Starting phenix.real_space_refine on Wed Mar 4 14:24:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z4j_14499/03_2026/7z4j_14499.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4j_14499/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7z4j_14499/03_2026/7z4j_14499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4j_14499/03_2026/7z4j_14499.map" model { file = "/net/cci-nas-00/data/ceres_data/7z4j_14499/03_2026/7z4j_14499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4j_14499/03_2026/7z4j_14499.cif" } 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-5986/lib/python3.9/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: 2.66, per 1000 atoms: 0.19 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: 1.21 Conformation dependent library (CDL) restraints added in 426.5 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: 1.80 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: 3.08 Time building geometry restraints manager: 1.61 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=" C ARG B1333 " pdb=" O ARG B1333 " ideal model delta sigma weight residual 1.235 1.254 -0.019 1.21e-02 6.83e+03 2.56e+00 bond pdb=" O5' DC C 17 " pdb=" C5' DC C 17 " ideal model delta sigma weight residual 1.423 1.375 0.048 3.00e-02 1.11e+03 2.56e+00 bond pdb=" C4' DG C 16 " pdb=" C3' DG C 16 " ideal model delta sigma weight residual 1.523 1.494 0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" O5' DC C 10 " pdb=" C5' DC C 10 " ideal model delta sigma weight residual 1.423 1.382 0.041 3.00e-02 1.11e+03 1.85e+00 bond pdb=" C4' DA C 8 " pdb=" C3' DA C 8 " ideal model delta sigma weight residual 1.523 1.498 0.025 2.00e-02 2.50e+03 1.61e+00 ... (remaining 14476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 19848 1.55 - 3.10: 274 3.10 - 4.65: 22 4.65 - 6.20: 1 6.20 - 7.75: 1 Bond angle restraints: 20146 Sorted by residual: angle pdb=" CA LEU B1312 " pdb=" CB LEU B1312 " pdb=" CG LEU B1312 " ideal model delta sigma weight residual 116.30 124.05 -7.75 3.50e+00 8.16e-02 4.90e+00 angle pdb=" C2' U A 59 " pdb=" C1' U A 59 " pdb=" N1 U A 59 " ideal model delta sigma weight residual 114.00 110.68 3.32 1.50e+00 4.44e-01 4.89e+00 angle pdb=" C2' U A 23 " pdb=" C1' U A 23 " pdb=" N1 U A 23 " ideal model delta sigma weight residual 112.00 114.97 -2.97 1.50e+00 4.44e-01 3.91e+00 angle pdb=" C2' G A 54 " pdb=" C1' G A 54 " pdb=" N9 G A 54 " ideal model delta sigma weight residual 112.00 114.81 -2.81 1.50e+00 4.44e-01 3.50e+00 angle pdb=" NE ARG B1333 " pdb=" CZ ARG B1333 " pdb=" NH1 ARG B1333 " ideal model delta sigma weight residual 121.50 119.73 1.77 1.00e+00 1.00e+00 3.12e+00 ... (remaining 20141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.77: 7965 19.77 - 39.53: 520 39.53 - 59.30: 228 59.30 - 79.07: 79 79.07 - 98.83: 6 Dihedral angle restraints: 8798 sinusoidal: 4846 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 8795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1409 0.028 - 0.056: 604 0.056 - 0.083: 203 0.083 - 0.111: 66 0.111 - 0.139: 23 Chirality restraints: 2305 Sorted by residual: chirality pdb=" C1' A A 51 " pdb=" O4' A A 51 " pdb=" C2' A A 51 " pdb=" N9 A A 51 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 4.83e-01 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 -2.66 -2.52 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA VAL B 870 " pdb=" N VAL B 870 " pdb=" C VAL B 870 " pdb=" CB VAL B 870 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.65e-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: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.530 Find NCS groups from input model: 0.060 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:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 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 0.048 14481 Z= 0.225 Angle : 0.477 7.748 20146 Z= 0.259 Chirality : 0.037 0.139 2305 Planarity : 0.003 0.026 2070 Dihedral : 16.164 98.833 6242 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 covalent geometry : bond 0.00465 (14481) covalent geometry : angle 0.47654 (20146) hydrogen bonds : bond 0.11265 ( 651) hydrogen bonds : angle 5.01801 ( 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 : 0.462 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: 0.7793 time to fit residues: 85.1208 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 : 0.435 ------------------------------------------------------------------------------- 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: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.0070 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 overall best weight: 1.