Starting phenix.real_space_refine on Fri Jul 3 12:53:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z4j_14499/07_2026/7z4j_14499.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4j_14499/07_2026/7z4j_14499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7z4j_14499/07_2026/7z4j_14499.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z4j_14499/07_2026/7z4j_14499.cif" model { file = "/net/cci-nas-00/data/ceres_data/7z4j_14499/07_2026/7z4j_14499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4j_14499/07_2026/7z4j_14499.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z4j_14499/07_2026/7z4j_14499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4j_14499/07_2026/7z4j_14499.map" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 138 5.49 5 Mg 4 5.21 5 S 22 5.16 5 C 8344 2.51 5 N 2443 2.21 5 O 2997 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 13948 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2081 Classifications: {'DNA': 1, 'RNA': 97} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 52, 'rna3p_pyr': 33} Link IDs: {'rna2p': 12, 'rna3p': 85} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G%5*END:plan': 1, ' G%5*END:plan2': 1} Unresolved non-hydrogen planarities: 14 Chain: "c" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 263 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "C" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 324 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DG%5*END:plan': 1, ' DG%5*END:plan2': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 269 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 10999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 10999 Classifications: {'peptide': 1345} Link IDs: {'PTRANS': 35, 'TRANS': 1309} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.40, per 1000 atoms: 0.17 Number of scatterers: 13948 At special positions: 0 Unit cell: (85.15, 119.6, 120.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 138 15.00 Mg 4 11.99 O 2997 8.00 N 2443 7.00 C 8344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 508.8 milliseconds 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2556 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 10 sheets defined 55.7% alpha, 9.7% beta 50 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'B' and resid 59 through 94 removed outlier: 4.818A pdb=" N ASN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS B 92 " --> pdb=" O ASN B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 104 Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 134 through 145 removed outlier: 3.706A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 Processing helix chain 'B' and resid 181 through 196 removed outlier: 3.835A pdb=" N LEU B 195 " --> pdb=" O THR B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 217 through 229 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.600A pdb=" N PHE B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 282 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 286 through 307 Processing helix chain 'B' and resid 315 through 343 Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 368 through 382 Proline residue: B 378 - end of helix Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.810A pdb=" N ASN B 407 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY B 408 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.157A pdb=" N HIS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 477 through 481 removed outlier: 3.545A pdb=" N VAL B 481 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 494 Processing helix chain 'B' and resid 512 through 526 removed outlier: 3.997A pdb=" N LYS B 526 " --> pdb=" O ASN B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 567 Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 603 through 609 removed outlier: 3.622A pdb=" N LEU B 607 " --> pdb=" O ASP B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 626 Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'B' and resid 664 through 668 Processing helix chain 'B' and resid 678 through 685 Processing helix chain 'B' and resid 692 through 698 Processing helix chain 'B' and resid 703 through 712 Processing helix chain 'B' and resid 713 through 715 No H-bonds generated for 'chain 'B' and resid 713 through 715' Processing helix chain 'B' and resid 719 through 727 Processing helix chain 'B' and resid 731 through 751 removed outlier: 4.385A pdb=" N LYS B 735 " --> pdb=" O PRO B 731 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 776 Processing helix chain 'B' and resid 779 through 792 removed outlier: 3.550A pdb=" N ARG B 783 " --> pdb=" O GLU B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 799 Processing helix chain 'B' and resid 804 through 807 Processing helix chain 'B' and