Starting phenix.real_space_refine on Fri Jul 3 05:49:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s4v_24835/07_2026/7s4v_24835.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s4v_24835/07_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_24835/07_2026/7s4v_24835.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s4v_24835/07_2026/7s4v_24835.cif" model { file = "/net/cci-nas-00/data/ceres_data/7s4v_24835/07_2026/7s4v_24835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s4v_24835/07_2026/7s4v_24835.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s4v_24835/07_2026/7s4v_24835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s4v_24835/07_2026/7s4v_24835.map" } 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-dev-6108/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: {'RNA': 98} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 52, 'rna3p_pyr': 33} Link IDs: {'rna2p': 13, 'rna3p': 84} 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: 2.35, per 1000 atoms: 0.19 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: 0.93 Conformation dependent library (CDL) restraints added in 504.8 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: 1.16 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: 2.63 Time building geometry restraints manager: 1.29 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: 17416 1.73 - 3.45: 365 3.45 - 5.18: 39 5.18 - 6.90: 6 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: 7085 35.01 - 70.03: 300 70.03 - 105.04: 13 105.04 - 140.06: 1 140.06 - 175.07: 7 Dihedral angle restraints: 7406 sinusoidal: 4107 harmonic: 3299 Sorted by residual: 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 54.05 145.95 1 1.50e+01 4.44e-03 7.80e+01 dihedral pdb=" CA LEU A 258 " pdb=" C LEU A 258 " pdb=" N ALA A 259 " pdb=" CA ALA A 259 " ideal model delta harmonic sigma weight residual 180.00 152.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" C4' DC D 2 " pdb=" C3' DC D 2 " pdb=" O3' DC D 2 " pdb=" P DT D 3 " ideal model delta sinusoidal sigma weight residual -140.00 35.07 -175.07 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1607 0.043 - 0.086: 372 0.086 - 0.129: 70 0.129 - 0.173: 10 0.173 - 0.216: 2 Chirality restraints: 2061 Sorted by residual: chirality pdb=" CB VAL A1259 " pdb=" CA VAL A1259 " pdb=" CG1 VAL A1259 " pdb=" CG2 VAL A1259 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA GLU A1260 " pdb=" N GLU A1260 " pdb=" C GLU A1260 " pdb=" CB GLU A1260 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" C3' A B 38 " pdb=" C4' A B 38 " pdb=" O3' A B 38 " pdb=" C2' A B 38 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 7.18e-01 ... (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: 6.060 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.380 Find NCS groups from input model: 0.040 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.840 ------------------------------------------------------------------------------- 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= 0.230 Angle : 0.576 8.627 17828 Z= 0.383 Chirality : 0.039 0.216 2061 Planarity : 0.004 0.067 1745 Dihedral : 17.534 175.071 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 0.00319 / 0.23 (12742) covalent geometry : angle 0.57582 / 0.38 (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 : 0.411 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: 0.1244 time to fit residues: 14.0114 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 : 0.269 ------------------------------------------------------------------------------- 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: 3.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 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: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 GLN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3803 r_free = 0.3803 target = 0.100519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.071757 restraints weight = 31305.769| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.50 r_work: 0.2964 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12742 Z= 0.223 Angle : 0.622 7.562 17828 Z= 0.338 Chirality : 0.042 0.235 2061 Planarity : 0.004 0.049 1745 Dihedral : 17.192 172.742 2888 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.40 % Allowed : 7.85 % Favored : 91.75 % 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: -0.04 (0.22), residues: 541 sheet: -0.70 (0.50), residues: 118 loop : -1.68 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 221 TYR 0.017 0.002 TYR A 325 PHE 0.021 0.002 PHE A 643 TRP 0.012 0.002 TRP A 476 HIS 0.008 0.002 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (12742) covalent geometry : angle 0.62249 / 0.34 (17828) hydrogen bonds : bond 0.06869 / 4.47 ( 430) hydrogen bonds : angle 4.91965 / 3.42 ( 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 : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 540 LEU cc_start: 0.6931 (tp) cc_final: 0.6568 (mp) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.0946 time to fit residues: 6.1215 Evaluate side-chains 41 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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: 0.6980 chunk 5 optimal weight: 0.6980 