Starting phenix.real_space_refine on Sat Sep 12 06:28:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z4j_14499/09_2026/7z4j_14499.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4j_14499/09_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_14499/09_2026/7z4j_14499.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z4j_14499/09_2026/7z4j_14499.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z4j_14499/09_2026/7z4j_14499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4j_14499/09_2026/7z4j_14499.map" model { file = "/net/cci-nas-00/data/ceres_data/7z4j_14499/09_2026/7z4j_14499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4j_14499/09_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-2.2.1-6174/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, 'RNAv2': 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: 1 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: 2.48, per 1000 atoms: 0.18 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: 1.09 Conformation dependent library (CDL) restraints added in 593.5 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: 2.34 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: 3.65 Time building geometry restraints manager: 1.52 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: 19476 1.55 - 3.10: 532 3.10 - 4.65: 116 4.65 - 6.20: 18 6.20 - 7.75: 1 Bond angle restraints: 20143 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 20138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 7590 17.28 - 34.55: 543 34.55 - 51.83: 237 51.83 - 69.11: 109 69.11 - 86.39: 18 Dihedral angle restraints: 8497 sinusoidal: 4545 harmonic: 3952 Sorted by residual: dihedral pdb=" C4' A A 57 " pdb=" C3' A A 57 " pdb=" C2' A A 57 " pdb=" C1' A A 57 " ideal model delta sinusoidal sigma weight residual 36.35 -37.73 74.07 1 3.10e+00 1.04e-01 7.25e+02 dihedral pdb=" C4' A A 88 " pdb=" C3' A A 88 " pdb=" C2' A A 88 " pdb=" C1' A A 88 " ideal model delta sinusoidal sigma weight residual 36.34 -37.54 73.88 1 3.10e+00 1.04e-01 7.22e+02 dihedral pdb=" C4' C A 55 " pdb=" C3' C A 55 " pdb=" C2' C A 55 " pdb=" C1' C A 55 " ideal model delta sinusoidal sigma weight residual 36.34 -37.43 73.78 1 3.10e+00 1.04e-01 7.20e+02 ... (remaining 8494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1921 0.060 - 0.120: 236 0.120 - 0.180: 32 0.180 - 0.240: 93 0.240 - 0.300: 23 Chirality restraints: 2305 Sorted by residual: chirality pdb=" C2' U A 59 " pdb=" C3' U A 59 " pdb=" O2' U A 59 " pdb=" C1' U A 59 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C2' G A 81 " pdb=" C3' G A 81 " pdb=" O2' G A 81 " pdb=" C1' G A 81 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C2' U A 44 " pdb=" C3' U A 44 " pdb=" O2' U A 44 " pdb=" C1' U A 44 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (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: 4.670 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 15.790 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.290 ------------------------------------------------------------------------------- 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 : 0.625 7.748 20143 Z= 0.366 Chirality : 0.065 0.300 2305 Planarity : 0.003 0.026 2070 Dihedral : 15.456 86.386 5941 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 0.00492 / 0.34 (14481) covalent geometry : angle 0.62529 / 0.37 (20143) hydrogen bonds : bond 0.11265 / 5.72 ( 651) hydrogen bonds : angle 5.01801 / 2.06 ( 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 : 0.573 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: 0.7282 time to fit residues: 79.9735 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 : 0.482 ------------------------------------------------------------------------------- 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: 0.2980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.072087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.050857 restraints weight = 39644.567| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.79 r_work: 0.2773 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14481 Z= 0.182 Angle : 0.871 16.023 20143 Z= 0.384 Chirality : 0.080 1.141 2305 Planarity : 0.003 0.036 2070 Dihedral : 16.131 125.873 3091 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.24 % Allowed : 10.43 % 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: 1.08 (0.23), residues: 1339 helix: 1.66 (0.20), residues: 693 sheet: -0.84 (0.46), residues: 119 loop : -0.07 (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 