Starting phenix.real_space_refine on Sun May 3 14:29:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8as7_15608/05_2026/8as7_15608.cif Found real_map, /net/cci-nas-00/data/ceres_data/8as7_15608/05_2026/8as7_15608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8as7_15608/05_2026/8as7_15608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8as7_15608/05_2026/8as7_15608.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8as7_15608/05_2026/8as7_15608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8as7_15608/05_2026/8as7_15608.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 39 5.49 5 Mg 2 5.21 5 S 73 5.16 5 C 8364 2.51 5 N 2339 2.21 5 O 2614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13431 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 12586 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1575, 12550 Classifications: {'peptide': 1575} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1515} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1575, 12550 Classifications: {'peptide': 1575} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1515} Chain breaks: 4 bond proxies already assigned to first conformer: 12775 Chain: "P" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 363 Classifications: {'RNA': 17} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 13} Chain: "T" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 361 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 8} Link IDs: {'rna2p': 4, 'rna3p': 12} Chain: "G" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'p5*END': 1, 'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 49 Unusual residues: {' MG': 2, '2KH': 1, 'EPE': 1} Classifications: {'undetermined': 4, 'water': 3} Link IDs: {None: 6} Chain: "P" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.55, per 1000 atoms: 0.41 Number of scatterers: 13431 At special positions: 0 Unit cell: (102.85, 107.95, 129.2, 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 73 16.00 P 39 15.00 Mg 2 11.99 O 2614 8.00 N 2339 7.00 C 8364 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: 1.23 Conformation dependent library (CDL) restraints added in 801.1 milliseconds 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2970 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 14 sheets defined 56.7% alpha, 10.2% beta 10 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 removed outlier: 3.856A pdb=" N LEU A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS A 7 " --> pdb=" O LEU A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 94 through 99 removed outlier: 4.148A pdb=" N VAL A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 158 removed outlier: 3.971A pdb=" N LEU A 138 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Proline residue: A 152 - end of helix removed outlier: 3.687A pdb=" N ASP A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 207 Processing helix chain 'A' and resid 208 through 213 removed outlier: 7.074A pdb=" N ASP A 211 " --> pdb=" O MET A 208 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 212 " --> pdb=" O ASP A 209 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A 213 " --> pdb=" O ALA A 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 213' Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'A' and resid 249 through 259 removed outlier: 4.158A pdb=" N LEU A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 285 Processing helix chain 'A' and resid 292 through 318 removed outlier: 3.703A pdb=" N ARG A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.650A pdb=" N MET A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 357' Processing helix chain 'A' and resid 358 through 374 Processing helix chain 'A' and resid 383 through 393 removed outlier: 3.531A pdb=" N GLU A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.706A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 447 removed outlier: 3.843A pdb=" N HIS A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 465 removed outlier: 3.748A pdb=" N GLY A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 492 Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 496 through 511 Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.680A pdb=" N TRP A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 602 through 611 removed outlier: 4.128A pdb=" N THR A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 627 Processing helix chain 'A' and resid 638 through 655 Processing helix chain 'A' and resid 656 through 665 removed outlier: 3.634A pdb=" N ILE A 663 " --> pdb=" O THR A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 672 removed outlier: 3.926A pdb=" N GLU A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 675 No H-bonds generated for 'chain 'A' and resid 673 through 675' Processing helix chain 'A' and resid 682 through 688 removed outlier: 3.537A pdb=" N LYS A 685 " --> pdb=" O LYS A 682 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY A 688 " --> pdb=" O LYS A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 716 Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 750 through 756 removed outlier: 4.750A pdb=" N GLY A 753 " --> pdb=" O TRP A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 779 removed outlier: 4.024A pdb=" N MET A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 774 " --> pdb=" O MET A 770 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N MET A 777 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 788 removed outlier: 4.532A pdb=" N PHE A 787 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 822 Processing helix chain 'A' and resid 824 through 840 removed outlier: 3.643A pdb=" N ASN A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A 840 " --> pdb=" O GLU A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 846 Processing helix chain 'A' and resid 855 through 859 Processing helix chain 'A' and resid 860 through 864 removed outlier: 3.703A pdb=" N GLU A 863 " --> pdb=" O LEU A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 884 Processing helix chain 'A' and resid 889 through 904 removed outlier: 4.521A pdb=" N GLY A 894 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLN A 895 " --> pdb=" O ASP A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 945 removed outlier: 4.039A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 973 removed outlier: 4.211A pdb=" N ILE A 961 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY A 966 " --> pdb=" O ILE A 962 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 967 " --> pdb=" O GLU A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 993 removed outlier: 3.707A pdb=" N HIS A 993 " --> pdb=" O TRP A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1005 removed outlier: 3.925A pdb=" N LEU A 998 " --> pdb=" O TYR A 994 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1009 No H-bonds generated for 'chain 'A' and resid 1007 through 1009' Processing helix chain 'A' and resid 1010 through 1020 removed outlier: 3.747A pdb=" N MET A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1038 removed outlier: 4.062A pdb=" N SER A1038 " --> pdb=" O ALA A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1057 removed outlier: 3.819A pdb=" N GLU A1050 " --> pdb=" O ASP A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1109 Processing helix chain 'A' and resid 1138 through 1155 Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1161 through 1164 Processing helix chain 'A' and resid 1194 through 1200 removed outlier: 3.988A pdb=" N TRP A1198 " --> pdb=" O PRO A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1228 removed outlier: 3.568A pdb=" N GLU A1216 " --> pdb=" O ALA A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1250 Processing helix chain 'A' and resid 1258 through 1266 Processing helix chain 'A' and resid 1270 through 1274 Processing helix chain 'A' and resid 1280 through 1284 removed outlier: 3.808A pdb=" N ALA A1284 " --> pdb=" O PRO A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1300 removed outlier: 3.666A pdb=" N ASN A1292 " --> pdb=" O GLY A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1316 removed outlier: 3.657A pdb=" N LYS A1316 " --> pdb=" O GLU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1336 removed outlier: 3.659A pdb=" N HIS A1336 " --> pdb=" O THR A1333 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1333 through 1336' Processing helix chain 'A' and resid 1342 through 1344 No H-bonds generated for 'chain 'A' and resid 1342 through 1344' Processing helix chain 'A' and resid 1345 through 1353 Processing helix chain 'A' and resid 1360 through 1368 Processing helix chain 'A' and resid 1369 through 1374 removed outlier: 3.746A pdb=" N ARG A1374 " --> pdb=" O VAL A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1391 Processing helix chain 'A' and resid 1392 through 1397 Processing helix chain 'A' and resid 1403 through 1411 removed outlier: 3.540A pdb=" N ARG A1407 " --> pdb=" O HIS A1403 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A1411 " --> pdb=" O ARG A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1412 through 1414 No H-bonds generated for 'chain 'A' and resid 1412 through 1414' Processing helix chain 'A' and resid 1437 through 1448 Processing helix chain 'A' and resid 1449 through 1451 No H-bonds generated for 'chain 'A' and resid 1449 through 1451' Processing helix chain 'A' and resid 1457 through 1464 Processing helix chain 'A' and resid 1467 through 1476 Processing helix chain 'A' and resid 1512 through 1523 removed outlier: 3.575A pdb=" N SER A1518 " --> pdb=" O GLU A1514 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A1520 " --> pdb=" O LEU A1516 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1546 removed outlier: 3.662A pdb=" N ALA A1543 " --> pdb=" O ASP A1539 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER A1544 " --> pdb=" O LYS A1540 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE A1545 " --> pdb=" O LEU A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1557 Processing helix chain 'A' and resid 1563 through 1575 removed outlier: 3.903A pdb=" N ASP A1575 " --> pdb=" O ILE A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1604 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 removed outlier: 3.637A pdb=" N PHE A 167 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 179 " --> pdb=" O GLY A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 17 removed outlier: 3.637A pdb=" N PHE A 167 " --> pdb=" O SER A 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 41 removed outlier: 3.624A pdb=" N ASP A 37 " --> pdb=" O ASP A 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 336 Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 411 removed outlier: 4.403A pdb=" N ARG A 409 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 411 removed outlier: 4.403A pdb=" N ARG A 409 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 719 through 723 Processing sheet with id=AA8, first strand: chain 'A' and resid 850 through 851 Processing sheet with id=AA9, first strand: chain 'A' and resid 921 through 925 removed outlier: 5.906A pdb=" N MET A 906 " --> pdb=" O LYS A1025 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N MET A1027 " --> pdb=" O MET A 906 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE A 908 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1117 through 1123 removed outlier: 7.140A pdb=" N ASN A 979 " --> pdb=" O VAL A1176 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL A1176 " --> pdb=" O ASN A 979 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ASN A 981 " --> pdb=" O ASN A1174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1178 through 1180 Processing sheet with id=AB3, first strand: chain 'A' and resid 1338 through 1340 Processing sheet with id=AB4, first strand: chain 'A' and resid 1486 through 1488 Processing sheet with id=AB5, first strand: chain 'A' and resid 1496 through 1503 removed outlier: 5.019A pdb=" N ARG A1497 " --> pdb=" O GLY A1585 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLY A1585 " --> pdb=" O ARG A1497 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ARG A1499 " --> pdb=" O LEU A1583 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU A1583 " --> pdb=" O ARG A1499 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP A1501 " --> pdb=" O VAL A1581 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL A1581 " --> pdb=" O ASP A1501 " (cutoff:3.500A) 632 hydrogen bonds defined for protein. 1786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2120 1.31 - 1.44: 3878 1.44 - 1.56: 7589 1.56 - 1.69: 74 1.69 - 1.81: 121 Bond restraints: 13782 Sorted by residual: bond pdb=" C3' 2KH A2104 " pdb=" C4' 2KH A2104 " ideal model delta sigma weight residual 1.550 1.297 0.253 2.00e-02 2.50e+03 1.60e+02 bond pdb=" N3A 2KH A2104 " pdb=" PA 2KH A2104 " ideal model delta sigma weight residual 1.933 1.704 0.229 2.00e-02 2.50e+03 1.32e+02 bond pdb=" N3A 2KH A2104 " pdb=" PB 2KH A2104 " ideal model delta sigma weight residual 1.890 1.706 0.184 2.00e-02 2.50e+03 8.45e+01 bond pdb=" O2G 2KH A2104 " pdb=" PG 2KH A2104 " ideal model delta sigma weight residual 1.682 1.510 0.172 2.00e-02 2.50e+03 7.44e+01 bond pdb=" O3G 2KH A2104 " pdb=" PG 2KH A2104 " ideal model delta sigma weight residual 1.669 1.510 0.159 2.00e-02 2.50e+03 6.32e+01 ... (remaining 13777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.35: 18780 12.35 - 24.70: 6 24.70 - 37.05: 0 37.05 - 49.40: 0 49.40 - 61.75: 2 Bond angle restraints: 18788 Sorted by residual: angle pdb=" N3A 2KH A2104 " pdb=" PA 2KH A2104 " pdb=" O2A 2KH A2104 " ideal model delta sigma weight residual 48.17 109.92 -61.75 3.00e+00 1.11e-01 4.24e+02 angle pdb=" O2G 2KH A2104 " pdb=" PG 2KH A2104 " pdb=" O3G 2KH A2104 " ideal model delta sigma weight residual 53.94 109.56 -55.62 3.00e+00 1.11e-01 3.44e+02 angle pdb=" O1A 2KH A2104 " pdb=" PA 2KH A2104 " pdb=" O2A 2KH A2104 " ideal model delta sigma weight residual 130.82 108.73 22.09 3.00e+00 1.11e-01 5.42e+01 angle pdb=" O1B 2KH A2104 " pdb=" PB 2KH A2104 " pdb=" O2B 2KH A2104 " ideal model delta sigma weight residual 130.56 109.43 21.13 3.00e+00 1.11e-01 4.96e+01 angle pdb=" O1G 2KH A2104 " pdb=" PG 2KH A2104 " pdb=" O2G 2KH A2104 " ideal model delta sigma weight residual 130.21 109.16 21.05 3.00e+00 1.11e-01 4.92e+01 ... (remaining 18783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.35: 8065 31.35 - 62.70: 291 62.70 - 94.05: 57 94.05 - 125.41: 2 125.41 - 156.76: 3 Dihedral angle restraints: 8418 sinusoidal: 3825 harmonic: 4593 Sorted by residual: dihedral pdb=" O4' C T 19 " pdb=" C1' C T 19 " pdb=" N1 C T 19 " pdb=" C2 C T 19 " ideal model delta sinusoidal sigma weight residual 200.00 43.24 156.76 1 1.50e+01 4.44e-03 8.19e+01 dihedral pdb=" CA ASN A 959 " pdb=" C ASN A 959 " pdb=" N SER A 960 " pdb=" CA SER A 960 " ideal model delta harmonic sigma weight residual -180.00 -156.76 -23.24 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" C3 EPE A2103 " pdb=" C2 EPE A2103 " pdb=" N1 EPE A2103 " pdb=" C6 EPE A2103 " ideal model delta sinusoidal sigma weight residual 58.34 -67.79 126.13 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 