resid 808 through 817 Processing helix chain 'B' and resid 851 through 853 No H-bonds generated for 'chain 'B' and resid 851 through 853' Processing helix chain 'B' and resid 860 through 867 Processing helix chain 'B' and resid 872 through 889 removed outlier: 5.303A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N TYR B 882 " --> pdb=" O LYS B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 901 Processing helix chain 'B' and resid 902 through 904 No H-bonds generated for 'chain 'B' and resid 902 through 904' Processing helix chain 'B' and resid 909 through 915 removed outlier: 4.417A pdb=" N GLY B 915 " --> pdb=" O ASP B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 940 removed outlier: 4.012A pdb=" N LEU B 921 " --> pdb=" O ILE B 917 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 922 " --> pdb=" O LYS B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 970 Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.458A pdb=" N ALA B 984 " --> pdb=" O ASN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1009 Processing helix chain 'B' and resid 1030 through 1043 removed outlier: 4.309A pdb=" N MET B1043 " --> pdb=" O TYR B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1047 Processing helix chain 'B' and resid 1078 through 1088 Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1170 through 1177 Processing helix chain 'B' and resid 1177 through 1186 Processing helix chain 'B' and resid 1229 through 1240 Processing helix chain 'B' and resid 1248 through 1262 Processing helix chain 'B' and resid 1263 through 1280 removed outlier: 4.326A pdb=" N ASP B1267 " --> pdb=" O LYS B1263 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1301 through 1313 Processing helix chain 'B' and resid 1314 through 1317 removed outlier: 3.575A pdb=" N ASN B1317 " --> pdb=" O THR B1314 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1314 through 1317' Processing helix chain 'B' and resid 1340 through 1344 Processing helix chain 'B' and resid 1363 through 1365 No H-bonds generated for 'chain 'B' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 959 removed outlier: 4.632A pdb=" N ILE B 11 " --> pdb=" O GLU B 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 46 removed outlier: 9.929A pdb=" N GLU B1357 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS B 33 " --> pdb=" O GLU B1357 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ARG B1359 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU B 35 " --> pdb=" O ARG B1359 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ASP B1361 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU B1219 " --> pdb=" O ALA B1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 507 through 509 removed outlier: 5.621A pdb=" N LEU B 662 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 539 Processing sheet with id=AA5, first strand: chain 'B' and resid 836 through 840 Processing sheet with id=AA6, first strand: chain 'B' and resid 1049 through 1050 Processing sheet with id=AA7, first strand: chain 'B' and resid 1063 through 1065 removed outlier: 3.881A pdb=" N TRP B1074 " --> pdb=" O GLU B1064 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1156 through 1163 removed outlier: 7.224A pdb=" N ILE B1166 " --> pdb=" O ALA B1140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1156 through 1163 Processing sheet with id=AB1, first strand: chain 'B' and resid 1324 through 1326 536 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 123 hydrogen bonds 238 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 1.32 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: 2474 1.33 - 1.45: 4187 1.45 - 1.57: 7502 1.57 - 1.69: 276 1.69 - 1.81: 42 Bond restraints: 14481 Sorted by residual: bond pdb=" C3' DG C 16 " pdb=" O3' DG C 16 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.27e+01 bond pdb=" C4' DG C 16 " pdb=" C3' DG C 16 " ideal model delta sigma weight residual 1.529 1.494 0.035 1.00e-02 1.00e+04 1.20e+01 bond pdb=" C3' DC C 17 " pdb=" O3' DC C 17 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" C4' DA C 8 " pdb=" C3' DA C 8 " ideal model delta sigma weight residual 1.529 1.498 0.031 1.00e-02 1.00e+04 9.86e+00 bond pdb=" C3' DA c 0 " pdb=" O3' DA c 0 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 9.74e+00 ... (remaining 14476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 19739 1.55 - 3.10: 379 3.10 - 4.65: 26 4.65 - 6.20: 1 6.20 - 7.75: 1 Bond angle restraints: 20146 Sorted by residual: angle pdb=" O4' DC C 7 " pdb=" C4' DC C 7 " pdb=" C3' DC C 7 " ideal model delta sigma weight residual 106.00 102.90 3.10 6.00e-01 2.78e+00 2.67e+01 angle pdb=" O4' DC c 2 " pdb=" C4' DC c 2 " pdb=" C3' DC c 2 " ideal model delta sigma weight residual 106.00 103.02 2.98 6.00e-01 2.78e+00 2.46e+01 angle