chunk 55 optimal weight: 9.9990 chunk 47 optimal weight: 0.0670 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 595 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.100802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.071323 restraints weight = 31813.898| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.40 r_work: 0.2974 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12742 Z= 0.144 Angle : 0.528 9.270 17828 Z= 0.288 Chirality : 0.039 0.229 2061 Planarity : 0.003 0.048 1745 Dihedral : 17.162 172.324 2888 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.99 % Allowed : 10.24 % Favored : 88.77 % 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: -0.87 (0.25), residues: 1110 helix: 0.40 (0.23), residues: 533 sheet: -0.69 (0.50), residues: 118 loop : -1.69 (0.25), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 221 TYR 0.014 0.001 TYR A 325 PHE 0.025 0.001 PHE A 643 TRP 0.010 0.001 TRP A 476 HIS 0.005 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (12742) covalent geometry : angle 0.52837 / 0.29 (17828) hydrogen bonds : bond 0.05469 / 3.58 ( 430) hydrogen bonds : angle 4.49226 / 3.14 ( 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 : 0.403 Fit side-chains revert: symmetry clash REVERT: A 321 MET cc_start: 0.8521 (mmt) cc_final: 0.8109 (mmm) REVERT: A 540 LEU cc_start: 0.7088 (tp) cc_final: 0.6724 (mp) REVERT: A 586 ARG cc_start: 0.7676 (ptt90) cc_final: 0.7362 (ptt90) REVERT: A 629 ARG cc_start: 0.7423 (mmm-85) cc_final: 0.7194 (mmt180) REVERT: A 631 MET cc_start: 0.8322 (mmm) cc_final: 0.8089 (mmm) outliers start: 10 outliers final: 7 residues processed: 49 average time/residue: 0.0986 time to fit residues: 7.1237 Evaluate side-chains 42 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 651 LEU Chi-restraints excluded: chain A residue 657 THR 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: 3.9990 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.097682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.068697 restraints weight = 31365.512| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.40 r_work: 0.2910 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12742 Z= 0.222 Angle : 0.595 7.645 17828 Z= 0.321 Chirality : 0.041 0.249 2061 Planarity : 0.004 0.049 1745 Dihedral : 17.242 171.949 2888 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.09 % Allowed : 12.33 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.24), residues: 1110 helix: 0.37 (0.22), residues: 541 sheet: -1.01 (0.52), residues: 108 loop : -1.74 (0.25), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 70 TYR 0.018 0.002 TYR A 325 PHE 0.019 0.002 PHE A 491 TRP 0.013 0.002 TRP A 476 HIS 0.008 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 (12742) covalent geometry : angle 0.59494 / 0.32 (17828) hydrogen bonds : bond 0.06437 / 4.17 ( 430) hydrogen bonds : angle 4.46549 / 3.11 ( 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 47 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 321 MET cc_start: 0.8621 (mmt) cc_final: 0.8237 (mmm) REVERT: A 531 THR cc_start: 0.5283 (OUTLIER) cc_final: 0.4982 (p) REVERT: A 540 LEU cc_start: 0.7107 (tp) cc_final: 0.6753 (mp) outliers start: 11 outliers final: 8 residues processed: 43 average time/residue: 0.0938 time to fit residues: 6.3767 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 : 0.401 ------------------------------------------------------------------------------- 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 305 ILE 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 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: 1.9990 chunk 58 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 86 optimal weight: 0.0010 chunk 72 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.099495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.066274 restraints weight = 31541.046| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.59 r_work: 0.2979 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2287 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= 0.117 Angle : 0.501 8.119 17828 Z= 0.274 Chirality : 0.038 0.227 2061 Planarity : 0.003 0.046 1745 Dihedral : 17.201 171.554 2888 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.49 % Allowed : 12.72 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.68 (0.25), residues: 1110 helix: 0.62 (0.23), residues: 537 sheet: -0.83 (0.49), residues: 118 loop : -1.63 (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 0.014 0.001 PHE A 643 TRP 0.009 0.001 TRP A 476 HIS 0.005 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 (12742) covalent geometry : angle 0.50070 / 0.27 (17828) hydrogen bonds : bond 0.04785 / 3.10 ( 430) hydrogen bonds : angle 4.21522 / 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 52 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8485 (mp0) REVERT: A 531 THR cc_start: 0.5515 (OUTLIER) cc_final: 0.5097 (p) REVERT: A 629 ARG cc_start: 0.7372 (mmm-85) cc_final: 0.7083 (mmt180) outliers start: 15 outliers final: 8 residues processed: 50 average time/residue: 0.0763 time to fit residues: 6.3388 Evaluate side-chains 44 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 404 THR 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 