155 PHE 0.025 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 0.00368 / 0.18 (14481) covalent geometry : angle 0.87115 / 0.38 (20143) hydrogen bonds : bond 0.04644 / 2.38 ( 651) hydrogen bonds : angle 4.25774 / 1.72 ( 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 50 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: B 216 LEU cc_start: 0.9038 (mt) cc_final: 0.8759 (pt) REVERT: B 221 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6857 (ptp-110) REVERT: B 248 LEU cc_start: 0.5762 (OUTLIER) cc_final: 0.5465 (tm) REVERT: B 534 MET cc_start: 0.7972 (mtp) cc_final: 0.7732 (mtm) REVERT: B 879 MET cc_start: 0.8376 (mmm) cc_final: 0.7913 (mmm) REVERT: B 1078 ARG cc_start: 0.8447 (ptp-110) cc_final: 0.7878 (ptm-80) REVERT: B 1189 GLU cc_start: 0.8292 (mp0) cc_final: 0.7968 (pm20) outliers start: 15 outliers final: 4 residues processed: 49 average time/residue: 0.6846 time to fit residues: 36.8825 Evaluate side-chains 38 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.071909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.050590 restraints weight = 39731.327| |-----------------------------------------------------------------------------| 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: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14481 Z= 0.175 Angle : 0.678 13.073 20143 Z= 0.315 Chirality : 0.057 0.705 2305 Planarity : 0.003 0.047 2070 Dihedral : 16.327 152.960 3087 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.57 % Allowed : 10.10 % 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: 1.66 (0.20), residues: 696 sheet: -0.83 (0.46), residues: 119 loop : -0.12 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (14481) covalent geometry : angle 0.67758 / 0.32 (20143) hydrogen bonds : bond 0.04355 / 2.22 ( 651) hydrogen bonds : angle 4.11539 / 1.66 ( 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 52 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 33 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: B 248 LEU cc_start: 0.5794 (OUTLIER) cc_final: 0.5521 (tm) REVERT: B 534 MET cc_start: 0.7860 (mtp) cc_final: 0.7619 (mtm) REVERT: B 628 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7005 (p0) REVERT: B 879 MET cc_start: 0.8372 (mmm) cc_final: 0.7908 (mmm) REVERT: B 1078 ARG cc_start: 0.8487 (ptp-110) cc_final: 0.7938 (ptm-80) outliers start: 19 outliers final: 7 residues processed: 51 average time/residue: 0.6270 time to fit residues: 35.6990 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 : 0.513 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 125 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 9 optimal weight: 20.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.071420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.050067 restraints weight = 39751.510| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.83 r_work: 0.2751 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14481 Z= 0.208 Angle : 0.658 11.381 20143 Z= 0.310 Chirality : 0.054 0.551 2305 Planarity : 0.003 0.041 2070 Dihedral : 16.211 162.409 3087 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.74 % Allowed : 10.76 % Favored : 87.50 % 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: 1.64 (0.20), residues: 696 sheet: -0.34 (0.56), residues: 79 loop : -0.28 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 220 TYR 0.022 0.001 TYR B1013 PHE 0.011 0.001 PHE B1204 TRP 0.005 0.001 TRP B 464 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (14481) covalent geometry : angle 0.65840 / 0.31 (20143) hydrogen bonds : bond 0.04361 / 2.23 ( 651) hydrogen bonds : angle 4.07395 / 1.64 ( 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 52 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 31 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: B 216 LEU cc_start: 0.9061 (mp) cc_final: 0.8729 (pp) REVERT: B 248 LEU cc_start: 0.5835 (OUTLIER) cc_final: 0.5570 (tm) REVERT: B 534 MET cc_start: 0.7874 (mtp) cc_final: 0.7642 (mtm) REVERT: B 628 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6813 (p0) REVERT: B 879 MET cc_start: 0.8501 (mmm) cc_final: 0.7987 (mmm) REVERT: B 1078 ARG cc_start: 0.8505 (ptp-110) cc_final: 0.7959 (ptm-80) outliers start: 21 outliers final: 10 residues processed: 51 average time/residue: 0.5791 time to fit residues: 33.1675 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 : 0.508 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 15 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 81 optimal