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN B 113 HIS ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3402 r_free = 0.3402 target = 0.072368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.051158 restraints weight = 39544.529| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.82 r_work: 0.2774 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14481 Z= 0.124 Angle : 0.473 6.604 20146 Z= 0.253 Chirality : 0.035 0.137 2305 Planarity : 0.003 0.034 2070 Dihedral : 17.996 96.292 3392 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.32 % Allowed : 10.35 % 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: 1.18 (0.23), residues: 1339 helix: 1.76 (0.20), residues: 694 sheet: -0.76 (0.46), residues: 119 loop : -0.06 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 535 TYR 0.010 0.001 TYR B 155 PHE 0.025 0.001 PHE B 290 TRP 0.003 0.001 TRP B 464 HIS 0.004 0.001 HIS B1297 Details of bonding type rmsd covalent geometry : bond 0.00269 (14481) covalent geometry : angle 0.47325 (20146) hydrogen bonds : bond 0.04069 ( 651) hydrogen bonds : angle 4.06968 ( 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 54 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.738 Fit side-chains REVERT: B 220 ARG cc_start: 0.8819 (mmm-85) cc_final: 0.8534 (tpp-160) REVERT: B 248 LEU cc_start: 0.5834 (OUTLIER) cc_final: 0.5550 (tm) REVERT: B 534 MET cc_start: 0.8123 (mtp) cc_final: 0.7805 (mtm) REVERT: B 879 MET cc_start: 0.8356 (mmm) cc_final: 0.7893 (mmm) REVERT: B 1078 ARG cc_start: 0.8456 (ptp-110) cc_final: 0.7894 (ptm-80) outliers start: 16 outliers final: 4 residues processed: 53 average time/residue: 0.7455 time to fit residues: 43.1810 Evaluate side-chains 35 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 627 GLU 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: 0.9990 chunk 5 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3419 r_free = 0.3419 target = 0.073067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.052035 restraints weight = 39612.806| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.82 r_work: 0.2798 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14481 Z= 0.105 Angle : 0.438 7.237 20146 Z= 0.234 Chirality : 0.034 0.136 2305 Planarity : 0.003 0.037 2070 Dihedral : 17.836 99.046 3387 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.57 % Allowed : 10.60 % Favored : 87.83 % 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: 1.84 (0.20), residues: 689 sheet: -0.69 (0.47), residues: 119 loop : -0.11 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 220 TYR 0.024 0.001 TYR B1013 PHE 0.028 0.001 PHE B 290 TRP 0.004 0.001 TRP B 476 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00224 (14481) covalent geometry : angle 0.43751 (20146) hydrogen bonds : bond 0.03724 ( 651) hydrogen bonds : angle 3.82768 ( 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 53 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 34 time to evaluate : 0.428 Fit side-chains REVERT: B 216 LEU cc_start: 0.9101 (mp) cc_final: 0.8488 (pp) REVERT: B 248 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5691 (tm) REVERT: B 534 MET cc_start: 0.8061 (mtp) cc_final: 0.7751 (mtm) REVERT: B 879 MET cc_start: 0.8489 (mmm) cc_final: 0.8051 (mmm) outliers start: 19 outliers final: 9 residues processed: 51 average time/residue: 0.5480 time to fit residues: 31.5062 Evaluate side-chains 41 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 282 ILE 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 1146 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 930 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.070795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.049543 restraints weight = 39836.816| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.80 r_work: 0.2738 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14481 Z= 0.206 Angle : 0.487 6.806 20146 Z= 0.259 Chirality : 0.037 0.135 2305 Planarity : 0.003 0.041 2070 Dihedral : 17.905 99.887 3387 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.90 % Allowed : 11.01 % Favored : 87.09 % 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: 1.16 (0.23), residues: 1339 helix: 1.74 (0.20), residues: 695 sheet: -0.63 (0.47), residues: 117 loop : -0.13 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 220 TYR 0.023 0.001 TYR B1013 PHE 0.013 0.001 PHE B1204 TRP 0.003 0.001 TRP B 476 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00462 (14481) covalent geometry : angle 0.48659 (20146) hydrogen bonds : bond 0.04279 ( 651) hydrogen bonds : angle 3.95452 ( 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 