start: 13 outliers final: 10 residues processed: 47 average time/residue: 0.1055 time to fit residues: 7.9160 Evaluate side-chains 47 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1177 ASN Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 119 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 chunk 93 optimal weight: 0.0570 chunk 71 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 86 optimal weight: 0.0050 chunk 88 optimal weight: 0.6980 overall best weight: 0.3712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.100549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.066500 restraints weight = 31239.487| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.65 r_work: 0.2947 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12742 Z= 0.108 Angle : 0.624 9.213 17828 Z= 0.290 Chirality : 0.050 0.330 2061 Planarity : 0.003 0.042 1745 Dihedral : 18.993 172.347 2888 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.99 % Allowed : 15.31 % Favored : 83.70 % 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: -0.24 (0.25), residues: 1110 helix: 1.01 (0.23), residues: 541 sheet: -0.70 (0.49), residues: 118 loop : -1.44 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 629 TYR 0.010 0.001 TYR A 325 PHE 0.007 0.001 PHE A1235 TRP 0.007 0.001 TRP A 476 HIS 0.003 0.001 HIS A 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.11 (12742) covalent geometry : angle 0.62416 / 0.29 (17828) hydrogen bonds : bond 0.04093 / 2.64 ( 430) hydrogen bonds : angle 3.93806 / 2.78 ( 1211) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 441 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8470 (mp0) REVERT: A 696 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8146 (mm) REVERT: A 1307 GLU cc_start: 0.8624 (tp30) cc_final: 0.8397 (tp30) outliers start: 10 outliers final: 7 residues processed: 44 average time/residue: 0.1045 time to fit residues: 7.3942 Evaluate side-chains 44 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.098312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.068354 restraints weight = 30896.577| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.28 r_work: 0.2892 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12742 Z= 0.160 Angle : 0.668 11.367 17828 Z= 0.310 Chirality : 0.052 0.365 2061 Planarity : 0.003 0.044 1745 Dihedral : 18.993 172.904 2888 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.19 % Allowed : 15.11 % Favored : 83.70 % 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: -0.39 (0.25), residues: 1110 helix: 0.88 (0.23), residues: 551 sheet: -0.73 (0.49), residues: 118 loop : -1.57 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 951 TYR 0.015 0.001 TYR A 325 PHE 0.014 0.001 PHE A 491 TRP 0.008 0.001 TRP A 476 HIS 0.006 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (12742) covalent geometry : angle 0.66814 / 0.31 (17828) hydrogen bonds : bond 0.04992 / 3.22 ( 430) hydrogen bonds : angle 4.00935 / 2.82 ( 1211) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2719.31 seconds wall clock time: 47 minutes 25.92 seconds (2845.92 seconds total)