Starting phenix.real_space_refine on Thu Jul 2 20:58:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wlj_32585/07_2026/7wlj_32585.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wlj_32585/07_2026/7wlj_32585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wlj_32585/07_2026/7wlj_32585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wlj_32585/07_2026/7wlj_32585.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wlj_32585/07_2026/7wlj_32585.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wlj_32585/07_2026/7wlj_32585.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wlj_32585/07_2026/7wlj_32585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wlj_32585/07_2026/7wlj_32585.map" } resolution = 3.9 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= 0.009 sd= 0.094 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 1 5.49 5 S 78 5.16 5 C 6272 2.51 5 N 1504 2.21 5 O 1593 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9450 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9111 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1135, 9100 Classifications: {'peptide': 1135} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 1103} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 1135, 9100 Classifications: {'peptide': 1135} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 1103} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 9289 Chain: "A" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 339 Unusual residues: {' CA': 1, '3PE': 5, 'MWV': 1, 'NAG': 2, 'Y01': 6} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'3PE:plan-1': 4, '3PE:plan-2': 4, 'Y01:plan-1': 3, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 41 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 854 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 854 " occ=0.50 Time building chain proxies: 3.70, per 1000 atoms: 0.39 Number of scatterers: 9450 At special positions: 0 Unit cell: (113.36, 123.76, 108.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 78 16.00 P 1 15.00 F 1 9.00 O 1593 8.00 N 1504 7.00 C 6272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A1335 " - pdb=" SG CYS A1349 " distance=2.03 Simple disulfide: pdb=" SG CYS A1646 " - pdb=" SG CYS A1652 " distance=2.03 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1698 " distance=2.03 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 Links applied NAG-ASN " NAG A2310 " - " ASN A1345 " " NAG A2312 " - " ASN A1342 " Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 758.3 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2150 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 2 sheets defined 77.9% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 66 through 78 removed outlier: 4.226A pdb=" N CYS A 72 " --> pdb=" O PRO A 68 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N MET A 75 " --> pdb=" O TRP A 71 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 76 " --> pdb=" O CYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 98 removed outlier: 3.853A pdb=" N GLU A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 136 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 148 through 170 Processing helix chain 'A' and resid 180 through 191 Proline residue: A 185 - end of helix removed outlier: 3.963A pdb=" N ILE A 189 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN A 190 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 206 Processing helix chain 'A' and resid 209 through 231 removed outlier: 3.812A pdb=" N PHE A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.547A pdb=" N ARG A 236 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 removed outlier: 3.706A pdb=" N ASP A 263 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.561A pdb=" N ARG A 321 " --> pdb=" O ASN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 355 removed outlier: 3.747A pdb=" N ALA A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 374 through 383 Processing helix chain 'A' and resid 389 through 413 Processing helix chain 'A' and resid 628 through 638 removed outlier: 3.808A pdb=" N LYS A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 660 removed outlier: 3.960A pdb=" N GLU A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 695 removed outlier: 3.586A pdb=" N ASN A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 702 removed outlier: 4.247A pdb=" N ASN A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 721 removed outlier: 3.935A pdb=" N ILE A 706 " --> pdb=" O ASN A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 730 removed outlier: 3.790A pdb=" N VAL A 729 " --> pdb=" O GLY A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 744 removed outlier: 3.865A pdb=" N LEU A 735 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 736 " --> pdb=" O PHE A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 785 removed outlier: 3.825A pdb=" N ARG A 749 " --> pdb=" O MET A 745 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASN A 761 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE A 765 " --> pdb=" O ASN A 761 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'A' and resid 806 through 819 Processing helix chain 'A' and resid 822 through 832 removed outlier: 4.318A