Starting phenix.real_space_refine on Sat Oct 24 14:01:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wbw_65850/10_2026/9wbw_65850_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wbw_65850/10_2026/9wbw_65850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wbw_65850/10_2026/9wbw_65850_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wbw_65850/10_2026/9wbw_65850_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wbw_65850/10_2026/9wbw_65850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wbw_65850/10_2026/9wbw_65850.map" } resolution = 3.44 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= 0.027 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: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 8381 2.51 5 N 2219 2.21 5 O 2418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13122 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1628, 13107 Classifications: {'peptide': 1628} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 70, 'TRANS': 1555} Chain breaks: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 2.84, per 1000 atoms: 0.22 Number of scatterers: 13122 At special positions: 0 Unit cell: (87.1, 132.66, 148.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 2418 8.00 N 2219 7.00 C 8381 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 518.6 milliseconds 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3116 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 11 sheets defined 62.9% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 21 through 31 removed outlier: 4.055A pdb=" N LEU A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 51 removed outlier: 3.678A pdb=" N ALA A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) Proline residue: A 48 - end of helix Processing helix chain 'A' and resid 58 through 70 Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 82 through 94 removed outlier: 3.609A pdb=" N CYS A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 131 through 136 Processing helix chain 'A' and resid 183 through 206 Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'A' and resid 252 through 267 Processing helix chain 'A' and resid 275 through 294 removed outlier: 3.705A pdb=" N VAL A 293 " --> pdb=" O HIS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 326 removed outlier: 3.508A pdb=" N SER A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 removed outlier: 3.590A pdb=" N ARG A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 359 through 362 Processing helix chain 'A' and resid 363 through 378 Processing helix chain 'A' and resid 381 through 395 removed outlier: 3.537A pdb=" N TYR A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 406 removed outlier: 3.621A pdb=" N LEU A 399 " --> pdb=" O TYR A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 417 removed outlier: 6.669A pdb=" N ILE A 414 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR A 415 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 removed outlier: 4.090A pdb=" N THR A 423 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 436 removed outlier: 3.557A pdb=" N ASN A 436 " --> pdb=" O ILE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 449 removed outlier: 3.713A pdb=" N LEU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 Processing helix chain 'A' and resid 465 through 472 Processing helix chain 'A' and resid 472 through 483 removed outlier: 4.238A pdb=" N ILE A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 513 removed outlier: 3.580A pdb=" N ILE A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 554 removed outlier: 3.622A pdb=" N ILE A 536 " --> pdb=" O TRP A 532 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASN A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 575 Processing helix chain 'A' and resid 576 through 578 No H-bonds generated for 'chain 'A' and resid 576 through 578' Processing helix chain 'A' and resid 609 through 626 removed outlier: 3.610A pdb=" N ARG A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 629 No H-bonds generated for 'chain 'A' and resid 627 through 629' Processing helix chain 'A' and resid 630 through 635 removed outlier: 4.121A pdb=" N PHE A 634 " --> pdb=" O ARG A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 removed outlier: 4.193A pdb=" N GLN A 641 " --> pdb=" O PHE A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 661 removed outlier: 4.459A pdb=" N TYR A 648 " --> pdb=" O VAL A 644 " (cutoff:3.500A) Proline residue: A 649 - end of helix Processing helix chain 'A' and resid 664 through 667 Processing helix chain 'A' and resid 668 through 679 removed outlier: 3.991A pdb=" N ILE A 672 " --> pdb=" O GLY A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 688 Processing helix chain 'A' and resid 688 through 702 Processing helix chain 'A' and resid 703 through 715 Processing helix chain 'A' and resid 729 through 753 Processing helix chain 'A' and resid 763 through 777 Processing helix chain 'A' and resid 783 through 789 Processing helix chain 'A' and resid 799 through 807 removed outlier: 4.020A pdb=" N VAL A 803 " --> pdb=" O GLY A 799 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ASN A 805 " --> pdb=" O GLU A 801 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LYS A 806 " --> pdb=" O ASN A 802 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 807 " --> pdb=" O VAL A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 831 removed outlier: 3.905A pdb=" N LYS A 829 " --> pdb=" O GLU A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 857 Processing helix chain 'A' and resid 872 through 883 removed outlier: 4.984A pdb=" N LYS A 877 " --> pdb=" O ALA A 874 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 879 " --> pdb=" O SER A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 