55 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 32 time to evaluate : 0.493 Fit side-chains REVERT: B 248 LEU cc_start: 0.5849 (OUTLIER) cc_final: 0.5618 (tm) REVERT: B 534 MET cc_start: 0.8097 (mtp) cc_final: 0.7702 (mtm) REVERT: B 879 MET cc_start: 0.8606 (mmm) cc_final: 0.8096 (mmm) REVERT: B 1242 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.7362 (m-80) outliers start: 23 outliers final: 9 residues processed: 52 average time/residue: 0.6078 time to fit residues: 35.2934 Evaluate side-chains 42 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 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 1164 LEU Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1240 SER Chi-restraints excluded: chain B residue 1242 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 80 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 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 = 0.3371 r_free = 0.3371 target = 0.070863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.049653 restraints weight = 40107.933| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.83 r_work: 0.2734 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14481 Z= 0.189 Angle : 0.472 6.697 20146 Z= 0.253 Chirality : 0.036 0.135 2305 Planarity : 0.003 0.041 2070 Dihedral : 17.909 99.830 3387 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.99 % Allowed : 11.59 % Favored : 86.42 % 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: 1.18 (0.23), residues: 1339 helix: 1.79 (0.20), residues: 689 sheet: -0.41 (0.53), residues: 91 loop : -0.22 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 221 TYR 0.024 0.001 TYR B1013 PHE 0.011 0.001 PHE B1204 TRP 0.005 0.001 TRP B 476 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00424 (14481) covalent geometry : angle 0.47192 (20146) hydrogen bonds : bond 0.04143 ( 651) hydrogen bonds : angle 3.93081 ( 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 54 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 30 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: B 248 LEU cc_start: 0.5836 (OUTLIER) cc_final: 0.5620 (tm) REVERT: B 534 MET cc_start: 0.8095 (mtp) cc_final: 0.7713 (mtm) REVERT: B 1242 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.7413 (m-80) REVERT: B 1333 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8492 (ptm-80) outliers start: 24 outliers final: 11 residues processed: 48 average time/residue: 0.6428 time to fit residues: 34.3265 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 : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 218 LYS 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 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 1240 SER Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1333 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 109 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 34 optimal weight: 0.0030 chunk 60 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 134 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3399 r_free = 0.3399 target = 0.072118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.051051 restraints weight = 39485.869| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.78 r_work: 0.2776 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14481 Z= 0.116 Angle : 0.436 6.894 20146 Z= 0.234 Chirality : 0.034 0.138 2305 Planarity : 0.003 0.038 2070 Dihedral : 17.832 99.887 3387 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.90 % Allowed : 12.09 % 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: 1.29 (0.23), residues: 1339 helix: 1.90 (0.20), residues: 687 sheet: -0.66 (0.49), residues: 115 loop : -0.09 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 220 TYR 0.024 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 covalent geometry : bond 0.00253 (14481) covalent geometry : angle 0.43566 (20146) hydrogen bonds : bond 0.03787 ( 651) hydrogen bonds : angle 3.78179 ( 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 53 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 30 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: B 218 LYS cc_start: 0.6713 (OUTLIER) cc_final: 0.6026 (mmmt) REVERT: B 221 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6288 (ptt-90) REVERT: B 248 LEU cc_start: 0.5876 (OUTLIER) cc_final: 0.5669 (tm) REVERT: B 534 MET cc_start: 0.8057 (mtp) cc_final: 0.7719 (mtm) REVERT: B 535 ARG cc_start: 0.7615 (tpm170) cc_final: 0.7371 (OUTLIER) REVERT: B 628 ASP cc_start: 0.6810 (OUTLIER) cc_final: 0.6482 (p0) REVERT: B 1242 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.7366 (m-80) outliers