pdb=" N VAL A 826 " --> pdb=" O ASP A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 838 through 851 removed outlier: 3.898A pdb=" N PHE A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 866 removed outlier: 3.504A pdb=" N VAL A 858 " --> pdb=" O BPHE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1188 Processing helix chain 'A' and resid 1198 through 1227 Processing helix chain 'A' and resid 1234 through 1237 removed outlier: 3.740A pdb=" N ARG A1237 " --> pdb=" O ALA A1234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1234 through 1237' Processing helix chain 'A' and resid 1238 through 1260 Processing helix chain 'A' and resid 1267 through 1281 Processing helix chain 'A' and resid 1284 through 1289 Processing helix chain 'A' and resid 1289 through 1304 removed outlier: 3.850A pdb=" N LYS A1304 " --> pdb=" O ILE A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1328 Processing helix chain 'A' and resid 1345 through 1353 Processing helix chain 'A' and resid 1365 through 1377 Processing helix chain 'A' and resid 1381 through 1392 removed outlier: 3.606A pdb=" N ILE A1385 " --> pdb=" O GLY A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1444 removed outlier: 4.012A pdb=" N TYR A1410 " --> pdb=" O TRP A1406 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A1415 " --> pdb=" O PHE A1411 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS A1440 " --> pdb=" O LYS A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1460 removed outlier: 3.621A pdb=" N ARG A1448 " --> pdb=" O GLU A1444 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A1450 " --> pdb=" O ALA A1446 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU A1451 " --> pdb=" O ARG A1447 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG A1453 " --> pdb=" O ARG A1449 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A1454 " --> pdb=" O GLU A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1463 No H-bonds generated for 'chain 'A' and resid 1461 through 1463' Processing helix chain 'A' and resid 1468 through 1473 removed outlier: 4.210A pdb=" N THR A1472 " --> pdb=" O PRO A1468 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A1473 " --> pdb=" O TYR A1469 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1468 through 1473' Processing helix chain 'A' and resid 1482 through 1485 Processing helix chain 'A' and resid 1486 through 1505 removed outlier: 3.704A pdb=" N ASP A1490 " --> pdb=" O SER A1486 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE A1492 " --> pdb=" O TYR A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1541 Processing helix chain 'A' and resid 1542 through 1549 removed outlier: 3.936A pdb=" N PHE A1546 " --> pdb=" O GLY A1542 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE A1547 " --> pdb=" O LEU A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1574 removed outlier: 3.597A pdb=" N LEU A1568 " --> pdb=" O MET A1564 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A1569 " --> pdb=" O GLY A1565 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A1570 " --> pdb=" O ILE A1566 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A1571 " --> pdb=" O THR A1567 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A1572 " --> pdb=" O LEU A1568 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A1574 " --> pdb=" O GLU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1591 Processing helix chain 'A' and resid 1592 through 1596 Processing helix chain 'A' and resid 1597 through 1602 removed outlier: 4.001A pdb=" N MET A1601 " --> pdb=" O LYS A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1602 through 1614 Processing helix chain 'A' and resid 1615 through 1642 Processing helix chain 'A' and resid 1663 through 1675 removed outlier: 3.668A pdb=" N ALA A1667 " --> pdb=" O ASN A1663 " (cutoff:3.500A) Processing helix chain 'A' and resid 1679 through 1688 Processing helix chain 'A' and resid 1695 through 1700 removed outlier: 4.063A pdb=" N LEU A1699 " --> pdb=" O GLU A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1701 through 1738 removed outlier: 3.619A pdb=" N VAL A1705 " --> pdb=" O SER A1701 " (cutoff:3.500A) Proline residue: A1707 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 238 through 239 removed outlier: 3.526A pdb=" N ARG A 238 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 327 " --> pdb=" O ARG A 238 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1333 through 1335 596 hydrogen bonds defined for protein. 