pdb=" O4' DA C 8 " pdb=" C4' DA C 8 " pdb=" C3' DA C 8 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.36e+01 angle pdb=" N3 DT C 4 " pdb=" C4 DT C 4 " pdb=" O4 DT C 4 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" O4' DT C 13 " pdb=" C4' DT C 13 " pdb=" C3' DT C 13 " ideal model delta sigma weight residual 106.00 103.26 2.74 6.00e-01 2.78e+00 2.08e+01 ... (remaining 20141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.77: 7860 19.77 - 39.53: 455 39.53 - 59.30: 165 59.30 - 79.07: 12 79.07 - 98.83: 6 Dihedral angle restraints: 8498 sinusoidal: 4546 harmonic: 3952 Sorted by residual: dihedral pdb=" O4' G A 82 " pdb=" C1' G A 82 " pdb=" N9 G A 82 " pdb=" C4 G A 82 " ideal model delta sinusoidal sigma weight residual 70.00 15.72 54.28 1 2.00e+01 2.50e-03 9.99e+00 dihedral pdb=" N ARG B 653 " pdb=" CA ARG B 653 " pdb=" CB ARG B 653 " pdb=" CG ARG B 653 " ideal model delta sinusoidal sigma weight residual -60.00 -119.38 59.38 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" O5' C A 91 " pdb=" C5' C A 91 " pdb=" C4' C A 91 " pdb=" C3' C A 91 " ideal model delta sinusoidal sigma weight residual -65.00 -123.58 58.58 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 8495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1784 0.042 - 0.084: 407 0.084 - 0.126: 92 0.126 - 0.168: 18 0.168 - 0.209: 4 Chirality restraints: 2305 Sorted by residual: chirality pdb=" C3' DC c -1 " pdb=" C4' DC c -1 " pdb=" O3' DC c -1 " pdb=" C2' DC c -1 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C3' DG C 16 " pdb=" C4' DG C 16 " pdb=" O3' DG C 16 " pdb=" C2' DG C 16 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" C3' DC C 17 " pdb=" C4' DC C 17 " pdb=" O3' DC C 17 " pdb=" C2' DC C 17 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 2302 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A 59 " 0.019 2.00e-02 2.50e+03 1.16e-02 3.04e+00 pdb=" N1 U A 59 " -0.029 2.00e-02 2.50e+03 pdb=" C2 U A 59 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U A 59 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U A 59 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U A 59 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U A 59 " 0.003 2.00e-02 2.50e+03 pdb=" C5 U A 59 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U A 59 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 23 " -0.020 2.00e-02 2.50e+03 1.12e-02 2.83e+00 pdb=" N1 U A 23 " 0.026 2.00e-02 2.50e+03 pdb=" C2 U A 23 " 0.000 2.00e-02 2.50e+03 pdb=" O2 U A 23 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U A 23 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U A 23 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U A 23 " -0.005 2.00e-02 2.50e+03 pdb=" C5 U A 23 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U A 23 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 54 " 0.022 2.00e-02 2.50e+03 9.66e-03 2.80e+00 pdb=" N9 G A 54 " -0.024 2.00e-02 2.50e+03 pdb=" C8 G A 54 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G A 54 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G A 54 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 54 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G A 54 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G A 54 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G A 54 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A 54 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G A 54 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G A 54 " -0.002 2.00e-02 2.50e+03 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 98 2.47 - 3.08: 9436 3.08 - 3.68: 22427 3.68 - 4.29: 33800 4.29 - 4.90: 53227 Nonbonded interactions: 118988 Sorted by model distance: nonbonded pdb=" OP2 DT C 4 " pdb="MG MG B1403 " model vdw 1.860 2.170 nonbonded pdb=" OP1 DT D -3 " pdb="MG MG B1401 " model vdw 1.889 2.170 nonbonded pdb="MG MG A 201 " pdb=" O HOH A 303 " model vdw 1.907 2.170 nonbonded pdb="MG MG B1403 " pdb=" O HOH B1501 " model vdw 1.932 2.170 nonbonded pdb="MG MG A 201 " pdb=" O HOH A 306 " model vdw 1.937 2.170 ... (remaining 118983 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=1.00 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.450 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 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 : 0.005 0.046 14481 Z= 0.337 Angle : 0.510 7.748 20146 Z= 0.349 Chirality : 0.040 0.209 2305 Planarity : 0.003 0.026 2070 Dihedral : 13.567 98.833 5942 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.15 % Allowed : 6.21 % Favored : 91.64 % 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: 0.96 (0.23), residues: 1339 helix: 1.51 (0.20), residues: 691 sheet: -0.59 (0.46), residues: 130 loop : -0.10 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 925 TYR 0.009 0.001 TYR B 155 