start: 23 outliers final: 9 residues processed: 50 average time/residue: 0.6083 time to fit residues: 34.0271 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 : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LYS 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 627 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 657 THR 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 Chi-restraints excluded: chain B residue 1242 TYR 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: 8.9990 chunk 101 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3380 r_free = 0.3380 target = 0.071285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.050057 restraints weight = 39790.020| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.82 r_work: 0.2742 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14481 Z= 0.162 Angle : 0.455 5.919 20146 Z= 0.244 Chirality : 0.036 0.134 2305 Planarity : 0.003 0.040 2070 Dihedral : 17.806 100.003 3387 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.90 % Allowed : 12.50 % Favored : 85.60 % 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: 1.26 (0.23), residues: 1339 helix: 1.88 (0.20), residues: 687 sheet: -0.67 (0.49), residues: 115 loop : -0.11 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 220 TYR 0.026 0.001 TYR B1013 PHE 0.011 0.001 PHE B1204 TRP 0.004 0.001 TRP B 464 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00361 (14481) covalent geometry : angle 0.45478 (20146) hydrogen bonds : bond 0.04005 ( 651) hydrogen bonds : angle 3.82704 ( 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 54 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 31 time to evaluate : 0.537 Fit side-chains REVERT: B 534 MET cc_start: 0.8098 (mtp) cc_final: 0.7763 (mtm) REVERT: B 535 ARG cc_start: 0.7675 (tpm170) cc_final: 0.7441 (OUTLIER) REVERT: B 628 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6606 (p0) REVERT: B 1242 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7409 (m-80) outliers start: 23 outliers final: 12 residues processed: 48 average time/residue: 0.5997 time to fit residues: 32.0614 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 : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 998 ILE 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 Chi-restraints excluded: chain B residue 1240 SER Chi-restraints excluded: chain B residue 1242 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 141 optimal weight: 0.2980 chunk 54 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3404 r_free = 0.3404 target = 0.072430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.051431 restraints weight = 39366.608| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.77 r_work: 0.2783 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14481 Z= 0.114 Angle : 0.432 10.156 20146 Z= 0.231 Chirality : 0.034 0.145 2305 Planarity : 0.003 0.037 2070 Dihedral : 17.724 99.612 3385 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.32 % Allowed : 13.08 % Favored : 85.60 % 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: 1.35 (0.23), residues: 1339 helix: 1.95 (0.20), residues: 687 sheet: -0.59 (0.49), residues: 115 loop : -0.09 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 220 TYR 0.028 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 covalent geometry : bond 0.00247 (14481) covalent geometry : angle 0.43194 (20146) hydrogen bonds : bond 0.03677 ( 651) hydrogen bonds : angle 3.72168 ( 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 47 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: B 183 LYS cc_start: 0.8758 (mmtm) cc_final: 0.8549 (tptt) REVERT: B 383 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8325 (mtm) REVERT: B 534 MET cc_start: 0.8112 (mtp) cc_final: 0.7783 (mtm) REVERT: B 535 ARG cc_start: 0.7682 (tpm170) cc_final: 0.7479 (tpm170) REVERT: B 628 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6633 (p0) REVERT: B 1242 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.7247 (m-80) outliers start: 16 outliers final: 9 residues processed: 45 average time/residue: 0.6350 time to fit residues: 32.0037 Evaluate side-chains 43 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 998 ILE 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 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: 5.9990 chunk 128 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 32 optimal weight: 30.0000 chunk 131 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3401 r_free = 0.3401 target = 0.072257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.051245 restraints weight = 