weight: 0.0970 chunk 107 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.072582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.051331 restraints weight = 39822.972| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.83 r_work: 0.2777 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14481 Z= 0.129 Angle : 0.603 10.128 20143 Z= 0.286 Chirality : 0.051 0.534 2305 Planarity : 0.003 0.039 2070 Dihedral : 16.189 162.989 3087 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.49 % Allowed : 11.34 % 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: 1.17 (0.23), residues: 1339 helix: 1.72 (0.20), residues: 696 sheet: -0.32 (0.56), residues: 79 loop : -0.20 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 220 TYR 0.023 0.001 TYR B1013 PHE 0.008 0.001 PHE B1204 TRP 0.004 0.001 TRP B 464 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (14481) covalent geometry : angle 0.60292 / 0.29 (20143) hydrogen bonds : bond 0.04050 / 2.06 ( 651) hydrogen bonds : angle 3.95636 / 1.59 ( 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 50 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 32 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: B 216 LEU cc_start: 0.9044 (mp) cc_final: 0.8823 (pp) REVERT: B 248 LEU cc_start: 0.5872 (OUTLIER) cc_final: 0.5597 (tm) REVERT: B 534 MET cc_start: 0.7900 (mtp) cc_final: 0.7697 (mtm) REVERT: B 535 ARG cc_start: 0.7742 (tpm170) cc_final: 0.7518 (OUTLIER) REVERT: B 628 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6830 (p0) REVERT: B 879 MET cc_start: 0.8493 (mmm) cc_final: 0.8021 (mmm) REVERT: B 1148 LYS cc_start: 0.9184 (mttt) cc_final: 0.8947 (mtmm) outliers start: 18 outliers final: 9 residues processed: 47 average time/residue: 0.6420 time to fit residues: 33.6711 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 : 0.503 ------------------------------------------------------------------------------- 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 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 1043 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 109 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 121 optimal weight: 0.0670 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 ASN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.072669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.051457 restraints weight = 39467.657| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.83 r_work: 0.2787 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14481 Z= 0.138 Angle : 0.593 9.041 20143 Z= 0.282 Chirality : 0.050 0.480 2305 Planarity : 0.003 0.039 2070 Dihedral : 16.115 165.724 3087 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.49 % Allowed : 11.92 % Favored : 86.59 % 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: 693 sheet: -0.34 (0.57), residues: 77 loop : -0.23 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 220 TYR 0.025 0.001 TYR B1013 PHE 0.009 0.001 PHE B 446 TRP 0.004 0.001 TRP B 464 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (14481) covalent geometry : angle 0.59307 / 0.28 (20143) hydrogen bonds : bond 0.03995 / 2.04 ( 651) hydrogen bonds : angle 3.88361 / 1.56 ( 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 52 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.469 Fit side-chains REVERT: B 216 LEU cc_start: 0.9043 (mp) cc_final: 0.8833 (pp) REVERT: B 248 LEU cc_start: 0.5866 (OUTLIER) cc_final: 0.5619 (tm) REVERT: B 534 MET cc_start: 0.7848 (mtp) cc_final: 0.7611 (mtm) REVERT: B 535 ARG cc_start: 0.7699 (tpm170) cc_final: 0.7481 (OUTLIER) REVERT: B 628 ASP cc_start: 0.6865 (OUTLIER) cc_final: 0.6632 (p0) REVERT: B 879 MET cc_start: 0.8534 (mmm) cc_final: 0.8059 (mmm) REVERT: B 1148 LYS cc_start: 0.9162 (mttt) cc_final: 0.8910 (mtmm) REVERT: B 1189 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8322 (pm20) outliers start: 18 outliers final: 8 residues processed: 51 average time/residue: 0.6048 time to fit residues: 34.2571 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 : 0.504 ------------------------------------------------------------------------------- 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 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 1164 LEU Chi-restraints excluded: chain B residue 1189 GLU 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: 0.6980 chunk 109 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3402 r_free = 0.3402 target = 0.072233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.051057 restraints