900 removed outlier: 3.583A pdb=" N MET A 888 " --> pdb=" O CYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 932 Processing helix chain 'A' and resid 933 through 937 Processing helix chain 'A' and resid 940 through 946 Processing helix chain 'A' and resid 954 through 963 Processing helix chain 'A' and resid 964 through 970 removed outlier: 6.196A pdb=" N GLN A 967 " --> pdb=" O GLY A 964 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY A 970 " --> pdb=" O GLN A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 994 Processing helix chain 'A' and resid 1165 through 1182 removed outlier: 3.512A pdb=" N ARG A1182 " --> pdb=" O SER A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1193 removed outlier: 3.886A pdb=" N SER A1192 " --> pdb=" O ASP A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1228 removed outlier: 4.309A pdb=" N GLN A1228 " --> pdb=" O ASP A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1249 Processing helix chain 'A' and resid 1271 through 1277 removed outlier: 4.086A pdb=" N ILE A1275 " --> pdb=" O PHE A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1307 Processing helix chain 'A' and resid 1316 through 1340 removed outlier: 3.777A pdb=" N GLU A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1365 Processing helix chain 'A' and resid 1370 through 1383 Processing helix chain 'A' and resid 1396 through 1400 removed outlier: 3.693A pdb=" N ILE A1400 " --> pdb=" O LEU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1401 through 1413 removed outlier: 3.649A pdb=" N VAL A1405 " --> pdb=" O ASP A1401 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1418 Processing helix chain 'A' and resid 1427 through 1453 removed outlier: 3.537A pdb=" N LEU A1452 " --> pdb=" O LEU A1448 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR A1453 " --> pdb=" O GLN A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1484 removed outlier: 3.707A pdb=" N HIS A1471 " --> pdb=" O SER A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1493 through 1521 Proline residue: A1507 - end of helix Processing helix chain 'A' and resid 1525 through 1530 Processing helix chain 'A' and resid 1535 through 1544 Processing helix chain 'A' and resid 1550 through 1557 removed outlier: 4.326A pdb=" N PHE A1554 " --> pdb=" O LEU A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1570 Proline residue: A1563 - end of helix Processing helix chain 'A' and resid 1571 through 1580 Processing helix chain 'A' and resid 1581 through 1584 removed outlier: 4.137A pdb=" N VAL A1584 " --> pdb=" O LYS A1581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1581 through 1584' Processing helix chain 'A' and resid 1600 through 1610 removed outlier: 4.153A pdb=" N LEU A1604 " --> pdb=" O ASP A1600 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS A1610 " --> pdb=" O ASN A1606 " (cutoff:3.500A) Processing helix chain 'A' and resid 1651 through 1661 removed outlier: 3.504A pdb=" N PHE A1655 " --> pdb=" O GLY A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1703 removed outlier: 4.310A pdb=" N LYS A1703 " --> pdb=" O PRO A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1711 through 1724 Processing helix chain 'A' and resid 1726 through 1738 Processing helix chain 'A' and resid 1745 through 1749 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 112 Processing sheet with id=AA2, first strand: chain 'A' and resid 268 through 274 removed outlier: 6.578A pdb=" N CYS A 228 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA A 273 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TYR A 226 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 583 through 588 removed outlier: 3.525A pdb=" N HIS A 591 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 781 through 782 removed outlier: 4.029A pdb=" N MET A 781 " --> pdb=" O TYR A 821 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 821 " --> pdb=" O MET A 781 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 820 " --> pdb=" O LYS A 811 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id=AA6, first strand: chain 'A' and resid 1153 through 1164 removed outlier: 3.605A pdb=" N CYS A1159 " --> pdb=" O SER A1117 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N SER A1117 " --> pdb=" O CYS A1159 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N HIS A1161 " --> pdb=" O VAL A1115 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A1115 " --> pdb=" O HIS A1161 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A1206 " --> pdb=" O ALA A1118 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1195 through 1196 Processing sheet with id=AA8, first strand: chain 'A' and resid 1280 through 1282 Processing sheet with id=AA9, first strand: chain 'A' and resid 1633 through 1636 removed outlier: 3.957A pdb=" N HIS A1623 " --> pdb=" O SER A1636 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A1683 " --> pdb=" O GLU A1679 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1643 through 1645 Processing sheet with id=AB2, first strand: chain 'A' and resid 1691 through 1692 713 hydrogen bonds defined for protein. 