953 VAL 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: 0.2980 chunk 40 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 980 ASN A1177 ASN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.098508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.069772 restraints weight = 31300.412| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.41 r_work: 0.2946 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2437 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= 0.149 Angle : 0.520 8.642 17828 Z= 0.282 Chirality : 0.039 0.226 2061 Planarity : 0.003 0.045 1745 Dihedral : 17.205 171.495 2888 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.79 % Allowed : 14.21 % 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: -0.65 (0.25), residues: 1110 helix: 0.63 (0.23), residues: 543 sheet: -0.85 (0.49), residues: 118 loop : -1.61 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 951 TYR 0.014 0.001 TYR A 325 PHE 0.013 0.001 PHE A 491 TRP 0.009 0.001 TRP A 476 HIS 0.005 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (12742) covalent geometry : angle 0.52037 / 0.28 (17828) hydrogen bonds : bond 0.05142 / 3.33 ( 430) hydrogen bonds : angle 4.19962 / 2.95 ( 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 53 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 35 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8555 (mp0) REVERT: A 534 MET cc_start: 0.2832 (ppp) cc_final: 0.0363 (ppp) REVERT: A 631 MET cc_start: 0.8500 (mmm) cc_final: 0.8160 (mmm) REVERT: A 696 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7973 (mm) outliers start: 18 outliers final: 13 residues processed: 50 average time/residue: 0.0966 time to fit residues: 7.4354 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 : 0.258 ------------------------------------------------------------------------------- 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 404 THR Chi-restraints excluded: chain A residue 441 GLU 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 696 LEU Chi-restraints excluded: chain A residue 751 MET 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 1318 LEU Chi-restraints excluded: chain A residue 1337 THR Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 40 optimal weight: 0.5980 chunk 123 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.098901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.069702 restraints weight = 31238.362| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.37 r_work: 0.2952 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12742 Z= 0.132 Angle : 0.502 7.523 17828 Z= 0.273 Chirality : 0.038 0.222 2061 Planarity : 0.003 0.044 1745 Dihedral : 17.210 171.478 2888 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.39 % Allowed : 14.41 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.25), residues: 1110 helix: 0.71 (0.23), residues: 537 sheet: -0.87 (0.49), residues: 118 loop : -1.56 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 629 TYR 0.013 0.001 TYR A 325 PHE 0.010 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 0.00275 / 0.13 (12742) covalent geometry : angle 0.50175 / 0.27 (17828) hydrogen bonds : bond 0.04850 / 3.14 ( 430) hydrogen bonds : angle 4.14524 / 2.91 ( 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 47 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8534 (mp0) REVERT: A 696 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8012 (mm) outliers start: 14 outliers final: 11 residues processed: 45 average time/residue: 0.0954 time to fit residues: 6.8597 Evaluate side-chains 46 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 404 THR Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 552 LEU 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 751 MET Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 6 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 107 optimal weight: 0.0670 chunk 36 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 69 optimal weight: 0.1980 chunk 115 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.100420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.071147 restraints weight = 31217.974| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.46 r_work: 0.2981 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12742 Z= 0.101 Angle : 0.470 7.297 17828 Z= 0.255 Chirality : 0.036 0.198 2061 Planarity : 0.003 0.043 1745 Dihedral : 17.167 171.364 2888 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.29 % Allowed : 14.51 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.25), residues: 1110 helix: 0.88 (0.23), residues: 540 sheet: -0.75 (0.49), residues: 118 loop : -1.50 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 535 TYR 0.010 0.001 TYR A 325 PHE 0.008 0.001 PHE A 97 TRP 0.006 0.001 TRP A 476 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.10 (12742) covalent geometry : angle 0.47047 / 0.26 (17828) hydrogen bonds : bond 0.03941 / 2.56 ( 430) hydrogen bonds : angle 3.99166 / 2.82 ( 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 47 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8516 (mp0) REVERT: A 631 MET cc_start: 0.8503 (mmm) cc_final: 0.8202 (mmm) REVERT: A 696 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8025 (mm) outliers start: 13 outliers final: 9 residues processed: 45 average time/residue: 0.0978 time to fit residues: 7.1172 Evaluate side-chains 44 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 404 THR 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 1318 LEU 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: 1.9990 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 103 optimal weight: 0.0670 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.098868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.070267 restraints weight = 31267.367| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.32 r_work: 0.2954 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12742 Z= 0.142 Angle : 0.500 6.874 17828 Z= 0.270 Chirality : 0.038 0.208 2061 Planarity : 0.003 0.045 1745 Dihedral : 17.166 171.812 2888 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.49 % Allowed : 14.71 % 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: -0.45 (0.25), residues: 1110 helix: 0.84 (0.23), residues: 550 sheet: -0.77 (0.49), residues: 118 loop : -1.62 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 40 TYR 0.014 0.001 TYR A 325 PHE 0.023 0.001 PHE A 432 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 0.00305 / 0.14 (12742) covalent geometry : angle 0.49989 / 0.27 (17828) hydrogen bonds : bond 0.04891 / 3.15 ( 430) hydrogen bonds : angle 4.04797 / 2.85 ( 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 48 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 629 ARG cc_start: 0.7181 (mmm160) cc_final: 0.6965 (mmm-85) REVERT: A 631 MET cc_start: 0.8543 (mmm) cc_final: 0.8247 (mmm) REVERT: A 696 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8160 (mm) outliers start: 15 outliers final: 11 residues processed: 46 average time/residue: 0.0905 time to fit residues: 6.6955 Evaluate side-chains 43 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 404 THR Chi-restraints excluded: chain A residue 552 LEU 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 1142 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 119 optimal weight: 5.9990 chunk 25 optimal weight: 0.0870 chunk 75 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 86 optimal weight: 0.0870 chunk 88 optimal weight: 0.5980 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.100025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.071442 restraints weight = 31317.680| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.40 r_work: 0.2972 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2787 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= 0.100 Angle : 0.478 9.416 17828 Z= 0.258 Chirality : 0.036 0.201 2061 Planarity : 0.003 0.043 1745 Dihedral : 17.123 171.801 2888 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.09 % Allowed : 15.11 % 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: -0.34 (0.25), residues: 1110 helix: 0.92 (0.23), residues: 546 sheet: -0.73 (0.49), residues: 118 loop : -1.53 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 221 TYR 0.011 0.001 TYR A 325 PHE 0.007 0.001 PHE A1235 TRP 0.008 0.001 TRP A 476 HIS 0.003 0.001 HIS A 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.10 (12742) covalent geometry : angle 0.47822 / 0.26 (17828) hydrogen bonds : bond 0.04111 / 2.64 ( 430) hydrogen bonds : angle 3.98808 / 2.81 ( 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 42 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 629 ARG cc_start: 0.7172 (mmm160) cc_final: 0.6951 (mmm-85) REVERT: A 631 MET cc_start: 0.8493 (mmm) cc_final: 0.8183 (mmm) REVERT: A 696 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8051 (mm) outliers start: 11 outliers final: 10 residues processed: 41 average time/residue: 0.0990 time to fit residues: 6.4209 Evaluate side-chains 43 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 404 THR 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 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 20 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 0.4980 chunk 3 optimal weight: 0.0270 chunk 116 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 overall best weight: 0.5840 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.099867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.071487 restraints weight = 31194.218| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.33 r_work: 0.2977 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12742 Z= 0.110 Angle : 0.485 12.627 17828 Z= 0.258 Chirality : 0.037 0.198 2061 Planarity : 0.003 0.043 1745 Dihedral : 17.063 172.007 2888 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.09 % Allowed : 15.31 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.25), residues: 1110 helix: 0.92 (0.23), residues: 553 sheet: -0.73 (0.49), residues: 118 loop : -1.54 (0.27), residues: 439 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 0.009 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 0.00221 / 0.11 (12742) covalent geometry : angle 0.48520 / 0.26 (17828) hydrogen bonds : bond 0.04188 / 2.69 ( 430) hydrogen bonds : angle 3.96128 / 2.79 ( 1211) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2470.76 seconds wall clock time: 43 minutes 7.99 seconds (2587.99 seconds total)