8415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1737 0.051 - 0.102: 300 0.102 - 0.154: 58 0.154 - 0.205: 2 0.205 - 0.256: 5 Chirality restraints: 2102 Sorted by residual: chirality pdb=" C3' 2KH A2104 " pdb=" C2' 2KH A2104 " pdb=" C4' 2KH A2104 " pdb=" O3' 2KH A2104 " both_signs ideal model delta sigma weight residual False -2.66 -2.41 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB ILE A 159 " pdb=" CA ILE A 159 " pdb=" CG1 ILE A 159 " pdb=" CG2 ILE A 159 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" C2' 2KH A2104 " pdb=" C1' 2KH A2104 " pdb=" C3' 2KH A2104 " pdb=" O2' 2KH A2104 " both_signs ideal model delta sigma weight residual False -2.85 -2.60 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2099 not shown) Planarity restraints: 2253 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 556 " 0.050 5.00e-02 4.00e+02 7.55e-02 9.11e+00 pdb=" N PRO A 557 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 557 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 557 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1457 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO A1458 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A1458 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1458 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 721 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 722 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 722 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 722 " -0.024 5.00e-02 4.00e+02 ... (remaining 2250 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 202 2.66 - 3.22: 11897 3.22 - 3.78: 21761 3.78 - 4.34: 30495 4.34 - 4.90: 48075 Nonbonded interactions: 112430 Sorted by model distance: nonbonded pdb=" OD1 ASP A1127 " pdb="MG MG A2102 " model vdw 2.100 2.170 nonbonded pdb=" OE1 GLU A 387 " pdb=" OG SER A1417 " model vdw 2.225 3.040 nonbonded pdb=" O ALA A 986 " pdb="MG MG A2101 " model vdw 2.241 2.170 nonbonded pdb=" O LEU A1416 " pdb=" OG SER A1437 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A1045 " pdb=" O2' A P 5 " model vdw 2.260 3.040 ... (remaining 112425 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.590 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.460 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 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 : 0.006 0.253 13782 Z= 0.282 Angle : 0.958 61.747 18788 Z= 0.416 Chirality : 0.041 0.256 2102 Planarity : 0.004 0.075 2253 Dihedral : 16.361 156.756 5448 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.29 % Allowed : 0.50 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.09 (0.20), residues: 1570 helix: 0.72 (0.18), residues: 777 sheet: 0.77 (0.44), residues: 143 loop : -1.19 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 481 TYR 0.015 0.001 TYR A1166 PHE 0.022 0.001 PHE A 649 TRP 0.022 0.002 TRP A 520 HIS 0.010 0.001 HIS A1190 Details of bonding type rmsd covalent geometry : bond 0.00566 (13782) covalent geometry : angle 0.95751 (18788) hydrogen bonds : bond 0.14908 ( 643) hydrogen bonds : angle 5.94959 ( 1836) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.464 Fit side-chains REVERT: A 294 GLN cc_start: 0.7106 (mp10) cc_final: 0.6886 (mp10) REVERT: A 887 MET cc_start: 0.7626 (tpp) cc_final: 0.7288 (tpp) REVERT: A 1344 ASP cc_start: 0.5874 (m-30) cc_final: 0.5575 (m-30) outliers start: 1 outliers final: 0 residues processed: 210 average time/residue: 0.7915 time to fit residues: 177.9057 Evaluate side-chains 169 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0270 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN A 853 ASN A 954 ASN A 959 ASN A1190 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.170482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.132414 restraints weight = 31944.390| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 4.59 r_work: 0.2955 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13782 Z= 0.135 Angle : 0.576 9.050 18788 Z= 0.297 Chirality : 0.040 0.210 2102 Planarity : 0.004 0.068 2253 Dihedral : 15.051 153.645 2339 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.45 % Allowed : 7.56 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.48 (0.21), residues: 1570 helix: 1.33 (0.19), residues: 770 sheet: 0.77 (0.42), residues: 145 loop : -1.01 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1304 TYR 0.019 0.002 TYR A1166 PHE 0.018 0.001 PHE A 649 TRP 0.014 0.001 TRP A 520 HIS 0.006 0.001 HIS A1091 Details of bonding type rmsd covalent geometry : bond 0.00299 (13782) covalent geometry : angle 0.57605 (18788) hydrogen bonds : bond 0.04516 ( 643) hydrogen bonds : angle 4.55575 ( 1836) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.404 Fit side-chains REVERT: A 139 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6561 (tm-30) REVERT: A 294 GLN cc_start: 0.7857 (mp10) cc_final: 0.7577 (mp10) REVERT: A 887 MET cc_start: 0.8489 (tpp) cc_final: 0.8248 (tpp) REVERT: A 1261 PHE cc_start: 0.7178 (t80) cc_final: 0.6910 (t80) REVERT: A 1304 ARG cc_start: 0.7040 (mtp-110) cc_final: 