Starting phenix.real_space_refine on Sat Aug 8 05:48:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/31mr_58555/08_2026/31mr_58555_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/31mr_58555/08_2026/31mr_58555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/31mr_58555/08_2026/31mr_58555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/31mr_58555/08_2026/31mr_58555.map" model { file = "/net/cci-nas-00/data/ceres_data/31mr_58555/08_2026/31mr_58555_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/31mr_58555/08_2026/31mr_58555_neut.cif" } resolution = 3.07 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: 5 Type Number sf(0) Gaussians S 37 5.16 5 C 7967 2.51 5 N 2167 2.21 5 O 2491 1.98 5 H 12465 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25127 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1468 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 20102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1304, 20102 Classifications: {'peptide': 1304} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1250} Chain: "H" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1850 Classifications: {'peptide': 122} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1707 Classifications: {'peptide': 113} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 4, 'PTRANS': 1, 'TRANS': 107} Time building chain proxies: 4.06, per 1000 atoms: 0.16 Number of scatterers: 25127 At special positions: 0 Unit cell: (96.75, 132, 145.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 O 2491 8.00 N 2167 7.00 C 7967 6.00 H 12465 1.00 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: 2.22 Conformation dependent library (CDL) restraints added in 758.8 milliseconds 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2992 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 32 sheets defined 14.7% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 141 through 153 Processing helix chain 'B' and resid 246 through 257 Processing helix chain 'B' and resid 286 through 291 removed outlier: 6.902A pdb=" N SER B 291 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 306 Processing helix chain 'B' and resid 326 through 339 Processing helix chain 'B' and resid 421 through 426 Processing helix chain 'B' and resid 441 through 448 removed outlier: 3.729A pdb=" N TYR B 445 " --> pdb=" O THR B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 474 removed outlier: 3.520A pdb=" N ALA B 472 " --> pdb=" O MET B 468 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 519 Processing helix chain 'B' and resid 520 through 522 No H-bonds generated for 'chain 'B' and resid 520 through 522' Processing helix chain 'B' and resid 583 through 606 removed outlier: 3.510A pdb=" N ALA B 587 " --> pdb=" O GLY B 583 " (cutoff:3.500A) Proline residue: B 589 - end of helix Processing helix chain 'B' and resid 610 through 625 removed outlier: 3.718A pdb=" N ALA B 615 " --> pdb=" O LYS B 611 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASP B 616 " --> pdb=" O GLU B 612 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 619 " --> pdb=" O ALA B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 644 Processing helix chain 'B' and resid 649 through 656 Processing helix chain 'B' and resid 746 through 754 removed outlier: 5.027A pdb=" N LYS B 752 " --> pdb=" O LYS B 748 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN B 753 " --> pdb=" O GLU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 791 Processing helix chain 'B' and resid 797 through 805 Processing helix chain 'B' and resid 1063 through 1068 Processing helix chain 'B' and resid 1089 through 1091 No H-bonds generated for 'chain 'B' and resid 1089 through 1091' Processing helix chain 'B' and resid 1189 through 1191 No H-bonds generated for 'chain 'B' and resid 1189 through 1191' Processing helix chain 'B' and resid 1208 through 1213 Processing helix chain 'B' and resid 1218 through 1222 removed outlier: 4.478A pdb=" N SER B1222 " --> pdb=" O ALA B1219 " (cutoff:3.500A) Processing helix chain 'B' and resid 1356 through 1361 Processing helix chain 'B' and resid 1378 through 1382 Processing helix chain 'B' and resid 1443 through 1446 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 85 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 164 through 169 removed outlier: 4.184A pdb=" N VAL A 164 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE B 280 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE A 166 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ARG B 282 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N HIS A 168 " --> pdb=" O ARG B 282 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL A 114 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ASN B 312 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA A 116 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE B 311 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ALA B 346 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LEU B 313 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL B 343 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL B 382 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL B 345 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ALA B 384 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N SER B 381 " --> pdb=" O ILE B 562 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA B 564 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA B 383 " --> pdb=" O ALA B 564 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLY B 566 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE B 385 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 389 through 392 Processing sheet with id=AA3, first strand: chain 'B' and resid 410 through 411 removed outlier: 6.981A pdb=" N GLN B 433 