1998 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: 2.71 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3832 1.33 - 1.45: 2072 1.45 - 1.57: 7369 1.57 - 1.69: 0 1.69 - 1.81: 149 Bond restraints: 13422 Sorted by residual: bond pdb=" CD2 TRP A1801 " pdb=" CE3 TRP A1801 " ideal model delta sigma weight residual 1.398 1.544 -0.146 1.60e-02 3.91e+03 8.35e+01 bond pdb=" CE2 TRP A1801 " pdb=" CZ2 TRP A1801 " ideal model delta sigma weight residual 1.394 1.559 -0.165 2.10e-02 2.27e+03 6.18e+01 bond pdb=" CZ2 TRP A1801 " pdb=" CH2 TRP A1801 " ideal model delta sigma weight residual 1.368 1.504 -0.136 1.90e-02 2.77e+03 5.13e+01 bond pdb=" CG TRP A1801 " pdb=" CD2 TRP A1801 " ideal model delta sigma weight residual 1.433 1.326 0.107 1.80e-02 3.09e+03 3.54e+01 bond pdb=" CE3 TRP A1801 " pdb=" CZ3 TRP A1801 " ideal model delta sigma weight residual 1.382 1.486 -0.104 3.00e-02 1.11e+03 1.20e+01 ... (remaining 13417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 17952 2.42 - 4.85: 197 4.85 - 7.27: 23 7.27 - 9.70: 3 9.70 - 12.12: 2 Bond angle restraints: 18177 Sorted by residual: angle pdb=" CG TRP A1801 " pdb=" CD2 TRP A1801 " pdb=" CE3 TRP A1801 " ideal model delta sigma weight residual 133.90 128.62 5.28 1.00e+00 1.00e+00 2.79e+01 angle pdb=" N LEU A 449 " pdb=" CA LEU A 449 " pdb=" C LEU A 449 " ideal model delta sigma weight residual 109.81 118.93 -9.12 2.21e+00 2.05e-01 1.70e+01 angle pdb=" CE2 TRP A1801 " pdb=" CD2 TRP A1801 " pdb=" CE3 TRP A1801 " ideal model delta sigma weight residual 118.80 122.91 -4.11 1.00e+00 1.00e+00 1.69e+01 angle pdb=" CB MET A1319 " pdb=" CG MET A1319 " pdb=" SD MET A1319 " ideal model delta sigma weight residual 112.70 100.58 12.12 3.00e+00 1.11e-01 1.63e+01 angle pdb=" CD2 TRP A1801 " pdb=" CE2 TRP A1801 " pdb=" CZ2 TRP A1801 " ideal model delta sigma weight residual 122.40 118.59 3.81 1.00e+00 1.00e+00 1.45e+01 ... (remaining 18172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 7387 16.03 - 32.06: 580 32.06 - 48.10: 130 48.10 - 64.13: 28 64.13 - 80.16: 9 Dihedral angle restraints: 8134 sinusoidal: 3332 harmonic: 4802 Sorted by residual: dihedral pdb=" CA LEU A 483 " pdb=" C LEU A 483 " pdb=" N ILE A 484 " pdb=" CA ILE A 484 " ideal model delta harmonic sigma weight residual -180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA LEU A 449 " pdb=" C LEU A 449 " pdb=" N PRO A 450 " pdb=" CA PRO A 450 " ideal model delta harmonic sigma weight residual -180.00 -158.11 -21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA PRO A1421 " pdb=" C PRO A1421 " pdb=" N VAL A1422 " pdb=" CA VAL A1422 " ideal model delta harmonic sigma weight residual -180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 8131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1326 0.034 - 0.068: 508 0.068 - 0.103: 141 0.103 - 0.137: 39 0.137 - 0.171: 4 Chirality restraints: 2018 Sorted by residual: chirality pdb=" CA LEU A 449 " pdb=" N LEU A 449 " pdb=" C LEU A 449 " pdb=" CB LEU A 449 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA MET A 981 " pdb=" N MET A 981 " pdb=" C MET A 981 " pdb=" CB MET A 981 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ASN A 796 " pdb=" N ASN A 796 " pdb=" C ASN A 796 " pdb=" CB ASN A 796 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 2015 not shown) Planarity restraints: 2328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1568 " 0.020 2.00e-02 2.50e+03 2.08e-02 1.08e+01 pdb=" CG TRP A1568 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP A1568 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A1568 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1568 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1568 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1568 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1568 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1568 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A1568 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 552 " 0.016 2.00e-02 2.50e+03 1.34e-02 4.46e+00 pdb=" CG TRP A 552 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 552 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 552 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 552 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 552 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 552 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 552 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 552 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 552 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 549 " 0.015 2.00e-02 2.50e+03 1.17e-02 2.39e+00 pdb=" CG PHE A 549 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 549 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 549 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 549 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 549 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 549 " -0.000 2.00e-02 2.50e+03 ... (remaining 2325 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 215 2.69 - 3.24: 13114 3.24 - 3.79: 20547 3.79 - 4.35: 25902 4.35 - 4.90: 43190 Nonbonded interactions: 102968 Sorted by model distance: nonbonded pdb=" NH2 ARG A 247 " pdb=" O HIS A 289 " model vdw 2.136 3.120 nonbonded pdb=" OH TYR A1246 " pdb=" O TRP A1418 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR A 598 " pdb=" O LEU A 604 " model vdw 2.187 3.040 nonbonded pdb=" NH1 ARG A1621 " pdb=" O GLN A1637 " model vdw 2.197 3.120 nonbonded pdb=" OG SER A 439 " pdb=" OE1 GLU A 500 " model vdw 2.207 3.040 ... (remaining 102963 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.740 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 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 : 0.004 0.165 13422 Z= 0.215 Angle : 0.645 12.120 18177 Z= 0.358 Chirality : 0.040 0.171 2018 Planarity : 0.003 0.042 2328 Dihedral : 12.584 80.162 5018 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.66 % Favored : 98.27 % Rotamer: Outliers : 0.07 % Allowed : 0.21 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.90 (0.21), residues: 1622 helix: 2.01 (0.18), residues: 862 sheet: 0.15 (0.51), residues: 99 loop : 0.57 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1586 TYR 0.014 0.001 TYR A 384 PHE 0.024 0.002 PHE A 549 TRP 0.056 0.002 TRP A1568 HIS 0.008 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.22 (13422) covalent geometry : angle 0.64546 / 0.36 (18177) hydrogen bonds : bond 0.15888 / 10.28 ( 713) hydrogen bonds : angle 5.79978 / 4.13 ( 1998) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 296 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8417 (tp40) cc_final: 0.8181 (tp40) REVERT: A 125 MET cc_start: 0.7892 (mmm) cc_final: 0.7669 (mmt) REVERT: A 234 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7749 (tm-30) REVERT: A 236 HIS cc_start: 0.6232 (m90) cc_final: 0.6032 (m170) REVERT: A 243 TYR cc_start: 0.8909 (t80) cc_final: 0.8652 (t80) REVERT: A 257 GLN cc_start: 0.6714 (mt0) cc_final: 0.6447 (mt0) REVERT: A 285 ASP cc_start: 0.9017 (m-30) cc_final: 0.8748 (m-30) REVERT: A 296 HIS cc_start: 0.8053 (m90) cc_final: 0.7732 (m-70) REVERT: A 361 LYS cc_start: 0.8157 (mttt) cc_final: 0.7868 (mtmm) REVERT: A 517 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7844 (mm-30) REVERT: A 551 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6268 (pt0) REVERT: A 719 GLU cc_start: 0.7537 (pm20) cc_final: 0.7088 (tm-30) REVERT: A 731 ASP cc_start: 0.7183 (t70) cc_final: 0.6780 (t70) REVERT: A 764 LYS cc_start: 0.6415 (mttt) cc_final: 0.6197 (tttt) REVERT: A 856 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7323 (pp30) REVERT: A 859 LYS cc_start: 0.7327 (mttt) cc_final: 0.6956 (mtmt) REVERT: A 861 GLU cc_start: 0.8275 (pp20) cc_final: 0.7753 (mp0) REVERT: A 910 MET cc_start: 0.7472 (ptp) cc_final: 0.7065 (ptp) REVERT: A 943 HIS cc_start: 0.8348 (t-90) cc_final: 0.7802 (m170) REVERT: A 953 MET cc_start: 0.8378 (mtp) cc_final: 0.7707 (mmm) REVERT: A 957 MET cc_start: 0.8916 (mtm) cc_final: 0.8263 (mtt) REVERT: A 968 LEU cc_start: 0.8913 (mt) cc_final: 0.8635 (mp) REVERT: A 1312 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8451 (pm20) REVERT: A 1441 LEU cc_start: 0.8508 (mp) cc_final: 0.8305 (tp) REVERT: A 1558 TRP cc_start: 0.8484 (t-100) cc_final: 0.8104 (t-100) REVERT: A 1674 ARG cc_start: 0.7643 (ttm170) cc_final: 0.7307 (ttt90) REVERT: A 1679 GLU cc_start: 0.5826 (pp20) cc_final: 0.5618 (pp20) REVERT: A 1740 MET cc_start: 0.0354 (pmm) cc_final: -0.0420 (mpp) outliers start: 1 outliers final: 1 residues processed: 297 average time/residue: 0.1251 time to fit residues: 52.1302 Evaluate side-chains 158 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1801 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 189 GLN ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN A 371 HIS A 462 GLN A 632 HIS ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 GLN A 930 GLN A 971 GLN A1375 GLN A1592 ASN A1724 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.171282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.137729 restraints weight = 22509.883| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 3.05 r_work: 0.3576 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13422 Z= 0.159 Angle : 0.610 10.197 18177 Z= 0.311 Chirality : 0.041 0.201 2018 Planarity : 0.004 0.047 2328 Dihedral : 4.556 51.248 1766 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.42 % Favored : 98.52 % Rotamer: Outliers : 1.71 % Allowed : 6.63 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.87 (0.21), residues: 1622 helix: 2.03 (0.17), residues: 875 sheet: -0.26 (0.45), residues: 123 loop : 0.56 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1182 TYR 0.020 0.002 TYR A 836 PHE 0.023 0.002 PHE A 388 TRP 0.028 0.002 TRP A1568 HIS 0.008 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (13422) covalent geometry : angle 0.60997 / 0.31 (18177) hydrogen bonds : bond 0.04973 / 3.32 ( 713) hydrogen bonds : angle 4.50282 / 3.21 ( 1998) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 ASP cc_start: 0.8606 (m-30) cc_final: 0.8389 (m-30) REVERT: A 457 ASN cc_start: 0.7689 (m-40) cc_final: 0.7398 (t0) REVERT: A 856 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7869 (pp30) REVERT: A 910 MET cc_start: 0.8099 (ptp) cc_final: 0.7691 (ptp) REVERT: A 943 HIS cc_start: 0.8109 (t-90) cc_final: 0.7901 (m170) REVERT: A 1312 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8297 (tp30) REVERT: A 1444 MET cc_start: 0.8496 (mmm) cc_final: 0.8073 (mmm) REVERT: A 1479 GLU cc_start: 0.8671 (pt0) cc_final: 0.7692 (pt0) REVERT: A 1558 TRP cc_start: 0.8326 (t-100) cc_final: 0.8024 (t-100) REVERT: A 1740 MET cc_start: 0.0841 (pmm) cc_final: -0.0167 (mpp) outliers start: 25 outliers final: 17 residues processed: 188 average time/residue: 0.1108 time to fit residues: 30.4724 Evaluate side-chains 162 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 930 GLN Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1396 CYS Chi-restraints excluded: chain A residue 1536 GLU Chi-restraints excluded: chain A residue 1659 HIS Chi-restraints excluded: chain A residue 1668 LEU Chi-restraints excluded: chain A residue 1669 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [53, 157, 103, 36, 21, 30, 156, 110, 148, 60, 79] chunk 53 optimal weight: 0.6980 chunk 157 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN A 667 ASN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 GLN ** A1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.168399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.126925 restraints weight = 22621.858| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.16 r_work: 0.3525 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13422 Z= 0.131 Angle : 0.555 10.443 18177 Z= 0.282 Chirality : 0.040 0.207 2018 Planarity : 0.003 0.050 2328 Dihedral : 4.277 51.575 1764 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.36 % Favored : 98.58 % Rotamer: Outliers : 2.12 % Allowed : 9.23 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.96 (0.21), residues: 1622 helix: 2.06 (0.17), residues: 877 sheet: -0.14 (0.47), residues: 113 loop : 0.63 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1182 