0.6167 (ptt-90) REVERT: A 1339 MET cc_start: 0.6445 (mtm) cc_final: 0.6170 (mtp) REVERT: A 1344 ASP cc_start: 0.5947 (m-30) cc_final: 0.5309 (p0) REVERT: A 1418 ARG cc_start: 0.6803 (mmt180) cc_final: 0.6590 (mpt-90) REVERT: A 1463 MET cc_start: 0.5427 (OUTLIER) cc_final: 0.5193 (tpt) outliers start: 31 outliers final: 13 residues processed: 189 average time/residue: 0.8058 time to fit residues: 162.9376 Evaluate side-chains 175 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1463 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 94 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 954 ASN A 959 ASN A 990 ASN A 991 GLN A1190 HIS A1467 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.166397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127222 restraints weight = 31931.518| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 4.40 r_work: 0.2843 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13782 Z= 0.257 Angle : 0.698 10.504 18788 Z= 0.362 Chirality : 0.047 0.240 2102 Planarity : 0.005 0.063 2253 Dihedral : 15.339 154.726 2339 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.02 % Allowed : 8.78 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.13 (0.20), residues: 1570 helix: 1.07 (0.18), residues: 770 sheet: 0.47 (0.42), residues: 142 loop : -1.18 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1189 TYR 0.027 0.003 TYR A1166 PHE 0.022 0.002 PHE A 934 TRP 0.015 0.002 TRP A 520 HIS 0.010 0.002 HIS A1091 Details of bonding type rmsd covalent geometry : bond 0.00606 (13782) covalent geometry : angle 0.69791 (18788) hydrogen bonds : bond 0.05714 ( 643) hydrogen bonds : angle 4.64318 ( 1836) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 139 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6585 (tm-30) REVERT: A 294 GLN cc_start: 0.7916 (mp10) cc_final: 0.7682 (mp10) REVERT: A 987 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8237 (ptpt) REVERT: A 1111 MET cc_start: 0.7291 (pp-130) cc_final: 0.7080 (pp-130) REVERT: A 1261 PHE cc_start: 0.7470 (t80) cc_final: 0.7253 (t80) REVERT: A 1304 ARG cc_start: 0.6973 (mtp-110) cc_final: 0.6089 (ptt-90) REVERT: A 1339 MET cc_start: 0.6371 (mtm) cc_final: 0.6090 (mtp) REVERT: A 1344 ASP cc_start: 0.5863 (m-30) cc_final: 0.5239 (p0) REVERT: A 1469 GLN cc_start: 0.7155 (tp-100) cc_final: 0.6200 (pm20) REVERT: A 1480 GLU cc_start: 0.7106 (pm20) cc_final: 0.5721 (mt-10) REVERT: A 1602 ARG cc_start: 0.7627 (ttt-90) cc_final: 0.7337 (ttt-90) outliers start: 39 outliers final: 24 residues processed: 187 average time/residue: 0.8134 time to fit residues: 162.8942 Evaluate side-chains 183 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1209 GLU Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1603 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 61 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 148 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1190 HIS A1467 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.169672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.133644 restraints weight = 40787.813| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 4.84 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13782 Z= 0.109 Angle : 0.532 8.576 18788 Z= 0.275 Chirality : 0.039 0.208 2102 Planarity : 0.004 0.061 2253 Dihedral : 14.992 153.414 2339 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.23 % Allowed : 10.66 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.54 (0.21), residues: 1570 helix: 1.51 (0.19), residues: 769 sheet: 0.71 (0.42), residues: 137 loop : -1.12 (0.21), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1189 TYR 0.017 0.001 TYR A1166 PHE 0.018 0.001 PHE A 649 TRP 0.020 0.001 TRP A 520 HIS 0.004 0.001 HIS A1190 Details of bonding type rmsd covalent geometry : bond 0.00238 (13782) covalent geometry : angle 0.53202 (18788) hydrogen bonds : bond 0.03967 ( 643) hydrogen bonds : angle 4.31318 ( 1836) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.473 Fit side-chains REVERT: A 139 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6891 (tm-30) REVERT: A 294 GLN cc_start: 0.7091 (mp10) cc_final: 0.6831 (mp10) REVERT: A 860 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8060 (mp) REVERT: A 1111 MET cc_start: 0.6886 (pp-130) cc_final: 0.6623 (pp-130) REVERT: A 1304 ARG cc_start: 0.7014 (mtp-110) cc_final: 0.6465 (ptt-90) REVERT: A 1339 MET cc_start: 0.5799 (mtm) cc_final: 0.5585 (mtp) REVERT: A 1344 ASP cc_start: 0.5770 (m-30) cc_final: 0.5380 (p0) REVERT: A 1463 MET cc_start: 0.5393 (tpt) cc_final: 0.5099 (tpt) REVERT: A 1469 GLN cc_start: 0.7058 (tp-100) cc_final: 0.6152 (pm20) REVERT: A 1480 GLU cc_start: 0.7048 (pm20) cc_final: 0.6789 (pm20) REVERT: A 1602 ARG cc_start: 0.7184 (ttt-90) cc_final: 0.6836 (ttt-90) outliers start: 28 outliers final: 13 residues processed: 182 average time/residue: 0.7947 time to fit residues: 155.0869 Evaluate side-chains 172 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1603 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 135 