PHE 0.010 0.001 PHE B1204 TRP 0.003 0.001 TRP B 476 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.34 (14481) covalent geometry : angle 0.50996 / 0.35 (20146) hydrogen bonds : bond 0.11265 / 6.64 ( 651) hydrogen bonds : angle 5.01801 / 2.94 ( 1786) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 216 LEU cc_start: 0.9175 (mt) cc_final: 0.8937 (mp) REVERT: B 248 LEU cc_start: 0.5687 (OUTLIER) cc_final: 0.5372 (tm) REVERT: B 879 MET cc_start: 0.8414 (mmm) cc_final: 0.7929 (mmm) REVERT: B 1078 ARG cc_start: 0.8304 (ptp-110) cc_final: 0.7776 (ptm-80) outliers start: 26 outliers final: 4 residues processed: 101 average time/residue: 0.6752 time to fit residues: 73.6415 Evaluate side-chains 36 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 1033 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 HIS ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 544 GLN B 588 ASN B 650 GLN B 668 ASN B 695 GLN B 805 GLN B 826 GLN B 844 GLN B 885 GLN B1262 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.071787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.050551 restraints weight = 39595.257| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.81 r_work: 0.2766 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14481 Z= 0.151 Angle : 0.512 7.127 20146 Z= 0.281 Chirality : 0.037 0.143 2305 Planarity : 0.003 0.037 2070 Dihedral : 13.800 97.134 3092 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.41 % Allowed : 10.26 % Favored : 88.33 % 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: 1.06 (0.23), residues: 1339 helix: 1.64 (0.20), residues: 693 sheet: -0.84 (0.46), residues: 119 loop : -0.09 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 220 TYR 0.010 0.001 TYR B 529 PHE 0.024 0.001 PHE B 290 TRP 0.004 0.001 TRP B 476 HIS 0.006 0.001 HIS B1297 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (14481) covalent geometry : angle 0.51233 / 0.28 (20146) hydrogen bonds : bond 0.04564 / 2.79 ( 651) hydrogen bonds : angle 4.24057 / 2.49 ( 1786) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 36 time to evaluate : 0.510 Fit side-chains REVERT: B 216 LEU cc_start: 0.9040 (mt) cc_final: 0.8757 (pt) REVERT: B 221 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6872 (ptp-110) REVERT: B 248 LEU cc_start: 0.5775 (OUTLIER) cc_final: 0.5477 (tm) REVERT: B 534 MET cc_start: 0.8011 (mtp) cc_final: 0.7751 (mtm) REVERT: B 879 MET cc_start: 0.8369 (mmm) cc_final: 0.7901 (mmm) REVERT: B 1078 ARG cc_start: 0.8437 (ptp-110) cc_final: 0.7867 (ptm-80) REVERT: B 1189 GLU cc_start: 0.8290 (mp0) cc_final: 0.7971 (pm20) outliers start: 17 outliers final: 6 residues processed: 52 average time/residue: 0.5808 time to fit residues: 33.2211 Evaluate side-chains 39 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 ARG Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1240 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 50 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 133 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 ASN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.071395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.050131 restraints weight = 39820.019| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.82 r_work: 0.2753 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14481 Z= 0.167 Angle : 0.483 6.354 20146 Z= 0.266 Chirality : 0.037 0.136 2305 Planarity : 0.003 0.044 2070 Dihedral : 13.756 97.209 3090 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.49 % Allowed : 10.35 % Favored : 88.16 % 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: 1.04 (0.23), residues: 1339 helix: 1.62 (0.20), residues: 702 sheet: -0.83 (0.46), residues: 119 loop : -0.12 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 220 TYR 0.020 0.001 TYR B1013 PHE 0.039 0.001 PHE B 290 TRP 0.004 0.001 TRP B 476 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (14481) covalent geometry : angle 0.48283 / 0.27 (20146) hydrogen bonds : bond 0.04326 / 2.66 ( 651) hydrogen bonds : angle 4.09464 / 2.40 ( 1786) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 31 time to evaluate : 0.446 Fit side-chains REVERT: B 216 LEU cc_start: 0.9043 (mt) cc_final: 0.8754 (mp) REVERT: B 220 ARG cc_start: 0.8867 (mmm-85) cc_final: 0.8571 (mmm-85) REVERT: B 221 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6582 (ptp-110) REVERT: B 248 LEU cc_start: 0.5803 (OUTLIER) cc_final: 0.5536 (tm) REVERT: B 534 MET cc_start: 0.7960 (mtp) cc_final: 0.7709 (mtm) REVERT: B 628 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6576 (p0) REVERT: B 879 MET cc_start: 0.8384 (mmm) cc_final: 0.7913 (mmm) REVERT: B 1078 ARG cc_start: 0.8475 (ptp-110) cc_final: 0.7931 (ptm-80) outliers start: 18 outliers final: 8 residues processed: 48 average time/residue: 0.5069 time to