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU B 456 " --> pdb=" O GLN B 433 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA B 435 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLU B 458 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL B 437 " --> pdb=" O GLU B 458 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA B 455 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE B 483 " --> pdb=" O ALA B 455 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE B 457 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL B 480 " --> pdb=" O ALA B 506 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE B 508 " --> pdb=" O VAL B 480 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE B 482 " --> pdb=" O ILE B 508 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 569 through 572 removed outlier: 3.972A pdb=" N ILE B 569 " --> pdb=" O GLN B 581 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN B 581 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 630 through 631 removed outlier: 3.645A pdb=" N THR B 636 " --> pdb=" O ASN B 631 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 658 through 661 Processing sheet with id=AA7, first strand: chain 'B' and resid 669 through 674 removed outlier: 5.601A pdb=" N SER B 670 " --> pdb=" O PRO B 780 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 782 " --> pdb=" O SER B 670 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY B 672 " --> pdb=" O VAL B 782 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N TYR B 759 " --> pdb=" O ASP B 703 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP B 703 " --> pdb=" O TYR B 759 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LYS B 692 " --> pdb=" O VAL B 727 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 727 " --> pdb=" O LYS B 692 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU B 694 " --> pdb=" O GLY B 725 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY B 725 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N TYR B 696 " --> pdb=" O GLN B 723 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLN B 723 " --> pdb=" O TYR B 696 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N THR B 698 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR B 721 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU B 700 " --> pdb=" O LEU B 719 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N THR B 715 " --> pdb=" O HIS B 704 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 847 through 850 removed outlier: 3.892A pdb=" N GLY B 847 " --> pdb=" O GLY B 833 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE B 888 " --> pdb=" O THR B 943 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR B 943 " --> pdb=" O PHE B 888 " (cutoff:3.500A) removed outlier: 11.699A pdb=" N GLY B 890 " --> pdb=" O LEU B 941 " (cutoff:3.500A) removed outlier: 10.536A pdb=" N LEU B 941 " --> pdb=" O GLY B 890 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 854 through 855 Processing sheet with id=AB1, first strand: chain 'B' and resid 873 through 875 removed outlier: 4.152A pdb=" N LEU B 873 " --> pdb=" O ASP B 981 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N TYR B 967 " --> pdb=" O GLY B 898 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLY B 898 " --> pdb=" O TYR B 967 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP B 916 " --> pdb=" O VAL B 903 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 873 through 875 removed outlier: 4.152A pdb=" N LEU B 873 " --> pdb=" O ASP B 981 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N TYR B 967 " --> pdb=" O GLY B 898 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLY B 898 " --> pdb=" O TYR B 967 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLN B 897 " --> pdb=" O GLY B 924 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N GLY B 924 " --> pdb=" O GLN B 897 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1060 through 1061 removed outlier: 3.594A pdb=" N SER B 992 " --> pdb=" O LEU B1105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1020 through 1023 Processing sheet with id=AB5, first strand: chain 'B' and resid 1032 through 1037 Processing sheet with id=AB6, first strand: chain 'B' and resid 1145 through 1148 removed outlier: 3.577A pdb=" N GLN B1145 " --> pdb=" O GLN B1133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1156 through 1157 removed outlier: 5.079A pdb=" N ARG B1236 " --> pdb=" O ASP B1180 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASP B1180 " --> pdb=" O ARG B1236 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TRP B1198 " --> pdb=" O VAL B1185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1156 through 1157 Processing sheet with id=AB9, first strand: chain 'B' and resid 1262 through 1266 removed outlier: 3.592A pdb=" N ASP B1264 " --> pdb=" O HIS B1271 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP B1270 " --> pdb=" O ILE B1329 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1317 through 1318 removed outlier: 5.506A pdb=" N ARG B1287 " --> pdb=" O GLU B1345 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU B1345 " --> pdb=" O ARG B1287 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU B1289 " --> pdb=" O LEU B1343 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1301 through 1306 Processing sheet with id=AC3, first strand: chain 'B' and resid 1410 through 1414 removed outlier: 9.073A pdb=" N GLN B1449 " --> pdb=" O LYS B1366 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B1368 " --> pdb=" O GLN B1449 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL B1451 " --> pdb=" O VAL B1368 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASN B1370 " --> pdb=" O VAL B1451 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1387 through 1391 removed outlier: 6.649A pdb=" N THR B1387 " --> pdb=" O LEU B1423 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1430 through 1432 Processing sheet with id=AC6, first strand: chain 'B' and resid 1498 through 1504 removed outlier: 9.039A pdb=" N HIS B1534 " --> pdb=" O THR B1460 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLN B1462 " --> pdb=" O HIS B1534 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU B1536 " --> pdb=" O GLN B1462 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N THR B1464 " --> pdb=" O LEU B1536 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU B1538 " --> pdb=" O THR B1464 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N HIS B1466 " --> pdb=" O LEU B1538 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU B1540 " --> pdb=" O HIS B1466 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1486 through 1489 removed outlier: 4.638A pdb=" N VAL B1477 " --> pdb=" O LEU B1489 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.612A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.786A pdb=" N ASN H 111 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AD4, first strand: chain 'L' and resid 59 through 60 removed outlier: 6.602A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N PHE L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU L 39 " --> pdb=" O PHE L 55 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR L 103 " --> pdb=" O GLN L 96 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 59 through 60 removed outlier: 6.602A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N PHE L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU L 39 " --> pdb=" O PHE L 55 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1059 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.28 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 12461 1.12 - 1.30: 2214 1.30 - 1.47: 4837 1.47 - 1.65: 5798 1.65 - 1.82: 70 Bond restraints: 25380 Sorted by residual: bond pdb=" ND2 ASN B 884 " pdb="HD21 ASN B 884 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" ND2 ASN B 884 " pdb="HD22 ASN B 884 " ideal model delta sigma weight residual 0.860 1.019 -0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" ND2 ASN H 30 " pdb="HD21 ASN H 30 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" NE2 GLN B1111 " pdb="HE22 GLN B1111 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N SER L 83 " pdb=" H SER L 83 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 25375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 42634 4.08 - 8.16: 3100 8.16 - 12.24: 79 12.24 - 16.32: 7 16.32 - 20.40: 1 Bond angle restraints: 45821 Sorted by residual: angle pdb=" N TYR B 353 " pdb=" CA TYR B 353 " pdb=" C TYR B 353 " ideal model delta sigma weight residual 110.43 124.96 -14.53 1.31e+00 5.83e-01 1.23e+02 angle pdb=" CA GLU B 761 " pdb=" CB GLU B 761 " pdb=" CG GLU B 761 " ideal model delta sigma weight residual 114.10 134.50 -20.40 2.00e+00 2.50e-01 1.04e+02 angle pdb=" N VAL B 352 " pdb=" CA VAL B 352 " pdb=" C VAL B 352 " ideal model delta sigma weight residual 109.30 96.94 12.36 1.25e+00 6.40e-01 9.78e+01 angle pdb=" N ARG B 351 " pdb=" CA ARG B 351 " pdb=" C ARG B 351 " ideal model delta sigma weight residual 107.93 123.35 -15.42 1.65e+00 3.67e-01 8.73e+01 angle pdb=" CA PHE H 67 " pdb=" CB PHE H 67 " pdb=" CG PHE H 67 " ideal model delta sigma weight residual 113.80 122.67 -8.87 1.00e+00 1.00e+00 7.87e+01 ... (remaining 45816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 10937 17.42 - 34.84: 607 34.84 - 52.27: 193 52.27 - 69.69: 243 69.69 - 87.11: 22 Dihedral angle restraints: 12002 sinusoidal: 6525 harmonic: 5477 Sorted by residual: dihedral pdb=" C TYR B 353 " pdb=" N TYR B 353 " pdb=" CA TYR B 353 " pdb=" CB TYR B 353 " ideal model delta harmonic sigma weight residual -122.60 -143.55 20.95 0 2.50e+00 1.60e-01 7.02e+01 dihedral pdb=" N TYR B 353 " pdb=" C TYR B 353 " pdb=" CA TYR B 353 " pdb=" CB TYR B 353 " ideal model delta harmonic sigma weight residual 122.80 143.08 -20.28 0 2.50e+00 1.60e-01 6.58e+01 dihedral pdb=" N GLU B 761 " pdb=" C GLU B 761 " pdb=" CA GLU B 761 " pdb=" CB GLU B 761 " ideal model delta harmonic sigma weight residual 122.80 103.36 19.44 0 2.50e+00 1.60e-01 6.05e+01 ... (remaining 11999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.193: 1800 0.193 - 0.387: 120 0.387 - 0.580: 8 0.580 - 0.773: 1 0.773 - 0.967: 1 Chirality restraints: 1930 Sorted by residual: chirality pdb=" CA TYR B 353 " pdb=" N TYR B 353 " pdb=" C TYR B 353 " pdb=" CB TYR B 353 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.34e+01 chirality pdb=" CA ASP B 421 " pdb=" N ASP B 421 " pdb=" C ASP B 421 " pdb=" CB ASP B 421 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.80e+00 chirality pdb=" CA LYS L 45 " pdb=" N LYS L 45 " pdb=" C LYS L 45 " pdb=" CB LYS L 45 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.21e+00 ... (remaining 1927 not shown) Planarity restraints: 3849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 550 " 0.372 2.00e-02 2.50e+03 1.53e-01 9.41e+02 pdb=" CG TRP B 550 " 0.152 2.00e-02 2.50e+03 pdb=" CD1 TRP B 550 " -0.144 2.00e-02 2.50e+03 pdb=" CD2 TRP B 550 " 0.060 2.00e-02 2.50e+03 pdb=" NE1 TRP B 550 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 TRP B 550 " 0.061 2.00e-02 2.50e+03 pdb=" CE3 TRP B 550 " -0.075 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 550 " 0.107 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 550 " -0.097 2.00e-02 2.50e+03 pdb=" CH2 TRP B 550 " 0.058 2.00e-02 2.50e+03 pdb=" HD1 TRP B 550 " -0.203 2.00e-02 2.50e+03 pdb=" HE1 TRP B 550 " -0.152 2.00e-02 2.50e+03 pdb=" HE3 TRP B 550 " -0.160 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 550 " 0.148 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 550 " -0.175 2.00e-02 2.50e+03 pdb=" HH2 TRP B 550 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 