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 4 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 ASN A 959 ASN A1190 HIS A1467 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.167828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.129064 restraints weight = 31603.075| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 4.26 r_work: 0.2897 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13782 Z= 0.168 Angle : 0.590 8.564 18788 Z= 0.305 Chirality : 0.042 0.222 2102 Planarity : 0.004 0.057 2253 Dihedral : 15.092 153.923 2339 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.52 % Allowed : 11.30 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.21), residues: 1570 helix: 1.43 (0.19), residues: 769 sheet: 0.64 (0.42), residues: 137 loop : -1.15 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1189 TYR 0.020 0.002 TYR A1166 PHE 0.019 0.002 PHE A 649 TRP 0.015 0.002 TRP A 520 HIS 0.005 0.001 HIS A1419 Details of bonding type rmsd covalent geometry : bond 0.00391 (13782) covalent geometry : angle 0.59027 (18788) hydrogen bonds : bond 0.04652 ( 643) hydrogen bonds : angle 4.34994 ( 1836) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 139 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6634 (mm-30) REVERT: A 294 GLN cc_start: 0.7893 (mp10) cc_final: 0.7666 (mp10) REVERT: A 987 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8409 (ptpt) REVERT: A 1111 MET cc_start: 0.7303 (pp-130) cc_final: 0.7038 (pp-130) REVERT: A 1304 ARG cc_start: 0.7088 (mtp-110) cc_final: 0.6181 (ptt-90) REVERT: A 1339 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5953 (mtp) REVERT: A 1344 ASP cc_start: 0.6045 (m-30) cc_final: 0.5372 (p0) REVERT: A 1352 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6513 (tp) REVERT: A 1469 GLN cc_start: 0.7201 (tp-100) cc_final: 0.6142 (pm20) outliers start: 32 outliers final: 18 residues processed: 179 average time/residue: 0.7475 time to fit residues: 143.7286 Evaluate side-chains 177 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1339 MET Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1603 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 49 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 959 ASN A1190 HIS A1467 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.167503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129209 restraints weight = 33342.613| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 4.51 r_work: 0.2892 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13782 Z= 0.170 Angle : 0.592 8.591 18788 Z= 0.307 Chirality : 0.042 0.222 2102 Planarity : 0.004 0.055 2253 Dihedral : 15.145 154.420 2339 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.59 % Allowed : 11.66 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.40 (0.21), residues: 1570 helix: 1.39 (0.19), residues: 773 sheet: 0.43 (0.42), residues: 144 loop : -1.16 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1189 TYR 0.020 0.002 TYR A1166 PHE 0.019 0.002 PHE A 649 TRP 0.017 0.002 TRP A 520 HIS 0.005 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00397 (13782) covalent geometry : angle 0.59221 (18788) hydrogen bonds : bond 0.04678 ( 643) hydrogen bonds : angle 4.35281 ( 1836) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 139 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6681 (mt-10) REVERT: A 192 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7018 (mpp) REVERT: A 294 GLN cc_start: 0.7968 (mp10) cc_final: 0.7730 (mp10) REVERT: A 987 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8293 (ptpt) REVERT: A 1111 MET cc_start: 0.7282 (pp-130) cc_final: 0.7018 (pp-130) REVERT: A 1262 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7772 (ttp) REVERT: A 1304 ARG cc_start: 0.7087 (mtp-110) cc_final: 0.6176 (ptt-90) REVERT: A 1339 MET cc_start: 0.6199 (OUTLIER) cc_final: 0.5961 (mtp) REVERT: A 1344 ASP cc_start: 0.6073 (m-30) cc_final: 0.5396 (p0) REVERT: A 1385 LYS cc_start: 0.6946 (mttp) cc_final: 0.6695 (mttp) REVERT: A 1469 GLN cc_start: 0.7189 (tp-100) cc_final: 0.6142 (pm20) REVERT: A 1480 GLU cc_start: 0.7145 (pm20) cc_final: 0.5743 (mt-10) REVERT: A 1582 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6139 (mmm160) outliers start: 33 outliers final: 21 residues processed: 176 average time/residue: 0.7813 time to fit residues: 147.4695 Evaluate side-chains 178 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1339 MET Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1582 ARG Chi-restraints excluded: chain A residue 1603 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 145 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 ASN A 959 ASN A1190 HIS A1467 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.167403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.128710 restraints weight = 30788.812| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 4.25 r_work: 0.2901 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13782 Z= 0.171 Angle : 0.597 8.421 18788 Z= 0.309 Chirality : 0.042 0.222 2102 Planarity : 0.004 0.054 2253 Dihedral : 