fit residues: 27.1637 Evaluate side-chains 41 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 221 ARG Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1240 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 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 = 0.3376 r_free = 0.3376 target = 0.071209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.049881 restraints weight = 39780.252| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.82 r_work: 0.2747 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14481 Z= 0.178 Angle : 0.477 6.564 20146 Z= 0.262 Chirality : 0.037 0.137 2305 Planarity : 0.003 0.041 2070 Dihedral : 13.760 98.160 3090 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.82 % Allowed : 10.60 % Favored : 87.58 % 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: 1.05 (0.23), residues: 1339 helix: 1.63 (0.20), residues: 702 sheet: -0.81 (0.47), residues: 119 loop : -0.14 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 629 TYR 0.022 0.001 TYR B1013 PHE 0.011 0.001 PHE B1204 TRP 0.005 0.001 TRP B 464 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (14481) covalent geometry : angle 0.47707 / 0.26 (20146) hydrogen bonds : bond 0.04280 / 2.64 ( 651) hydrogen bonds : angle 4.02836 / 2.36 ( 1786) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 31 time to evaluate : 0.326 Fit side-chains REVERT: B 248 LEU cc_start: 0.5839 (OUTLIER) cc_final: 0.5580 (tm) REVERT: B 534 MET cc_start: 0.7932 (mtp) cc_final: 0.7671 (mtm) REVERT: B 879 MET cc_start: 0.8473 (mmm) cc_final: 0.7964 (mmm) REVERT: B 1078 ARG cc_start: 0.8503 (ptp-110) cc_final: 0.7956 (ptm-80) outliers start: 22 outliers final: 9 residues processed: 52 average time/residue: 0.4903 time to fit residues: 28.9401 Evaluate side-chains 40 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1240 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 80 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 81 optimal weight: 0.0980 chunk 107 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.071871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.050651 restraints weight = 40016.934| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.83 r_work: 0.2765 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14481 Z= 0.130 Angle : 0.455 6.729 20146 Z= 0.251 Chirality : 0.036 0.137 2305 Planarity : 0.003 0.055 2070 Dihedral : 13.743 98.300 3090 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.32 % Allowed : 11.51 % Favored : 87.17 % 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: 1.15 (0.23), residues: 1339 helix: 1.70 (0.20), residues: 702 sheet: -0.78 (0.47), residues: 119 loop : -0.07 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 220 TYR 0.022 0.001 TYR B1013 PHE 0.009 0.001 PHE B1204 TRP 0.004 0.001 TRP B 476 HIS 0.005 0.001 HIS B1297 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (14481) covalent geometry : angle 0.45535 / 0.25 (20146) hydrogen bonds : bond 0.04078 / 2.52 ( 651) hydrogen bonds : angle 3.93574 / 2.30 ( 1786) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 30 time to evaluate : 0.331 Fit side-chains REVERT: B 216 LEU cc_start: 0.9052 (mp) cc_final: 0.8540 (pp) REVERT: B 248 LEU cc_start: 0.5790 (OUTLIER) cc_final: 0.5540 (tm) REVERT: B 534 MET cc_start: 0.7880 (mtp) cc_final: 0.7632 (mtm) REVERT: B 535 ARG cc_start: 0.7682 (tpm170) cc_final: 0.7466 (OUTLIER) REVERT: B 879 MET cc_start: 0.8460 (mmm) cc_final: 0.8011 (mmm) outliers start: 16 outliers final: 8 residues processed: 45 average time/residue: 0.4667 time to fit residues: 23.5840 Evaluate side-chains 37 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1240 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 109 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 121 optimal weight: 0.0170 chunk 25 optimal weight: 0.4980 chunk 23 optimal weight: 0.3980 chunk 134 optimal weight: 0.0470 chunk 10 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.073371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.052346 restraints weight = 39375.997| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.84 r_work: 0.2808 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14481 Z= 0.095 Angle : 0.433 6.385 20146 Z= 0.241 Chirality : 0.035 0.137 2305 Planarity : 0.003 0.038 2070 Dihedral : 13.677 98.437 3090 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.82 % Allowed : 11.34 % Favored : 86.84 % 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: 1.23 (0.23), residues: 1339 helix: 1.79 (0.20), residues: 694 sheet: -0.51 (0.51), residues: 107 loop : -0.11 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 220 TYR 0.026 0.001 TYR B1013 PHE 0.008 0.001 PHE B1045 TRP 0.005 0.001 TRP B 476 HIS 0.004 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.09 (14481) covalent