weight = 39639.401| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.79 r_work: 0.2769 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1889 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= 0.170 Angle : 0.606 9.253 20143 Z= 0.287 Chirality : 0.050 0.501 2305 Planarity : 0.003 0.040 2070 Dihedral : 16.106 166.413 3087 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.66 % Allowed : 12.09 % Favored : 86.26 % 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: 1.17 (0.23), residues: 1339 helix: 1.76 (0.20), residues: 695 sheet: -0.35 (0.58), residues: 77 loop : -0.25 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 220 TYR 0.025 0.001 TYR B1013 PHE 0.010 0.001 PHE B1204 TRP 0.003 0.001 TRP B 476 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (14481) covalent geometry : angle 0.60596 / 0.29 (20143) hydrogen bonds : bond 0.04083 / 2.08 ( 651) hydrogen bonds : angle 3.88927 / 1.57 ( 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: 20 poor density : 34 time to evaluate : 0.506 Fit side-chains REVERT: B 221 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6494 (ptp-110) REVERT: B 248 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.5648 (tm) REVERT: B 534 MET cc_start: 0.7816 (mtp) cc_final: 0.7586 (mtm) REVERT: B 535 ARG cc_start: 0.7695 (tpm170) cc_final: 0.7486 (tpm170) REVERT: B 628 ASP cc_start: 0.6879 (OUTLIER) cc_final: 0.6678 (p0) REVERT: B 879 MET cc_start: 0.8568 (mmm) cc_final: 0.8093 (mmm) REVERT: B 1148 LYS cc_start: 0.9174 (mttt) cc_final: 0.8910 (mtmm) REVERT: B 1189 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8388 (pm20) outliers start: 20 outliers final: 10 residues processed: 51 average time/residue: 0.6152 time to fit residues: 35.0099 Evaluate side-chains 46 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 616 LEU 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 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1189 GLU 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: 4.9990 chunk 100 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.073090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.051842 restraints weight = 39251.375| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.82 r_work: 0.2794 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2006 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= 0.120 Angle : 0.577 8.976 20143 Z= 0.275 Chirality : 0.049 0.474 2305 Planarity : 0.003 0.039 2070 Dihedral : 16.047 168.195 3087 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: 1.23 (0.23), residues: 1339 helix: 1.82 (0.20), residues: 693 sheet: -0.30 (0.58), residues: 77 loop : -0.22 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 215 TYR 0.026 0.001 TYR B1013 PHE 0.009 0.001 PHE B 446 TRP 0.004 0.001 TRP B 464 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (14481) covalent geometry : angle 0.57693 / 0.28 (20143) hydrogen bonds : bond 0.03878 / 1.97 ( 651) hydrogen bonds : angle 3.81976 / 1.53 ( 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 50 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 31 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: B 248 LEU cc_start: 0.5899 (OUTLIER) cc_final: 0.5654 (tm) REVERT: B 534 MET cc_start: 0.7856 (mtp) cc_final: 0.7609 (mtm) REVERT: B 879 MET cc_start: 0.8524 (mmm) cc_final: 0.8032 (mmm) REVERT: B 1148 LYS cc_start: 0.9157 (mttt) cc_final: 0.8864 (mtmm) REVERT: B 1189 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8392 (pm20) outliers start: 19 outliers final: 9 residues processed: 48 average time/residue: 0.6021 time to fit residues: 32.5862 Evaluate side-chains 40 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 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 1189 GLU Chi-restraints excluded: chain B residue 1216 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.072823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.051623 restraints weight = 39653.056| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.82 r_work: 0.2787 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14481 Z= 0.144 Angle : 0.594 8.757 20143 Z= 0.283 Chirality : 0.049 0.469 2305 Planarity : 0.003 0.040 2070 Dihedral : 16.020 168.928 3087 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.99 % Allowed : 13.25 % Favored : 85.76 % 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: 1.83 (0.20), residues: 696 sheet: -0.31 (0.58), residues: 77 loop : -0.24 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 535 TYR 0.028 0.001 TYR