TYR 0.017 0.001 TYR A 243 PHE 0.016 0.001 PHE A 148 TRP 0.018 0.001 TRP A1568 HIS 0.005 0.001 HIS A1659 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (13422) covalent geometry : angle 0.55522 / 0.28 (18177) hydrogen bonds : bond 0.04252 / 2.85 ( 713) hydrogen bonds : angle 4.22395 / 3.01 ( 1998) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8105 (mt) cc_final: 0.7880 (tp) REVERT: A 285 ASP cc_start: 0.8732 (m-30) cc_final: 0.8459 (m-30) REVERT: A 321 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8329 (tpt) REVERT: A 457 ASN cc_start: 0.7707 (m-40) cc_final: 0.7373 (t0) REVERT: A 856 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7811 (pp30) REVERT: A 861 GLU cc_start: 0.7868 (mp0) cc_final: 0.7613 (mp0) REVERT: A 910 MET cc_start: 0.8057 (ptp) cc_final: 0.7574 (ptp) REVERT: A 1312 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8251 (tp30) REVERT: A 1444 MET cc_start: 0.8544 (mmm) cc_final: 0.7998 (mmm) REVERT: A 1495 TRP cc_start: 0.6895 (p-90) cc_final: 0.6570 (p-90) REVERT: A 1554 PHE cc_start: 0.7981 (m-80) cc_final: 0.7771 (m-10) REVERT: A 1558 TRP cc_start: 0.8386 (t-100) cc_final: 0.8139 (t-100) REVERT: A 1562 ARG cc_start: 0.8652 (mtp180) cc_final: 0.8316 (ttt-90) REVERT: A 1674 ARG cc_start: 0.8354 (mtp85) cc_final: 0.7777 (ttp80) REVERT: A 1733 ARG cc_start: 0.7659 (ttp80) cc_final: 0.7383 (ttp80) REVERT: A 1740 MET cc_start: 0.0867 (pmm) cc_final: -0.0051 (mpp) outliers start: 31 outliers final: 16 residues processed: 172 average time/residue: 0.1035 time to fit residues: 26.6094 Evaluate side-chains 154 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1152 TYR Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1396 CYS Chi-restraints excluded: chain A residue 1659 HIS Chi-restraints excluded: chain A residue 1668 LEU Chi-restraints excluded: chain A residue 1669 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [100, 95, 36, 7, 157, 43, 50, 135, 32, 142, 81] chunk 100 optimal weight: 0.0370 chunk 95 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 157 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 240 HIS A 296 HIS A 667 ASN A 818 HIS A1164 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.167991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.132336 restraints weight = 22484.857| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 3.49 r_work: 0.3476 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13422 Z= 0.128 Angle : 0.540 10.406 18177 Z= 0.273 Chirality : 0.040 0.195 2018 Planarity : 0.003 0.050 2328 Dihedral : 4.212 51.819 1764 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.66 % Favored : 98.27 % Rotamer: Outliers : 1.98 % Allowed : 10.26 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 2.02 (0.21), residues: 1622 helix: 2.19 (0.17), residues: 870 sheet: -0.24 (0.48), residues: 114 loop : 0.56 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1182 TYR 0.017 0.001 TYR A1171 PHE 0.024 0.001 PHE A 941 TRP 0.016 0.001 TRP A 552 HIS 0.006 0.001 HIS A1659 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (13422) covalent geometry : angle 0.53972 / 0.27 (18177) hydrogen bonds : bond 0.04049 / 2.71 ( 713) hydrogen bonds : angle 4.08525 / 2.92 ( 1998) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 CYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7018 (p) REVERT: A 266 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7509 (mm-30) REVERT: A 285 ASP cc_start: 0.8783 (m-30) cc_final: 0.8503 (m-30) REVERT: A 457 ASN cc_start: 0.7825 (m-40) cc_final: 0.7415 (t0) REVERT: A 856 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7776 (pp30) REVERT: A 910 MET cc_start: 0.8103 (ptp) cc_final: 0.7603 (ptp) REVERT: A 986 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7595 (ttpp) REVERT: A 1312 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8213 (tp30) REVERT: A 1441 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8535 (tp) REVERT: A 1444 MET cc_start: 0.8600 (mmm) cc_final: 0.8192 (mmm) REVERT: A 1452 LEU cc_start: 0.8696 (mm) cc_final: 0.8471 (mp) REVERT: A 1495 TRP cc_start: 0.6878 (p-90) cc_final: 0.6499 (p-90) REVERT: A 1562 ARG cc_start: 0.8759 (mtp180) cc_final: 0.8441 (ttt-90) REVERT: A 1733 ARG cc_start: 0.7714 (ttp80) cc_final: 0.7497 (ttp80) REVERT: A 1740 MET cc_start: 0.0917 (pmm) cc_final: -0.0008 (mpp) outliers start: 29 outliers final: 18 residues processed: 169 average time/residue: 0.1049 time to fit residues: 26.2998 Evaluate side-chains 155 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 986 LYS Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1152 TYR Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1396 CYS Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1633 ILE Chi-restraints excluded: chain A residue 1659 HIS Chi-restraints excluded: chain A residue 1669 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [112, 141, 52, 159, 57, 134, 153, 27, 70, 32, 24] chunk 112 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 159 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 153 optimal weight: 0.2980 chunk 27 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN A 129 GLN A 322 ASN A 667 ASN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.163837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.116774 restraints weight = 22596.311| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.93 r_work: 0.3437 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13422 Z= 0.232 Angle : 0.642 10.698 18177 Z= 0.326 Chirality : 0.043 0.215 2018 Planarity : 0.004 0.049 2328 Dihedral : 4.449 54.009 1764 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.40 % Favored : 97.53 % Rotamer: Outliers : 2.26 % Allowed : 11.90 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.64 (0.21), residues: 1622 helix: 1.94 (0.17), residues: 863 sheet: -0.46 (0.46), residues: 114 loop : 0.31 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 665 TYR 0.026 0.002 TYR A 678 PHE 0.031 0.002 PHE A 148 TRP 0.021 0.002 TRP A 552 HIS 0.008 0.002 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.23 (13422) covalent geometry : angle 0.64232 / 0.33 (18177) hydrogen bonds : bond 0.05190 / 3.50 ( 713) hydrogen bonds : angle 4.33528 / 3.09 ( 1998) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8799 (ttp80) cc_final: 0.8528 (ttp80) REVERT: A 228 CYS cc_start: 0.7329 (OUTLIER) cc_final: 0.7003 (p) REVERT: A 285 ASP cc_start: 0.8733 (m-30) cc_final: 0.8484 (m-30) REVERT: A 457 ASN cc_start: 0.7894 (m-40) cc_final: 0.7532 (t0) REVERT: A 731 ASP cc_start: 0.6837 (OUTLIER) cc_final: 0.5870 (t0) REVERT: A 856 GLN cc_start: 0.8379 (mm-40) cc_final: 0.7881 (pp30) REVERT: A 910 MET cc_start: 0.8214 (ptp) cc_final: 0.7741 (ptp) REVERT: A 980 GLN cc_start: 0.8436 (tm-30) cc_final: 0.7791 (tm-30) REVERT: A 1312 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8209 (tp30) REVERT: A 1444 MET cc_start: 0.8713 (mmm) cc_final: 0.8211 (mmm) REVERT: A 1452 LEU cc_start: 0.8686 (mm) cc_final: 0.8452 (mp) REVERT: A 1495 TRP cc_start: 0.6914 (p-90) cc_final: 0.6521 (p-90) REVERT: A 1562 ARG cc_start: 0.8706 (mtp180) cc_final: 0.8403 (ttt-90) REVERT: A 1740 MET cc_start: 0.1010 (pmm) cc_final: 0.0105 (mpp) outliers start: 33 outliers final: 20 residues processed: 168 average time/residue: 0.1058 time to fit residues: 26.9093 Evaluate side-chains 156 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 982 PHE Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1127 THR Chi-restraints excluded: chain A residue 1152 TYR Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1396 CYS Chi-restraints excluded: chain A residue 1633 ILE Chi-restraints excluded: chain A residue 1659 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [122, 141, 57, 8, 67, 160, 99, 133, 85, 158, 155] chunk 122 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 133 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN A 818 HIS A1738 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.166141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.119924 restraints weight = 22443.763| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.92 r_work: 0.3487 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13422 Z= 0.132 Angle : 0.556 10.869 18177 Z= 0.280 Chirality : 0.039 0.199 2018 Planarity : 0.003 0.050 2328 Dihedral : 4.296 53.634 1764 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.10 % Favored : 97.84 % Rotamer: Outliers : 2.26 % Allowed : 12.24 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.86 (0.21), residues: 1622 helix: 2.14 (0.18), residues: 862 sheet: -0.36 (0.47), residues: 114 loop : 0.39 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1674 TYR 0.017 0.001 TYR A1171 PHE 0.015 0.001 PHE A 148 TRP 0.014 0.001 TRP A1558 HIS 0.007 0.001 HIS A1659 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (13422) covalent geometry : angle 0.55587 / 0.28 (18177) hydrogen bonds : bond 0.04071 / 2.72 ( 713) hydrogen bonds : angle 4.07979 / 2.90 ( 1998) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 228 CYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6921 (p) REVERT: A 266 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7627 (mm-30) REVERT: A 285 ASP cc_start: 0.8711 (m-30) cc_final: 0.8464 (m-30) REVERT: A 457 ASN cc_start: 0.7898 (m-40) cc_final: 0.7542 (t0) REVERT: A 856 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7757 (pp30) REVERT: A 910 MET cc_start: 0.8139 (ptp) cc_final: 0.7669 (ptp) REVERT: A 1312 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8189 (tp30) REVERT: A 1375 GLN cc_start: 0.8705 (tm130) cc_final: 0.8072 (tm-30) REVERT: A 1444 MET cc_start: 0.8703 (mmm) cc_final: 0.8296 (mmm) REVERT: A 1452 LEU cc_start: 0.8672 (mm) cc_final: 0.8422 (mp) REVERT: A 1495 TRP cc_start: 0.6822 (p-90) cc_final: 0.6447 (p-90) REVERT: A 1562 ARG cc_start: 0.8779 (mtp180) cc_final: 0.8513 (ttt-90) REVERT: A 1740 MET cc_start: 0.1004 (pmm) cc_final: 0.0145 (mpp) outliers start: 33 outliers final: 22 residues processed: 163 average time/residue: 0.1004 time to fit residues: 24.8858 Evaluate side-chains 154 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 982 PHE Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1152 TYR Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1396 CYS Chi-restraints excluded: chain A residue 1633 ILE Chi-restraints excluded: chain A residue 1659 HIS Chi-restraints excluded: chain A residue 1731 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [158, 99, 113, 149, 40, 5, 116, 97, 143, 7, 14] chunk 158 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 14 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN A 818 HIS A1449 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.166770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.132137 restraints weight = 22308.051| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 3.74 r_work: 0.3437 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13422 Z= 0.113 Angle : 0.534 10.229 18177 Z= 0.269 Chirality : 0.039 0.195 2018 Planarity : 0.003 0.050 2328 Dihedral : 4.231 52.844 1764 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.97 % Favored : 97.97 % Rotamer: Outliers : 2.05 % Allowed : 12.52 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 2.00 (0.21), residues: 1622 helix: 2.22 (0.18), residues: 867 sheet: -0.24 (0.49), residues: 112 loop : 0.48 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1674 TYR 0.014 0.001 TYR A 384 PHE 0.015 0.001 PHE A 52 TRP 0.013 0.001 TRP A1558 HIS 0.006 0.001 HIS A1659 