15.159 154.687 2339 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.66 % Allowed : 11.66 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.38 (0.21), residues: 1570 helix: 1.37 (0.19), residues: 775 sheet: 0.38 (0.42), residues: 144 loop : -1.16 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1189 TYR 0.020 0.002 TYR A1166 PHE 0.019 0.002 PHE A 649 TRP 0.017 0.002 TRP A 520 HIS 0.005 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00400 (13782) covalent geometry : angle 0.59715 (18788) hydrogen bonds : bond 0.04683 ( 643) hydrogen bonds : angle 4.34596 ( 1836) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 139 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6495 (mm-30) REVERT: A 192 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.6950 (mpp) REVERT: A 294 GLN cc_start: 0.7941 (mp10) cc_final: 0.7702 (mp10) REVERT: A 860 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8351 (mp) REVERT: A 1111 MET cc_start: 0.7253 (pp-130) cc_final: 0.7007 (pp-130) REVERT: A 1262 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7738 (ttp) REVERT: A 1339 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5966 (mtp) REVERT: A 1344 ASP cc_start: 0.6044 (m-30) cc_final: 0.5395 (p0) REVERT: A 1385 LYS cc_start: 0.6880 (mttp) cc_final: 0.6598 (mttp) REVERT: A 1469 GLN cc_start: 0.7253 (tp-100) cc_final: 0.6185 (pm20) REVERT: A 1480 GLU cc_start: 0.7140 (pm20) cc_final: 0.5774 (mt-10) outliers start: 34 outliers final: 23 residues processed: 174 average time/residue: 0.8343 time to fit residues: 155.7650 Evaluate side-chains 179 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1339 MET Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1603 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 8 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 138 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 43 optimal weight: 0.0010 chunk 158 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS A 959 ASN A1190 HIS A1467 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.168213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.129663 restraints weight = 31875.414| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 4.47 r_work: 0.2860 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13782 Z= 0.142 Angle : 0.566 8.616 18788 Z= 0.292 Chirality : 0.041 0.217 2102 Planarity : 0.004 0.055 2253 Dihedral : 15.085 154.609 2339 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.30 % Allowed : 12.38 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.49 (0.21), residues: 1570 helix: 1.47 (0.19), residues: 775 sheet: 0.45 (0.43), residues: 134 loop : -1.11 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1304 TYR 0.018 0.002 TYR A1166 PHE 0.020 0.002 PHE A 649 TRP 0.019 0.001 TRP A 520 HIS 0.005 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00330 (13782) covalent geometry : angle 0.56601 (18788) hydrogen bonds : bond 0.04356 ( 643) hydrogen bonds : angle 4.27713 ( 1836) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 139 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6523 (mm-30) REVERT: A 192 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.6893 (mpp) REVERT: A 294 GLN cc_start: 0.7903 (mp10) cc_final: 0.7646 (mp10) REVERT: A 860 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8324 (mp) REVERT: A 1061 ASP cc_start: 0.6964 (m-30) cc_final: 0.6697 (m-30) REVERT: A 1111 MET cc_start: 0.7241 (pp-130) cc_final: 0.6991 (pp-130) REVERT: A 1262 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7720 (ttp) REVERT: A 1304 ARG cc_start: 0.7140 (mtp-110) cc_final: 0.6207 (ptt90) REVERT: A 1344 ASP cc_start: 0.6081 (m-30) cc_final: 0.5421 (p0) REVERT: A 1385 LYS cc_start: 0.6823 (mttp) cc_final: 0.6516 (mttp) REVERT: A 1469 GLN cc_start: 0.7199 (tp-100) cc_final: 0.6136 (pm20) REVERT: A 1480 GLU cc_start: 0.7136 (pm20) cc_final: 0.5732 (mt-10) outliers start: 29 outliers final: 21 residues processed: 176 average time/residue: 0.8257 time to fit residues: 155.9383 Evaluate side-chains 179 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1603 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 122 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 ASN A 959 ASN A1190 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.168338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.129995 restraints weight = 31496.052| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 4.33 r_work: 0.2897 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13782 Z= 0.142 Angle : 0.565 9.120 18788 Z= 0.291 Chirality : 0.041 0.217 2102 Planarity : 0.004 0.054 2253 Dihedral : 15.067 154.592 2339 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.16 % Allowed : 12.74 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.21), residues: 1570 helix: 1.45 (0.19), residues: 781 sheet: 0.44 (0.43), residues: 134 loop : -1.14 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1304 TYR 0.018 0.002 TYR A1166 PHE 0.020 0.001 PHE A 649 TRP 0.019 0.001 TRP A 520 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00329 (13782) covalent geometry : angle 0.56497 (18788) hydrogen bonds : bond 0.04356 ( 643) hydrogen bonds : angle 4.27175 ( 1836) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 139 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6515 (mm-30) REVERT: A 192 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.6934 (mpp) REVERT: A 294 GLN cc_start: 0.7917 (mp10) cc_final: 0.7667 (mp10) REVERT: A 860 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8328 (mp) REVERT: A 1061 ASP cc_start: 0.6909 (m-30) cc_final: 0.6641 (m-30) REVERT: A 1111 MET cc_start: 0.7223 (pp-130) cc_final: 0.6977 (pp-130) REVERT: A 1262 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7745 (ttp) REVERT: A 1304 ARG cc_start: 0.7145 (mtp-110) cc_final: 0.6201 (ptt90) REVERT: A 1344 ASP cc_start: 0.6111 (m-30) cc_final: 0.5432 (p0) REVERT: A 1385 LYS cc_start: 0.6885 (mttp) cc_final: 0.6575 (mttp) REVERT: A 1469 GLN cc_start: 0.7199 (tp-100) cc_final: 0.6151 (pm20) outliers start: 27 outliers final: 19 residues processed: 174 average time/residue: 0.7719 time to fit residues: 144.4207 Evaluate side-chains 180 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1456 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 81 optimal weight: 0.3980 chunk 152 optimal weight: 10.0000 chunk 134 optimal weight: 0.0070 chunk 144 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 114 optimal weight: 0.4980 chunk 140 optimal weight: 10.0000 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 ASN ** A1182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.168681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130040 restraints weight = 29280.229| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 4.13 r_work: 0.2915 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13782 Z= 0.132 Angle : 0.556 12.302 18788 Z= 0.285 Chirality : 0.040 0.214 2102 Planarity : 0.004 0.055 2253 Dihedral : 14.998 154.508 2339 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.94 % Allowed : 13.17 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.21), residues: 1570 helix: 1.52 (0.19), residues: 781 sheet: 0.44 (0.43), residues: 134 loop : -1.13 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1304 TYR 0.018 0.001 TYR A1166 PHE 0.020 0.001 PHE A 649 TRP 0.019 0.001 TRP A 520 HIS 0.004 0.001 HIS A1190 Details of bonding type rmsd covalent geometry : bond 0.00304 (13782) covalent geometry : angle 0.55620 (18788) hydrogen bonds : bond 0.04193 ( 643) hydrogen bonds : angle 4.22130 ( 1836) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 139 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6616 (mm-30) REVERT: A 192 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.6810 (mpp) REVERT: A 221 LEU cc_start: 0.7225 (mt) cc_final: 0.6997 (mt) REVERT: A 294 GLN cc_start: 0.7884 (mp10) cc_final: 0.7557 (mp10) REVERT: A 1061 ASP cc_start: 0.6893 (m-30) cc_final: 0.6635 (m-30) REVERT: A 1111 MET cc_start: 0.7208 (pp-130) cc_final: 0.6983 (pp-130) REVERT: A 1262 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7732 (ttp) REVERT: A 1304 ARG cc_start: 0.7139 (mtp-110) cc_final: 0.6255 (ptt90) REVERT: A 1344 ASP cc_start: 0.6138 (m-30) cc_final: 0.5433 (p0) REVERT: A 1385 LYS cc_start: 0.6894 (mttp) cc_final: 0.6572 (mttp) REVERT: A 1418 ARG cc_start: 0.6871 (mmt180) cc_final: 0.6646 (mpt-90) REVERT: A 1469 GLN cc_start: 0.7204 (tp-100) cc_final: 0.6168 (pm20) REVERT: A 1582 ARG cc_start: 0.6971 (mmm160) cc_final: 0.6311 (mmm160) outliers start: 24 outliers final: 19 residues processed: 179 average time/residue: 0.7846 time to fit residues: 151.0607 Evaluate side-chains 182 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1456 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 6 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 5 optimal weight: 30.0000 chunk 99 optimal weight: 0.3980 chunk 83 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 ASN ** A1182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.166491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.127690 restraints weight = 31867.030| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 4.53 r_work: 0.2873 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13782 Z= 0.225 Angle : 0.652 11.185 18788 Z= 0.334 Chirality : 0.045 0.229 2102 Planarity : 0.005 0.052 2253 Dihedral : 15.097 153.071 2339 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.09 % Allowed : 13.17 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.20), residues: 1570 helix: 1.23 (0.18), residues: 783 sheet: 0.10 (0.42), residues: 139 loop : -1.15 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1304 TYR 0.021 0.002 TYR A1166 PHE 0.025 0.002 PHE A 234 TRP 0.015 0.002 TRP A 520 HIS 0.006 0.002 HIS A1419 Details of bonding type rmsd covalent geometry : bond 0.00532 (13782) covalent geometry : angle 0.65182 (18788) hydrogen bonds : bond 0.05105 ( 643) hydrogen bonds : angle 4.36759 ( 1836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5412.74 seconds wall clock time: 92 minutes 59.70 seconds (5579.70 seconds total)