353 " 0.413 2.00e-02 2.50e+03 1.55e-01 7.20e+02 pdb=" CG TYR B 353 " -0.098 2.00e-02 2.50e+03 pdb=" CD1 TYR B 353 " -0.141 2.00e-02 2.50e+03 pdb=" CD2 TYR B 353 " -0.116 2.00e-02 2.50e+03 pdb=" CE1 TYR B 353 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR B 353 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR B 353 " 0.051 2.00e-02 2.50e+03 pdb=" OH TYR B 353 " 0.209 2.00e-02 2.50e+03 pdb=" HD1 TYR B 353 " -0.108 2.00e-02 2.50e+03 pdb=" HD2 TYR B 353 " -0.111 2.00e-02 2.50e+03 pdb=" HE1 TYR B 353 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR B 353 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 97 " 0.227 2.00e-02 2.50e+03 1.02e-01 4.19e+02 pdb=" CG TRP A 97 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP A 97 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 97 " -0.074 2.00e-02 2.50e+03 pdb=" NE1 TRP A 97 " -0.080 2.00e-02 2.50e+03 pdb=" CE2 TRP A 97 " -0.056 2.00e-02 2.50e+03 pdb=" CE3 TRP A 97 " -0.106 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 97 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 97 " -0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP A 97 " 0.085 2.00e-02 2.50e+03 pdb=" HD1 TRP A 97 " 0.082 2.00e-02 2.50e+03 pdb=" HE1 TRP A 97 " -0.107 2.00e-02 2.50e+03 pdb=" HE3 TRP A 97 " -0.146 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 97 " -0.003 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 97 " -0.024 2.00e-02 2.50e+03 pdb=" HH2 TRP A 97 " 0.204 2.00e-02 2.50e+03 ... (remaining 3846 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 2153 2.20 - 2.80: 47012 2.80 - 3.40: 71036 3.40 - 4.00: 96032 4.00 - 4.60: 140448 Nonbonded interactions: 356681 Sorted by model distance: nonbonded pdb=" OD1 ASP B1057 " pdb=" HG SER B1059 " model vdw 1.595 2.450 nonbonded pdb=" HG SER B 381 " pdb=" OD1 ASP B 561 " model vdw 1.597 2.450 nonbonded pdb=" O THR B 637 " pdb=" HG SER B 716 " model vdw 1.600 2.450 nonbonded pdb=" OD2 ASP B 429 " pdb=" HG SER B 531 " model vdw 1.600 2.450 nonbonded pdb=" OD1 ASP B 742 " pdb=" HG SER B 744 " model vdw 1.601 2.450 ... (remaining 356676 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.960 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: 0.180 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.540 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.012 0.047 12915 Z= 0.708 Angle : 1.995 20.398 17475 Z= 1.324 Chirality : 0.113 0.967 1930 Planarity : 0.016 0.331 2283 Dihedral : 11.855 87.111 4756 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 1.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.20), residues: 1626 helix: -1.64 (0.34), residues: 165 sheet: -0.34 (0.22), residues: 457 loop : -0.74 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG B1357 TYR 0.350 0.028 TYR B 353 PHE 0.123 0.019 PHE B 507 TRP 0.212 0.033 TRP B 550 HIS 0.016 0.004 HIS B 911 Details of bonding type rmsd/Z covalent geometry : bond 0.01172 / 0.71 (12915) covalent geometry : angle 1.99457 / 1.32 (17475) hydrogen bonds : bond 0.15547 / 10.45 ( 378) hydrogen bonds : angle 8.37328 / 6.02 ( 1059) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASN cc_start: 0.8263 (t0) cc_final: 0.7364 (t0) REVERT: B 243 LYS cc_start: 0.9151 (mmtp) cc_final: 0.8335 (tptp) REVERT: H 111 ASN cc_start: 0.8322 (m-40) cc_final: 0.8023 (m110) REVERT: H 119 THR cc_start: 0.9274 (m) cc_final: 0.8950 (p) REVERT: L 92 TYR cc_start: 0.7454 (m-80) cc_final: 0.6917 (m-80) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.3238 time to fit residues: 164.8974 Evaluate side-chains 248 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 GLN B 286 ASN B 312 ASN B 475 HIS B1446 ASN H 81 GLN L 97 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.088856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.070248 restraints weight = 97501.645| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.79 r_work: 0.3154 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12915 Z= 0.185 Angle : 0.720 10.266 17475 Z= 0.400 Chirality : 0.046 0.175 1930 Planarity : 0.005 0.105 2283 Dihedral : 5.559 44.133 1755 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.16 % Allowed : 7.73 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.84 (0.20), residues: 1626 helix: -0.20 (0.41), residues: 155 sheet: -0.57 (0.21), residues: 491 loop : -0.54 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 53 TYR 0.049 0.002 TYR B 353 PHE 0.030 0.002 PHE H 67 TRP 0.019 0.002 TRP B 550 HIS 0.008 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (12915) covalent geometry : angle 0.72048 / 0.40 (17475) hydrogen bonds : bond 0.04662 / 3.05 ( 378) hydrogen bonds : angle 6.71340 / 4.79 ( 1059) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 254 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8185 (mp0) cc_final: 0.7951 (mp0) REVERT: A 180 ASN cc_start: 0.8327 (t0) cc_final: 0.7707 (t0) REVERT: B 243 LYS cc_start: 0.8910 (mmtp) cc_final: 0.8272 (tttp) REVERT: B 558 LEU cc_start: 0.8819 (tp) cc_final: 0.8619 (tt) REVERT: B 806 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8596 (mtmm) REVERT: B 1119 ASN cc_start: 0.8879 (m-40) cc_final: 0.8358 (p0) REVERT: B 1316 LYS cc_start: 0.9003 (ttmt) cc_final: 0.8786 (tppt) REVERT: B 1422 LEU cc_start: 0.8863 (tp) cc_final: 0.8644 (tt) REVERT: H 111 ASN cc_start: 0.8251 (m-40) cc_final: 0.7703 (m-40) REVERT: H 119 THR cc_start: 0.9523 (m) cc_final: 0.9112 (p) REVERT: L 52 LEU cc_start: 0.8857 (tp) cc_final: 0.8517 (tp) REVERT: L 66 ASP cc_start: 0.9187 (t0) cc_final: 0.8833 (t0) REVERT: L 75 THR cc_start: 0.8919 (m) cc_final: 0.8678 (m) REVERT: L 80 THR cc_start: 0.9202 (m) cc_final: 0.8910 (p) outliers start: 16 outliers final: 9 residues processed: 259 average time/residue: 0.3056 time to fit residues: 111.1410 Evaluate side-chains 231 