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (13422) covalent geometry : angle 0.53425 / 0.27 (18177) hydrogen bonds : bond 0.03751 / 2.48 ( 713) hydrogen bonds : angle 3.98967 / 2.84 ( 1998) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.477 Fit side-chains REVERT: A 228 CYS cc_start: 0.7349 (OUTLIER) cc_final: 0.7028 (p) REVERT: A 266 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7706 (mm-30) REVERT: A 285 ASP cc_start: 0.8779 (m-30) cc_final: 0.8517 (m-30) REVERT: A 457 ASN cc_start: 0.7983 (m-40) cc_final: 0.7584 (t0) REVERT: A 731 ASP cc_start: 0.6754 (OUTLIER) cc_final: 0.5607 (t0) REVERT: A 856 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7735 (pp30) REVERT: A 910 MET cc_start: 0.8184 (ptp) cc_final: 0.7707 (ptp) REVERT: A 1312 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8178 (tp30) REVERT: A 1375 GLN cc_start: 0.8716 (tm130) cc_final: 0.8080 (tm-30) REVERT: A 1452 LEU cc_start: 0.8633 (mm) cc_final: 0.8383 (mp) REVERT: A 1495 TRP cc_start: 0.6834 (p-90) cc_final: 0.6486 (p-90) REVERT: A 1562 ARG cc_start: 0.8850 (mtp180) cc_final: 0.8604 (ttt-90) REVERT: A 1674 ARG cc_start: 0.8619 (ttm110) cc_final: 0.8408 (ttp-110) REVERT: A 1740 MET cc_start: 0.0951 (pmm) cc_final: -0.0042 (mpp) outliers start: 30 outliers final: 19 residues processed: 160 average time/residue: 0.0972 time to fit residues: 23.7257 Evaluate side-chains 157 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 982 PHE Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1152 TYR Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1396 CYS Chi-restraints excluded: chain A residue 1633 ILE Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1659 HIS Chi-restraints excluded: chain A residue 1731 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [103, 122, 42, 15, 79, 55, 100, 94, 4, 73, 136] chunk 103 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN A 818 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.166446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.131450 restraints weight = 22236.355| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 3.56 r_work: 0.3440 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13422 Z= 0.121 Angle : 0.540 10.961 18177 Z= 0.271 Chirality : 0.039 0.190 2018 Planarity : 0.003 0.050 2328 Dihedral : 4.181 52.710 1764 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 1.85 % Allowed : 13.00 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.98 (0.21), residues: 1622 helix: 2.21 (0.18), residues: 866 sheet: -0.21 (0.49), residues: 112 loop : 0.46 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1674 TYR 0.018 0.001 TYR A1171 PHE 0.029 0.001 PHE A 676 TRP 0.025 0.001 TRP A1558 HIS 0.006 0.001 HIS A1659 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (13422) covalent geometry : angle 0.53959 / 0.27 (18177) hydrogen bonds : bond 0.03816 / 2.55 ( 713) hydrogen bonds : angle 3.96719 / 2.82 ( 1998) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8920 (ttp80) cc_final: 0.8573 (ptp90) REVERT: A 228 CYS cc_start: 0.7325 (OUTLIER) cc_final: 0.7019 (p) REVERT: A 266 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7723 (mm-30) REVERT: A 285 ASP cc_start: 0.8791 (m-30) cc_final: 0.8523 (m-30) REVERT: A 457 ASN cc_start: 0.7973 (m-40) cc_final: 0.7599 (t0) REVERT: A 856 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7742 (pp30) REVERT: A 910 MET cc_start: 0.8169 (ptp) cc_final: 0.7677 (ptp) REVERT: A 980 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7708 (tm-30) REVERT: A 1168 TRP cc_start: 0.7832 (t-100) cc_final: 0.7185 (t-100) REVERT: A 1375 GLN cc_start: 0.8718 (tm130) cc_final: 0.8077 (tm-30) REVERT: A 1452 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8360 (mp) REVERT: A 1495 TRP cc_start: 0.6828 (p-90) cc_final: 0.6445 (p-90) REVERT: A 1562 ARG cc_start: 0.8875 (mtp180) cc_final: 0.8543 (ttt-90) REVERT: A 1740 MET cc_start: 0.0955 (pmm) cc_final: -0.0115 (mpp) outliers start: 27 outliers final: 20 residues processed: 157 average time/residue: 0.0967 time to fit residues: 23.1234 Evaluate side-chains 151 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 982 PHE Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1152 TYR Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1396 CYS Chi-restraints excluded: chain A residue 1452 LEU Chi-restraints excluded: chain A residue 1633 ILE Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1659 HIS Chi-restraints excluded: chain A residue 1731 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [55, 0, 13, 20, 143, 106, 70, 61, 46, 17, 125] chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 0.0570 chunk 46 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 HIS A1449 GLN A1566 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.166311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.131510 restraints weight = 22370.306| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.68 r_work: 0.3431 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13422 Z= 0.126 Angle : 0.554 11.150 18177 Z= 0.277 Chirality : 0.039 0.189 2018 Planarity : 0.004 0.054 2328 Dihedral : 4.200 52.977 1764 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 1.64 % Allowed : 13.61 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.95 (0.21), residues: 1622 helix: 2.19 (0.18), residues: 867 sheet: -0.21 (0.50), residues: 112 loop : 0.43 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1674 TYR 0.018 0.001 TYR A1437 PHE 0.027 0.001 PHE A 676 TRP 0.025 0.001 TRP A1558 HIS 0.006 0.001 HIS A1659 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (13422) covalent geometry : angle 0.55393 / 0.28 (18177) hydrogen bonds : bond 0.03842 / 2.57 ( 713) hydrogen bonds : angle 3.97811 / 2.83 ( 1998) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8955 (ttp80) cc_final: 0.8591 (ptp90) REVERT: A 228 CYS cc_start: 0.7310 (OUTLIER) cc_final: 0.7027 (p) REVERT: A 266 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7753 (mm-30) REVERT: A 285 ASP cc_start: 0.8782 (m-30) cc_final: 0.8522 (m-30) REVERT: A 390 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7287 (mpp) REVERT: A 457 ASN cc_start: 0.8004 (m-40) cc_final: 0.7649 (t0) REVERT: A 856 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7768 (pp30) REVERT: A 910 MET cc_start: 0.8179 (ptp) cc_final: 0.7675 (ptp) REVERT: A 1168 TRP cc_start: 0.7873 (t-100) cc_final: 0.7378 (t-100) REVERT: A 1375 GLN cc_start: 0.8726 (tm130) cc_final: 0.8085 (tm-30) REVERT: A 1444 MET cc_start: 0.9080 (mmm) cc_final: 0.8407 (mmm) REVERT: A 1452 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8373 (mp) REVERT: A 1495 TRP cc_start: 0.6816 (p-90) cc_final: 0.6500 (p-90) REVERT: A 1562 ARG cc_start: 0.8923 (mtp180) cc_final: 0.8658 (ttt-90) REVERT: A 1674 ARG cc_start: 0.8375 (ttp-110) cc_final: 0.7911 (ttp-110) REVERT: A 1740 MET cc_start: 0.0915 (pmm) cc_final: -0.0159 (mpp) outliers start: 24 outliers final: 20 residues processed: 149 average time/residue: 0.1042 time to fit residues: 23.2862 Evaluate side-chains 153 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 982 PHE Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1152 TYR Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1452 LEU Chi-restraints excluded: chain A residue 1633 ILE Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1659 HIS Chi-restraints excluded: chain A residue 1731 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [17, 161, 146, 63, 89, 78, 124, 152, 132, 116, 70] chunk 17 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.165330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.118546 restraints weight = 22402.411| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.95 r_work: 0.3457 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13422 Z= 0.152 Angle : 0.578 11.332 18177 Z= 0.289 Chirality : 0.040 0.193 2018 Planarity : 0.004 0.059 2328 Dihedral : 4.282 53.954 1764 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.65 % Favored : 97.29 % Rotamer: Outliers : 1.71 % Allowed : 13.54 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.81 (0.21), residues: 1622 helix: 2.09 (0.18), residues: 867 sheet: -0.25 (0.49), residues: 114 loop : 0.34 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1674 TYR 0.018 0.001 TYR A 384 PHE 0.027 0.002 PHE A 676 TRP 0.019 0.001 TRP A1558 HIS 0.006 0.001 HIS A1659 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (13422) covalent geometry : angle 0.57794 / 0.29 (18177) hydrogen bonds : bond 0.04192 / 2.81 ( 713) hydrogen bonds : angle 4.06173 / 2.90 ( 1998) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.489 Fit side-chains REVERT: A 228 CYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6921 (p) REVERT: A 266 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7747 (mm-30) REVERT: A 285 ASP cc_start: 0.8782 (m-30) cc_final: 0.8524 (m-30) REVERT: A 390 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7445 (mpp) REVERT: A 457 ASN cc_start: 0.7954 (m-40) cc_final: 0.7674 (t0) REVERT: A 856 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7779 (pp30) REVERT: A 910 MET cc_start: 0.8159 (ptp) cc_final: 0.7631 (ptp) REVERT: A 957 MET cc_start: 0.8580 (pmm) cc_final: 0.7798 (pmm) REVERT: A 980 GLN cc_start: 0.8313 (tm-30) cc_final: 0.7681 (tm-30) REVERT: A 1168 TRP cc_start: 0.7912 (t-100) cc_final: 0.7390 (t-100) REVERT: A 1375 GLN cc_start: 0.8699 (tm130) cc_final: 0.8060 (tm-30) REVERT: A 1444 MET cc_start: 0.9058 (mmm) cc_final: 0.8421 (mmm) REVERT: A 1495 TRP cc_start: 0.6814 (p-90) cc_final: 0.6440 (p-90) REVERT: A 1562 ARG cc_start: 0.8916 (mtp180) cc_final: 0.8590 (ttt-90) REVERT: A 1740 MET cc_start: 0.1026 (pmm) cc_final: -0.0134 (mpp) outliers start: 25 outliers final: 20 residues processed: 145 average time/residue: 0.1010 time to fit residues: 22.2893 Evaluate side-chains 145 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 982 PHE Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1152 TYR Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1633 ILE Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1659 HIS Chi-restraints excluded: chain A residue 1731 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [57, 10, 13, 19, 55, 22, 12, 95, 78, 83, 68] chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.0050 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 78 optimal weight: 0.0370 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.167596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.125512 restraints weight = 22227.797| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 3.27 r_work: 0.3505 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13422 Z= 0.108 Angle : 0.555 11.240 18177 Z= 0.275 Chirality : 0.038 0.187 2018 Planarity : 0.004 0.060 2328 Dihedral : 4.199 53.060 1764 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.91 % Favored : 98.03 % Rotamer: Outliers : 1.57 % Allowed : 13.89 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.99 (0.22), residues: 1622 helix: 2.25 (0.18), residues: 867 sheet: -0.29 (0.49), residues: 114 loop : 0.43 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1674 TYR 0.013 0.001 TYR A 384 PHE 0.026 0.001 PHE A 676 TRP 0.019 0.001 TRP A1558 HIS 0.006 0.001 HIS A1659 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (13422) covalent geometry : angle 0.55470 / 0.28 (18177) hydrogen bonds : bond 0.03488 / 2.32 ( 713) hydrogen bonds : angle 3.91854 / 2.79 ( 1998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3147.75 seconds wall clock time: 54 minutes 53.25 seconds (3293.25 seconds total)