39692.289| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.78 r_work: 0.2779 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2143 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= 0.127 Angle : 0.439 9.255 20146 Z= 0.234 Chirality : 0.035 0.139 2305 Planarity : 0.003 0.036 2070 Dihedral : 17.694 99.415 3385 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.32 % Allowed : 13.08 % Favored : 85.60 % 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: 1.34 (0.23), residues: 1339 helix: 1.95 (0.20), residues: 686 sheet: -0.60 (0.49), residues: 115 loop : -0.09 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 220 TYR 0.026 0.001 TYR B1013 PHE 0.009 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 covalent geometry : bond 0.00279 (14481) covalent geometry : angle 0.43922 (20146) hydrogen bonds : bond 0.03774 ( 651) hydrogen bonds : angle 3.72219 ( 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 47 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 0.487 Fit side-chains REVERT: B 534 MET cc_start: 0.8174 (mtp) cc_final: 0.7866 (mtm) REVERT: B 628 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6952 (p0) REVERT: B 1242 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.7230 (m-80) outliers start: 16 outliers final: 10 residues processed: 47 average time/residue: 0.5761 time to fit residues: 30.2940 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 : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 998 ILE 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 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: 5.9990 chunk 76 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 115 optimal weight: 0.0670 chunk 87 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.073169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.052223 restraints weight = 39212.930| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.86 r_work: 0.2820 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14481 Z= 0.095 Angle : 0.430 10.195 20146 Z= 0.229 Chirality : 0.034 0.143 2305 Planarity : 0.003 0.035 2070 Dihedral : 17.641 98.946 3385 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.16 % Allowed : 13.33 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.23), residues: 1339 helix: 2.02 (0.20), residues: 686 sheet: -0.52 (0.49), residues: 115 loop : -0.03 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 220 TYR 0.028 0.001 TYR B1013 PHE 0.007 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 covalent geometry : bond 0.00204 (14481) covalent geometry : angle 0.43003 (20146) hydrogen bonds : bond 0.03501 ( 651) hydrogen bonds : angle 3.63408 ( 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 45 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: B 534 MET cc_start: 0.8139 (mtp) cc_final: 0.7767 (mtm) REVERT: B 628 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6717 (p0) REVERT: B 879 MET cc_start: 0.8486 (mmm) cc_final: 0.8062 (mmm) REVERT: B 1242 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.7038 (m-80) outliers start: 14 outliers final: 7 residues processed: 44 average time/residue: 0.6434 time to fit residues: 31.5418 Evaluate side-chains 38 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 801 VAL 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 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: 0.8980 chunk 39 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 106 optimal weight: 0.3980 chunk 11 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3378 r_free = 0.3378 target = 0.071150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.049943 restraints weight = 39638.271| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.84 r_work: 0.2752 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14481 Z= 0.172 Angle : 0.467 9.236 20146 Z= 0.248 Chirality : 0.036 0.135 2305 Planarity : 0.003 0.055 2070 Dihedral : 17.697 98.802 3385 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.91 % Allowed : 13.74 % Favored : 85.35 % 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: 1.36 (0.23), residues: 1339 helix: 1.94 (0.20), residues: 686 sheet: -0.54 (0.49), residues: 115 loop : -0.05 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 629 TYR 0.026 0.001 TYR B1013 PHE 0.011 0.001 PHE B1204 TRP 0.003 0.001 TRP B 476 HIS 0.005 0.001 HIS B 983 Details of bonding type rmsd covalent geometry : bond 0.00383 (14481) covalent geometry : angle 0.46748 (20146) hydrogen bonds : bond 0.04023 ( 651) hydrogen bonds : angle 3.78549 ( 1786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3231.57 seconds wall clock time: 56 minutes 13.06 seconds (3373.06 seconds total)