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 221 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 806 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 58 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 8 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 117 optimal weight: 0.0770 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 ASN B 883 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.086732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.067648 restraints weight = 97585.093| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.87 r_work: 0.3069 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12915 Z= 0.207 Angle : 0.647 9.106 17475 Z= 0.352 Chirality : 0.044 0.166 1930 Planarity : 0.005 0.081 2283 Dihedral : 5.400 37.215 1755 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.37 % Allowed : 9.46 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.72 (0.20), residues: 1626 helix: 0.20 (0.44), residues: 155 sheet: -0.54 (0.22), residues: 499 loop : -0.48 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 3 TYR 0.047 0.002 TYR B 353 PHE 0.029 0.002 PHE H 67 TRP 0.011 0.002 TRP B 550 HIS 0.005 0.001 HIS B 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (12915) covalent geometry : angle 0.64691 / 0.35 (17475) hydrogen bonds : bond 0.03844 / 2.52 ( 378) hydrogen bonds : angle 6.19882 / 4.41 ( 1059) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 230 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASN cc_start: 0.8469 (t0) cc_final: 0.7829 (t0) REVERT: B 243 LYS cc_start: 0.8909 (mmtp) cc_final: 0.8355 (tttp) REVERT: B 749 GLU cc_start: 0.9039 (tt0) cc_final: 0.8764 (tp30) REVERT: B 806 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8751 (mtmm) REVERT: B 1104 LYS cc_start: 0.9155 (ptmm) cc_final: 0.8885 (pttp) REVERT: B 1119 ASN cc_start: 0.8981 (m-40) cc_final: 0.8465 (p0) REVERT: B 1225 MET cc_start: 0.8817 (mmm) cc_final: 0.8534 (mmp) REVERT: B 1316 LYS cc_start: 0.9082 (ttmt) cc_final: 0.8870 (tppp) REVERT: H 111 ASN cc_start: 0.8247 (m-40) cc_final: 0.7113 (m-40) REVERT: H 119 THR cc_start: 0.9433 (m) cc_final: 0.9010 (p) REVERT: L 52 LEU cc_start: 0.8963 (tp) cc_final: 0.8720 (tp) REVERT: L 67 ARG cc_start: 0.8722 (mpp-170) cc_final: 0.7748 (ptp-170) outliers start: 19 outliers final: 13 residues processed: 236 average time/residue: 0.2831 time to fit residues: 96.0385 Evaluate side-chains 225 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 211 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 806 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 931 ASP Chi-restraints excluded: chain B residue 1374 ASP Chi-restraints excluded: chain B residue 1386 PHE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 43 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 57 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN B1192 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.087466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.067459 restraints weight = 97372.172| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 4.02 r_work: 0.3071 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12915 Z= 0.151 Angle : 0.589 7.902 17475 Z= 0.316 Chirality : 0.043 0.159 1930 Planarity : 0.004 0.068 2283 Dihedral : 5.219 36.596 1755 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.81 % Allowed : 10.11 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.21), residues: 1626 helix: 0.40 (0.44), residues: 156 sheet: -0.56 (0.22), residues: 508 loop : -0.42 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1026 TYR 0.039 0.002 TYR B 353 PHE 0.027 0.002 PHE H 67 TRP 0.010 0.001 TRP A 159 HIS 0.003 0.001 HIS B1534 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (12915) covalent geometry : angle 0.58885 / 0.32 (17475) hydrogen bonds : bond 0.03279 / 2.15 ( 378) hydrogen bonds : angle 5.89551 / 4.21 ( 1059) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 214 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASN cc_start: 0.8452 (t0) cc_final: 0.7787 (t0) REVERT: B 243 LYS cc_start: 0.8883 (mmtp) cc_final: 0.8326 (tttp) REVERT: B 474 LYS cc_start: 0.9057 (mttt) cc_final: 0.8739 (mmtm) REVERT: B 501 MET cc_start: 0.7379 (mtt) cc_final: 0.7038 (mtt) REVERT: B 604 LYS cc_start: 0.8980 (mmtt) cc_final: 0.8692 (tttt) REVERT: B 749 GLU cc_start: 0.9088 (tt0) cc_final: 0.8807 (tp30) REVERT: B 806 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8780 (mtmm) REVERT: B 1104 LYS cc_start: 0.9180 (ptmm) cc_final: 0.8948 (ptmm) REVERT: B 1119 ASN cc_start: 0.8972 (m-40) cc_final: 0.8510 (p0) REVERT: B 1122 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8555 (mmp) REVERT: B 1225 MET cc_start: 0.8757 (mmm) cc_final: 0.8370 (mmp) REVERT: B 1316 LYS cc_start: 0.9085 (ttmt) cc_final: 0.8862 (tppp) REVERT: H 111 ASN cc_start: 0.7948 (m-40) cc_final: 0.7382 (m-40) REVERT: H 119 THR cc_start: 0.9418 (m) cc_final: 0.8968 (p) REVERT: L 52 LEU cc_start: 0.9022 (tp) cc_final: 0.8699 (tp) outliers start: 25 outliers final: 20 residues processed: 223 average time/residue: 0.2708 time to fit residues: 87.6337 Evaluate side-chains 223 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 806 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 931 ASP Chi-restraints excluded: chain B residue 1071 ASP Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1122 MET Chi-restraints excluded: chain B residue 1192 GLN Chi-restraints excluded: chain B residue 1386 PHE Chi-restraints excluded: chain B residue 1428 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 43 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 131 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN B1322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.087245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.067308 restraints weight = 