B1013 PHE 0.009 0.001 PHE B 446 TRP 0.003 0.001 TRP B 464 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (14481) covalent geometry : angle 0.59387 / 0.28 (20143) hydrogen bonds : bond 0.03925 / 2.00 ( 651) hydrogen bonds : angle 3.81555 / 1.53 ( 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 43 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.422 Fit side-chains REVERT: B 221 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6275 (ptp-110) REVERT: B 248 LEU cc_start: 0.5914 (OUTLIER) cc_final: 0.5682 (tm) REVERT: B 534 MET cc_start: 0.7919 (mtp) cc_final: 0.7587 (mtm) REVERT: B 879 MET cc_start: 0.8546 (mmm) cc_final: 0.8052 (mmm) REVERT: B 1148 LYS cc_start: 0.9154 (mttt) cc_final: 0.8864 (mtmm) REVERT: B 1189 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8397 (pm20) outliers start: 12 outliers final: 10 residues processed: 41 average time/residue: 0.6825 time to fit residues: 31.2988 Evaluate side-chains 44 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 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 1189 GLU Chi-restraints excluded: chain B residue 1216 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 14 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 49 optimal weight: 0.2980 chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.073593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.052416 restraints weight = 39311.172| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.82 r_work: 0.2813 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 14481 Z= 0.113 Angle : 0.579 9.021 20143 Z= 0.277 Chirality : 0.048 0.455 2305 Planarity : 0.003 0.053 2070 Dihedral : 15.985 170.061 3087 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.08 % Allowed : 13.08 % 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: 1.26 (0.23), residues: 1339 helix: 1.86 (0.20), residues: 692 sheet: -0.27 (0.58), residues: 77 loop : -0.24 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 215 TYR 0.028 0.001 TYR B1013 PHE 0.008 0.001 PHE B 446 TRP 0.004 0.001 TRP B 464 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (14481) covalent geometry : angle 0.57911 / 0.28 (20143) hydrogen bonds : bond 0.03799 / 1.93 ( 651) hydrogen bonds : angle 3.79730 / 1.52 ( 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: 13 poor density : 32 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: B 248 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5690 (tm) REVERT: B 534 MET cc_start: 0.7990 (mtp) cc_final: 0.7681 (mtm) REVERT: B 879 MET cc_start: 0.8548 (mmm) cc_final: 0.8054 (mmm) REVERT: B 1148 LYS cc_start: 0.9156 (mttt) cc_final: 0.8865 (mtmm) REVERT: B 1189 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8413 (pm20) outliers start: 13 outliers final: 8 residues processed: 44 average time/residue: 0.6148 time to fit residues: 30.3143 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 : 0.482 ------------------------------------------------------------------------------- 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 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 1189 GLU Chi-restraints excluded: chain B residue 1216 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 38 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 81 optimal weight: 0.4980 chunk 15 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 overall best weight: 3.8586 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.071009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.049602 restraints weight = 39918.571| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.81 r_work: 0.2739 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 14481 Z= 0.263 Angle : 0.677 11.411 20143 Z= 0.319 Chirality : 0.053 0.537 2305 Planarity : 0.003 0.044 2070 Dihedral : 16.051 168.403 3087 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.91 % Allowed : 13.25 % 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: 1.08 (0.23), residues: 1339 helix: 1.72 (0.20), residues: 699 sheet: -0.47 (0.58), residues: 78 loop : -0.34 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 535 TYR 0.026 0.001 TYR B1013 PHE 0.015 0.001 PHE B1235 TRP 0.006 0.001 TRP B1074 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.26 (14481) covalent geometry : angle 0.67661 / 0.32 (20143) hydrogen bonds : bond 0.04517 / 2.32 ( 651) hydrogen bonds : angle 3.99964 / 1.61 ( 1786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3286.77 seconds wall clock time: 57 minutes 20.21 seconds (3440.21 seconds total)