geometry : angle 0.43335 / 0.24 (20146) hydrogen bonds : bond 0.03792 / 2.35 ( 651) hydrogen bonds : angle 3.80646 / 2.20 ( 1786) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 35 time to evaluate : 0.354 Fit side-chains REVERT: B 216 LEU cc_start: 0.9096 (mp) cc_final: 0.8838 (pp) REVERT: B 248 LEU cc_start: 0.5875 (OUTLIER) cc_final: 0.5623 (tm) REVERT: B 402 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.8466 (mp10) REVERT: B 534 MET cc_start: 0.7839 (mtp) cc_final: 0.7610 (mtm) REVERT: B 535 ARG cc_start: 0.7685 (tpm170) cc_final: 0.7475 (OUTLIER) REVERT: B 879 MET cc_start: 0.8450 (mmm) cc_final: 0.8006 (mmm) outliers start: 22 outliers final: 8 residues processed: 51 average time/residue: 0.4852 time to fit residues: 27.7157 Evaluate side-chains 40 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1043 MET Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1216 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 25 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 ASN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 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 = 0.3408 r_free = 0.3408 target = 0.072617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.051513 restraints weight = 39670.203| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.82 r_work: 0.2789 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14481 Z= 0.122 Angle : 0.439 5.981 20146 Z= 0.242 Chirality : 0.035 0.154 2305 Planarity : 0.003 0.039 2070 Dihedral : 13.641 99.502 3090 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.49 % Allowed : 12.42 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.23), residues: 1339 helix: 1.81 (0.20), residues: 701 sheet: -0.65 (0.48), residues: 116 loop : -0.10 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 832 TYR 0.025 0.001 TYR B1013 PHE 0.008 0.001 PHE B1045 TRP 0.004 0.001 TRP B 476 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (14481) covalent geometry : angle 0.43928 / 0.24 (20146) hydrogen bonds : bond 0.03861 / 2.39 ( 651) hydrogen bonds : angle 3.76926 / 2.19 ( 1786) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 31 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: B 248 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5689 (tm) REVERT: B 402 GLN cc_start: 0.9324 (OUTLIER) cc_final: 0.8397 (mp10) REVERT: B 534 MET cc_start: 0.7911 (mtp) cc_final: 0.7662 (mtm) REVERT: B 535 ARG cc_start: 0.7660 (tpm170) cc_final: 0.7444 (OUTLIER) REVERT: B 628 ASP cc_start: 0.6917 (OUTLIER) cc_final: 0.6621 (p0) REVERT: B 879 MET cc_start: 0.8485 (mmm) cc_final: 0.8020 (mmm) outliers start: 18 outliers final: 11 residues processed: 46 average time/residue: 0.5029 time to fit residues: 26.1730 Evaluate side-chains 43 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1216 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 HIS B1297 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.072120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.051046 restraints weight = 39480.876| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.81 r_work: 0.2777 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14481 Z= 0.140 Angle : 0.446 6.663 20146 Z= 0.245 Chirality : 0.035 0.149 2305 Planarity : 0.003 0.039 2070 Dihedral : 13.649 99.696 3090 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.57 % Allowed : 12.42 % Favored : 86.01 % 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: 1.27 (0.23), residues: 1339 helix: 1.83 (0.20), residues: 701 sheet: -0.62 (0.49), residues: 115 loop : -0.09 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 653 TYR 0.026 0.001 TYR B1013 PHE 0.009 0.001 PHE B1204 TRP 0.004 0.001 TRP B 883 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (14481) covalent geometry : angle 0.44638 / 0.25 (20146) hydrogen bonds : bond 0.03934 / 2.44 ( 651) hydrogen bonds : angle 3.79122 / 2.21 ( 1786) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 30 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: B 248 LEU cc_start: 0.5942 (OUTLIER) cc_final: 0.5699 (tm) REVERT: B 402 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.8343 (mp10) REVERT: B 534 MET cc_start: 0.7912 (mtp) cc_final: 0.7652 (mtm) REVERT: B 535 ARG cc_start: 0.7666 (tpm170) cc_final: 0.7458 (tpm170) REVERT: B 628 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6715 (p0) REVERT: B 879 MET cc_start: 0.8530 (mmm) cc_final: 0.8057 (mmm) REVERT: B 1242 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.7163 (m-80) outliers start: 19 outliers final: 9 residues processed: 46 average time/residue: 0.5064 time to fit residues: 26.1964 Evaluate side-chains 43 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1242 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 32 optimal weight: 0.2980 chunk 131 