97280.370| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 4.01 r_work: 0.3068 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12915 Z= 0.149 Angle : 0.571 7.609 17475 Z= 0.306 Chirality : 0.043 0.155 1930 Planarity : 0.004 0.070 2283 Dihedral : 5.087 35.913 1755 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.37 % Allowed : 11.19 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.61 (0.21), residues: 1626 helix: 0.52 (0.44), residues: 156 sheet: -0.57 (0.22), residues: 518 loop : -0.38 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 53 TYR 0.036 0.002 TYR B 353 PHE 0.026 0.001 PHE H 67 TRP 0.009 0.001 TRP A 159 HIS 0.003 0.001 HIS B1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (12915) covalent geometry : angle 0.57060 / 0.31 (17475) hydrogen bonds : bond 0.03122 / 2.05 ( 378) hydrogen bonds : angle 5.74221 / 4.09 ( 1059) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASN cc_start: 0.8419 (t0) cc_final: 0.7739 (t0) REVERT: B 243 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8276 (tttp) REVERT: B 474 LYS cc_start: 0.9057 (mttt) cc_final: 0.8739 (mmtm) REVERT: B 501 MET cc_start: 0.7383 (mtt) cc_final: 0.7018 (mtt) REVERT: B 544 MET cc_start: 0.9236 (mmm) cc_final: 0.9020 (mmt) REVERT: B 604 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8684 (tttt) REVERT: B 749 GLU cc_start: 0.9119 (tt0) cc_final: 0.8806 (tp30) REVERT: B 806 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8793 (mtmm) REVERT: B 1104 LYS cc_start: 0.9201 (ptmm) cc_final: 0.8952 (ptmm) REVERT: B 1119 ASN cc_start: 0.8974 (m-40) cc_final: 0.8535 (p0) REVERT: B 1122 MET cc_start: 0.8801 (mmp) cc_final: 0.8543 (mmp) REVERT: B 1192 GLN cc_start: 0.8428 (tp-100) cc_final: 0.8109 (mp-120) REVERT: B 1316 LYS cc_start: 0.9089 (ttmt) cc_final: 0.8864 (tppp) REVERT: H 82 MET cc_start: 0.8157 (mtm) cc_final: 0.7723 (mmm) REVERT: H 111 ASN cc_start: 0.7921 (m-40) cc_final: 0.7366 (m-40) REVERT: H 119 THR cc_start: 0.9415 (m) cc_final: 0.8993 (p) REVERT: L 52 LEU cc_start: 0.8984 (tp) cc_final: 0.8663 (tp) outliers start: 19 outliers final: 15 residues processed: 213 average time/residue: 0.2862 time to fit residues: 87.6272 Evaluate side-chains 218 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 806 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 931 ASP Chi-restraints excluded: chain B residue 1071 ASP Chi-restraints excluded: chain B residue 1386 PHE Chi-restraints excluded: chain B residue 1428 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 43 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.084897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.064866 restraints weight = 98146.370| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.99 r_work: 0.3014 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12915 Z= 0.225 Angle : 0.588 8.408 17475 Z= 0.316 Chirality : 0.043 0.154 1930 Planarity : 0.004 0.068 2283 Dihedral : 5.122 34.820 1755 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.44 % Allowed : 12.06 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.79 (0.20), residues: 1626 helix: 0.32 (0.42), residues: 161 sheet: -0.72 (0.22), residues: 517 loop : -0.47 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 53 TYR 0.040 0.002 TYR B 353 PHE 0.027 0.002 PHE H 67 TRP 0.008 0.001 TRP B 550 HIS 0.004 0.001 HIS B 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.22 (12915) covalent geometry : angle 0.58779 / 0.32 (17475) hydrogen bonds : bond 0.03175 / 2.10 ( 378) hydrogen bonds : angle 5.74530 / 4.09 ( 1059) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASN cc_start: 0.8391 (t0) cc_final: 0.7744 (t0) REVERT: B 243 LYS cc_start: 0.8859 (mmtp) cc_final: 0.8271 (tttp) REVERT: B 474 LYS cc_start: 0.9077 (mttt) cc_final: 0.8764 (mmtm) REVERT: B 501 MET cc_start: 0.7627 (mtt) cc_final: 0.7277 (mtt) REVERT: B 749 GLU cc_start: 0.9185 (tt0) cc_final: 0.8848 (tp30) REVERT: B 806 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8828 (mtmm) REVERT: B 1104 LYS cc_start: 0.9211 (ptmm) cc_final: 0.9007 (ptmm) REVERT: B 1119 ASN cc_start: 0.9009 (m-40) cc_final: 0.8593 (p0) REVERT: B 1122 MET cc_start: 0.8855 (mmp) cc_final: 0.8514 (mmp) REVERT: B 1225 MET cc_start: 0.8424 (mmp) cc_final: 0.8147 (mmp) REVERT: B 1287 ARG cc_start: 0.8871 (ttp-110) cc_final: 0.8594 (ttp80) REVERT: B 1316 LYS cc_start: 0.9093 (ttmt) cc_final: 0.8875 (tppp) REVERT: H 4 LEU cc_start: 0.7892 (mm) cc_final: 0.7657 (mm) REVERT: H 119 THR cc_start: 0.9433 (m) cc_final: 0.9028 (p) REVERT: L 52 LEU cc_start: 0.8992 (tp) cc_final: 0.8726 (tp) outliers start: 20 outliers final: 17 residues processed: 218 average time/residue: 0.2976 time to fit residues: 92.1744 Evaluate side-chains 218 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 806 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 931 ASP Chi-restraints excluded: chain B residue 1071 ASP Chi-restraints excluded: chain B residue 1386 PHE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 43 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.085676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.065829 restraints weight = 96713.246| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.99 r_work: 0.3032 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12915 Z= 0.156 Angle : 0.563 7.769 17475 Z= 0.301 Chirality : 0.043 0.156 1930 Planarity : 0.004 0.068 2283 Dihedral : 5.018 34.559 1755 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.30 % Allowed : 13.00 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.71 (0.20), residues: 1626 helix: 0.75 (0.43), residues: 155 sheet: -0.67 (0.22), residues: 511 loop : -0.48 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 60 TYR 0.034 0.002 TYR B 353 PHE 0.026 0.001 PHE H 67 TRP 0.008 0.001 TRP A 159 HIS 0.003 0.001 HIS B 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (12915) covalent geometry : angle 0.56293 / 0.30 (17475) hydrogen bonds : bond 0.02930 / 1.93 ( 378) hydrogen bonds : angle 5.60749 / 3.99 ( 1059) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASN cc_start: 0.8334 (t0) cc_final: 0.7663 (t0) REVERT: B 243 LYS cc_start: 0.8826 (mmtp) cc_final: 0.8206 (tttp) REVERT: B 474 LYS cc_start: 0.9054 (mttt) cc_final: 0.8724 (mmtm) REVERT: B 501 MET cc_start: 0.7514 (mtt) cc_final: 0.7163 (mtt) REVERT: B 604 LYS cc_start: 0.8923 (mmtt) cc_final: 0.8655 (tttt) REVERT: B 749 GLU cc_start: 0.9195 (tt0) cc_final: 0.8859 (tp30) REVERT: B 806 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8871 (mtmm) REVERT: B 913 ASN cc_start: 0.9043 (m-40) cc_final: 0.8501 (p0) REVERT: B 1104 LYS cc_start: 0.9204 (ptmm) cc_final: 0.8990 (ptmm) REVERT: B 1119 ASN cc_start: 0.8988 (m-40) cc_final: 0.8598 (p0) REVERT: B 1122 MET cc_start: 0.8839 (mmp) cc_final: 0.8407 (mmp) REVERT: B 1225 MET cc_start: 0.8376 (mmp) cc_final: 0.8158 (mmp) REVERT: B 1287 ARG cc_start: 0.8836 (ttp-110) cc_final: 0.8552 (ttp80) REVERT: B 1316 LYS cc_start: 0.9115 (ttmt) cc_final: 0.8866 (tppp) REVERT: H 4 LEU cc_start: 0.7961 (mm) cc_final: 0.7703 (mm) REVERT: H 82 MET cc_start: 0.8214 (mtm) cc_final: 0.7796 (mmm) REVERT: H 119 THR cc_start: 0.9428 (m) cc_final: 0.9040 (p) REVERT: L 52 LEU cc_start: 0.8965 (tp) cc_final: 0.8697 (tp) REVERT: L 66 ASP cc_start: 0.8946 (t0) cc_final: 0.8635 (t0) outliers start: 18 outliers final: 14 residues processed: 210 average time/residue: 0.2464 time to fit residues: 74.0801 Evaluate side-chains 209 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 806 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 931 ASP Chi-restraints excluded: chain B residue 1071 ASP Chi-restraints excluded: chain B residue 1374 ASP Chi-restraints excluded: chain B residue 1386 PHE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 43 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 119 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 134 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 95 optimal weight: 0.0980 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.086110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.066352 restraints weight = 97227.804| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 4.00 r_work: 0.3046 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12915 Z= 0.135 Angle : 0.556 7.347 17475 Z= 0.296 Chirality : 0.043 0.153 1930 Planarity : 0.004 0.067 2283 Dihedral : 4.904 34.315 1755 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.08 % Allowed : 13.00 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.21), residues: 1626 helix: 0.77 (0.43), residues: 156 sheet: -0.66 (0.23), residues: 498 loop : -0.43 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 53 TYR 0.032 0.002 TYR B 353 PHE 0.026 0.001 PHE H 67 TRP 0.008 0.001 TRP A 159 HIS 0.003 0.001 HIS B 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (12915) covalent geometry : angle 0.55616 / 0.30 (17475) hydrogen bonds : bond 0.02818 / 1.87 ( 378) hydrogen bonds : angle 5.49708 / 3.92 ( 1059) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASN cc_start: 0.8239 (t0) cc_final: 0.7589 (t0) REVERT: B 243 LYS cc_start: 0.8803 (mmtp) cc_final: 0.8188 (tttp) REVERT: B 474 LYS cc_start: 0.9040 (mttt) cc_final: 0.8705 (mmtm) REVERT: B 501 MET cc_start: 0.7497 (mtt) cc_final: 0.7148 (mtt) REVERT: B 604 LYS cc_start: 0.8902 (mmtt) cc_final: 0.8634 (tttt) REVERT: B 749 GLU cc_start: 0.9218 (tt0) cc_final: 0.8918 (tp30) REVERT: B 806 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8873 (mtmm) REVERT: B 913 ASN cc_start: 0.9049 (m-40) cc_final: 0.8536 (p0) REVERT: B 1053 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8201 (tm-30) REVERT: B 1104 LYS cc_start: 0.9208 (ptmm) cc_final: 0.8987 (ptmm) REVERT: B 1119 ASN cc_start: 0.8962 (m-40) cc_final: 0.8620 (p0) REVERT: B 1122 MET cc_start: 0.8809 (mmp) cc_final: 0.8224 (mmp) REVERT: B 1287 ARG cc_start: 0.8879 (ttp-110) cc_final: 0.8597 (ttp80) REVERT: H 4 LEU cc_start: 0.7973 (mm) cc_final: 0.7695 (mm) REVERT: H 82 MET cc_start: 0.8219 (mtm) cc_final: 0.7816 (mmm) REVERT: H 119 THR cc_start: 0.9413 (m) cc_final: 0.9022 (p) REVERT: L 52 LEU cc_start: 0.8926 (tp) cc_final: 0.8672 (tp) outliers start: 15 outliers final: 13 residues processed: 207 average time/residue: 0.2585 time to fit residues: 76.4817 Evaluate side-chains 208 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 806 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 931 ASP Chi-restraints excluded: chain B residue 1023 TYR Chi-restraints excluded: chain B residue 1386 PHE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 43 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN B 723 GLN B1055 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.084903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.065414 restraints weight = 97377.923| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.94 r_work: 0.3052 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12915 Z= 0.165 Angle : 0.569 7.591 17475 Z= 0.304 Chirality : 0.043 0.152 1930 Planarity : 0.004 0.067 2283 Dihedral : 4.900 34.101 1755 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.16 % Allowed : 13.29 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.74 (0.21), residues: 1626 helix: 0.59 (0.43), residues: 162 sheet: -0.68 (0.23), residues: 499 loop : -0.49 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 53 TYR 0.034 0.002 TYR B 353 PHE 0.025 0.001 PHE H 67 TRP 0.007 0.001 TRP B 550 HIS 0.003 0.001 HIS B 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (12915) covalent geometry : angle 0.56850 / 0.30 (17475) hydrogen bonds : bond 0.02858 / 1.91 ( 378) hydrogen bonds : angle 5.47971 / 3.91 ( 1059) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASN cc_start: 0.8249 (t0) cc_final: 0.7583 (t0) REVERT: B 243 LYS cc_start: 0.8806 (mmtp) cc_final: 0.8192 (tttp) REVERT: B 474 LYS cc_start: 0.9054 (mttt) cc_final: 0.8725 (mmtm) REVERT: B 501 MET cc_start: 0.7590 (mtt) cc_final: 0.7240 (mtt) REVERT: B 604 LYS cc_start: 0.8917 (mmtt) cc_final: 0.8654 (tttt) REVERT: B 749 GLU cc_start: 0.9202 (tt0) cc_final: 0.8926 (tp30) REVERT: B 806 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8897 (mtmm) REVERT: B 913 ASN cc_start: 0.9044 (m-40) cc_final: 0.8541 (p0) REVERT: B 1053 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8198 (tm-30) REVERT: B 1104 LYS cc_start: 0.9203 (ptmm) cc_final: 0.8977 (ptmm) REVERT: B 1119 ASN cc_start: 0.8986 (m-40) cc_final: 0.8660 (p0) REVERT: B 1122 MET cc_start: 0.8824 (mmp) cc_final: 0.8187 (mmp) REVERT: B 1287 ARG cc_start: 0.8872 (ttp-110) cc_final: 0.8592 (ttp80) REVERT: H 4 LEU cc_start: 0.8003 (mm) cc_final: 0.7728 (mm) REVERT: H 82 MET cc_start: 0.8266 (mtm) cc_final: 0.7842 (mmm) REVERT: H 119 THR cc_start: 0.9406 (m) cc_final: 0.9022 (p) REVERT: L 52 LEU cc_start: 0.8933 (tp) cc_final: 0.8716 (tp) outliers start: 16 outliers final: 13 residues processed: 206 average time/residue: 0.2827 time to fit residues: 83.6439 Evaluate side-chains 204 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 806 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 849 HIS Chi-restraints excluded: chain B residue 931 ASP Chi-restraints excluded: chain B residue 1386 PHE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 43 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 70 optimal weight: 0.0770 chunk 5 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 126 optimal weight: 0.0670 chunk 33 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 GLN ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.086720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066886 restraints weight = 96931.559| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 4.02 r_work: 0.3063 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12915 Z= 0.119 Angle : 0.560 6.988 17475 Z= 0.298 Chirality : 0.043 0.154 1930 Planarity : 0.004 0.066 2283 Dihedral : 4.840 34.270 1755 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.16 % Allowed : 13.57 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.69 (0.21), residues: 1626 helix: 0.62 (0.43), residues: 162 sheet: -0.66 (0.23), residues: 501 loop : -0.46 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 53 TYR 0.030 0.002 TYR B 353 PHE 0.025 0.001 PHE H 67 TRP 0.007 0.001 TRP A 159 HIS 0.004 0.001 HIS B 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (12915) covalent geometry : angle 0.56046 / 0.30 (17475) hydrogen bonds : bond 0.02760 / 1.86 ( 378) hydrogen bonds : angle 5.39657 / 3.84 ( 1059) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASN cc_start: 0.8147 (t0) cc_final: 0.7637 (t0) REVERT: B 243 LYS cc_start: 0.8805 (mmtp) cc_final: 0.8205 (tttp) REVERT: B 474 LYS cc_start: 0.9034 (mttt) cc_final: 0.8692 (mmtm) REVERT: B 501 MET cc_start: 0.7505 (mtt) cc_final: 0.7165 (mtt) REVERT: B 604 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8627 (tttt) REVERT: B 749 GLU cc_start: 0.9224 (tt0) cc_final: 0.8924 (tp30) REVERT: B 806 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8878 (mtmm) REVERT: B 913 ASN cc_start: 0.9054 (m-40) cc_final: 0.8565 (p0) REVERT: B 1053 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8170 (tm-30) REVERT: B 1104 LYS cc_start: 0.9195 (ptmm) cc_final: 0.8967 (ptmm) REVERT: B 1119 ASN cc_start: 0.8953 (m-40) cc_final: 0.8663 (p0) REVERT: B 1122 MET cc_start: 0.8804 (mmp) cc_final: 0.8015 (mmp) REVERT: B 1287 ARG cc_start: 0.8845 (ttp-110) cc_final: 0.8564 (ttp80) REVERT: H 4 LEU cc_start: 0.7973 (mm) cc_final: 0.7700 (mm) REVERT: H 82 MET cc_start: 0.8206 (mtm) cc_final: 0.7810 (mmm) REVERT: H 119 THR cc_start: 0.9398 (m) cc_final: 0.9053 (p) REVERT: L 52 LEU cc_start: 0.8931 (tp) cc_final: 0.8706 (tp) REVERT: L 66 ASP cc_start: 0.8747 (t0) cc_final: 0.8523 (t0) outliers start: 16 outliers final: 13 residues processed: 202 average time/residue: 0.2445 time to fit residues: 71.2102 Evaluate side-chains 205 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 806 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 931 ASP Chi-restraints excluded: chain B residue 1023 TYR Chi-restraints excluded: chain B residue 1386 PHE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 43 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 99 optimal weight: 0.9980 chunk 132 optimal weight: 0.0010 chunk 117 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 128 optimal weight: 0.0970 chunk 152 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.086722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.067566 restraints weight = 96040.980| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.92 r_work: 0.3077 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12915 Z= 0.118 Angle : 0.550 6.804 17475 Z= 0.292 Chirality : 0.043 0.153 1930 Planarity : 0.004 0.066 2283 Dihedral : 4.756 34.001 1755 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.30 % Allowed : 13.72 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.62 (0.21), residues: 1626 helix: 0.63 (0.44), residues: 162 sheet: -0.57 (0.23), residues: 496 loop : -0.43 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 53 TYR 0.030 0.001 TYR B 353 PHE 0.024 0.001 PHE H 67 TRP 0.006 0.001 TRP A 159 HIS 0.005 0.001 HIS B 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (12915) covalent geometry : angle 0.54981 / 0.29 (17475) hydrogen bonds : bond 0.02773 / 1.88 ( 378) hydrogen bonds : angle 5.33938 / 3.80 ( 1059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6347.27 seconds wall clock time: 108 minutes 48.90 seconds (6528.90 seconds total)