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.072754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.051716 restraints weight = 39640.192| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.83 r_work: 0.2793 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14481 Z= 0.106 Angle : 0.434 7.865 20146 Z= 0.240 Chirality : 0.035 0.141 2305 Planarity : 0.003 0.037 2070 Dihedral : 13.626 99.389 3090 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.57 % Allowed : 12.58 % Favored : 85.84 % 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: 1.33 (0.23), residues: 1339 helix: 1.88 (0.20), residues: 693 sheet: -0.39 (0.51), residues: 105 loop : -0.10 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 653 TYR 0.028 0.001 TYR B1013 PHE 0.008 0.001 PHE B 626 TRP 0.004 0.001 TRP B 476 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.11 (14481) covalent geometry : angle 0.43434 / 0.24 (20146) hydrogen bonds : bond 0.03838 / 2.38 ( 651) hydrogen bonds : angle 3.75398 / 2.18 ( 1786) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 32 time to evaluate : 0.396 Fit side-chains REVERT: B 248 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.5712 (tm) REVERT: B 402 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.8377 (mp10) REVERT: B 534 MET cc_start: 0.7896 (mtp) cc_final: 0.7638 (mtm) REVERT: B 879 MET cc_start: 0.8503 (mmm) cc_final: 0.8011 (mmm) REVERT: B 1242 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.7174 (m-80) outliers start: 19 outliers final: 9 residues processed: 47 average time/residue: 0.4835 time to fit residues: 25.4581 Evaluate side-chains 42 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1242 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 14 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 99 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.073146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.052160 restraints weight = 39390.904| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.84 r_work: 0.2803 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 14481 Z= 0.104 Angle : 0.442 10.014 20146 Z= 0.245 Chirality : 0.035 0.142 2305 Planarity : 0.003 0.039 2070 Dihedral : 13.600 99.424 3090 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.16 % Allowed : 13.00 % Favored : 85.84 % 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: 1.30 (0.23), residues: 1339 helix: 1.90 (0.20), residues: 692 sheet: -0.42 (0.51), residues: 106 loop : -0.16 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 535 TYR 0.027 0.001 TYR B1013 PHE 0.007 0.001 PHE B1045 TRP 0.004 0.001 TRP B 464 HIS 0.004 0.001 HIS B 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (14481) covalent geometry : angle 0.44220 / 0.24 (20146) hydrogen bonds : bond 0.03751 / 2.33 ( 651) hydrogen bonds : angle 3.75737 / 2.18 ( 1786) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: B 248 LEU cc_start: 0.5967 (OUTLIER) cc_final: 0.5742 (tm) REVERT: B 402 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.8375 (mp10) REVERT: B 534 MET cc_start: 0.7970 (mtp) cc_final: 0.7725 (mtm) REVERT: B 879 MET cc_start: 0.8507 (mmm) cc_final: 0.8006 (mmm) REVERT: B 1242 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.7106 (m-80) outliers start: 14 outliers final: 7 residues processed: 43 average time/residue: 0.5108 time to fit residues: 24.8230 Evaluate side-chains 40 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1242 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 38 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 53 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 15 optimal weight: 0.0770 chunk 35 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.073570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.052770 restraints weight = 39519.307| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.81 r_work: 0.2822 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14481 Z= 0.096 Angle : 0.420 5.744 20146 Z= 0.235 Chirality : 0.034 0.137 2305 Planarity : 0.003 0.036 2070 Dihedral : 13.563 99.404 3090 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.08 % Allowed : 13.00 % Favored : 85.93 % 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: 1.33 (0.23), residues: 1339 helix: 1.93 (0.20), residues: 692 sheet: -0.37 (0.52), residues: 106 loop : -0.16 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 535 TYR 0.026 0.001 TYR B1013 PHE 0.007 0.001 PHE B1045 TRP 0.003 0.001 TRP B 476 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.10 (14481) covalent geometry : angle 0.42037 / 0.24 (20146) hydrogen bonds : bond 0.03667 / 2.28 ( 651) hydrogen bonds : angle 3.73851 / 2.17 ( 1786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2733.91 seconds wall clock time: 47 minutes 46.99 seconds (2866.99 seconds total)