1725 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: 1.41 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1432 1.32 - 1.44: 2587 1.44 - 1.57: 5459 1.57 - 1.69: 64 1.69 - 1.82: 127 Bond restraints: 9669 Sorted by residual: bond pdb=" C21 3PE A2302 " pdb=" O21 3PE A2302 " ideal model delta sigma weight residual 1.316 1.465 -0.149 2.00e-02 2.50e+03 5.56e+01 bond pdb=" C31 3PE A2302 " pdb=" O31 3PE A2302 " ideal model delta sigma weight residual 1.331 1.469 -0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" C04 MWV A2301 " pdb=" O06 MWV A2301 " ideal model delta sigma weight residual 1.322 1.432 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C21 3PE A2302 " pdb=" C22 3PE A2302 " ideal model delta sigma weight residual 1.502 1.602 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C31 3PE A2306 " pdb=" C32 3PE A2306 " ideal model delta sigma weight residual 1.504 1.604 -0.100 2.00e-02 2.50e+03 2.48e+01 ... (remaining 9664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 12782 2.87 - 5.75: 283 5.75 - 8.62: 42 8.62 - 11.50: 10 11.50 - 14.37: 2 Bond angle restraints: 13119 Sorted by residual: angle pdb=" O12 3PE A2302 " pdb=" P 3PE A2302 " pdb=" O14 3PE A2302 " ideal model delta sigma weight residual 123.79 109.42 14.37 3.00e+00 1.11e-01 2.30e+01 angle pdb=" N ILE A 177 " pdb=" CA ILE A 177 " pdb=" C ILE A 177 " ideal model delta sigma weight residual 113.39 106.40 6.99 1.47e+00 4.63e-01 2.26e+01 angle pdb=" C ARG A1341 " pdb=" N ASN A1342 " pdb=" CA ASN A1342 " ideal model delta sigma weight residual 122.61 129.43 -6.82 1.56e+00 4.11e-01 1.91e+01 angle pdb=" N ALA A 176 " pdb=" CA ALA A 176 " pdb=" C ALA A 176 " ideal model delta sigma weight residual 114.39 108.37 6.02 1.45e+00 4.76e-01 1.73e+01 angle pdb=" CB MET A 687 " pdb=" CG MET A 687 " pdb=" SD MET A 687 " ideal model delta sigma weight residual 112.70 124.37 -11.67 3.00e+00 1.11e-01 1.51e+01 ... (remaining 13114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.22: 5274 24.22 - 48.45: 328 48.45 - 72.67: 35 72.67 - 96.89: 5 96.89 - 121.12: 2 Dihedral angle restraints: 5644 sinusoidal: 2325 harmonic: 3319 Sorted by residual: dihedral pdb=" CB CYS A1646 " pdb=" SG CYS A1646 " pdb=" SG CYS A1652 " pdb=" CB CYS A1652 " ideal model delta sinusoidal sigma weight residual 93.00 166.57 -73.57 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS A 239 " pdb=" SG CYS A 239 " pdb=" SG CYS A 280 " pdb=" CB CYS A 280 " ideal model delta sinusoidal sigma weight residual 93.00 146.34 -53.34 1 1.00e+01 1.00e-02 3.87e+01 dihedral pdb=" CB CYS A1691 " pdb=" SG CYS A1691 " pdb=" SG CYS A1698 " pdb=" CB CYS A1698 " ideal model delta sinusoidal sigma weight residual -86.00 -40.00 -46.00 1 1.00e+01 1.00e-02 2.93e+01 ... (remaining 5641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.953: 1536 0.953 - 1.906: 0 1.906 - 2.859: 0 2.859 - 3.812: 0 3.812 - 4.766: 1 Chirality restraints: 1537 Sorted by residual: chirality pdb=" C33 MWV A2301 " pdb=" C07 MWV A2301 " pdb=" C27 MWV A2301 " pdb=" C34 MWV A2301 " both_signs ideal model delta sigma weight residual False 2.33 -2.44 4.77 2.00e-01 2.50e+01 5.68e+02 chirality pdb=" CBG Y01 A2311 " pdb=" CAQ Y01 A2311 " pdb=" CBD Y01 A2311 " pdb=" CBI Y01 A2311 " both_signs ideal model delta sigma weight residual False -2.33 -2.84 0.51 2.00e-01 2.50e+01 6.48e+00 chirality pdb=" CBG Y01 A2313 " pdb=" CAQ Y01 A2313 " pdb=" CBD Y01 A2313 " pdb=" CBI Y01 A2313 " both_signs ideal model delta sigma weight residual False -2.33 -2.83 0.50 2.00e-01 2.50e+01 6.26e+00 ... (remaining 1534 not shown) Planarity restraints: 1582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 702 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 703 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 703 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 703 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 192 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO A 193 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A1191 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A1192 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A1192 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1192 " -0.026 5.00e-02 4.00e+02 ... (remaining 1579 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 57 2.51 - 3.11: 7724 3.11 - 3.70: 14803 3.70 - 4.30: 20488 4.30 - 4.90: 32605 Nonbonded interactions: 75677 Sorted by model distance: nonbonded pdb=" CD ARG A1191 " pdb=" CA ASN A1663 " model vdw 1.912 3.870 nonbonded pdb=" CG ARG A1191 " pdb=" O GLU A1662 " model vdw 2.067 3.440 nonbonded pdb=" CD1 LEU A 861 " pdb=" CD2 LEU A1423 " model vdw 2.092 3.880 nonbonded pdb=" O TYR A1633 " pdb=" OH TYR A1709 " model vdw 2.130 3.040 nonbonded pdb=" OD1 ASP A1380 " pdb=" ND2 ASN A1681 " model vdw 2.185 3.120 ... (remaining 75672 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.010 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.009 0.149 9676 Z= 0.437 Angle : 1.015 14.374 13135 Z= 0.497 Chirality : 0.138 4.766 1537 Planarity : 0.004 0.050 1580 Dihedral : 14.589 121.117 3479 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.10 % Allowed : 0.20 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.26), residues: 1130 helix: 0.85 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -1.61 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1278 TYR 0.014 0.002 TYR A1473 PHE 0.029 0.002 PHE A 772 TRP 0.020 0.002 TRP A 231 HIS 0.014 0.001 HIS A1440 Details of bonding type rmsd/Z covalent geometry : bond 0.00884 / 0.44 ( 9669) covalent geometry : angle 1.01173 / 0.50 (13119) SS BOND : bond 0.00145 / 0.08 ( 5) SS BOND : angle 0.77660 / 0.45 ( 10) hydrogen bonds : bond 0.14507 / 9.61 ( 596) hydrogen bonds : angle 6.12922 / 4.54 ( 1725) link_NAG-ASN : bond 0.00651 / 0.34 ( 2) link_NAG-ASN : angle 4.01906 / 2.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 208 MET cc_start: 0.7518 (mtm) cc_final: 0.6461 (mtm) REVERT: A 373 TYR cc_start: 0.8538 (m-80) cc_final: 0.8123 (m-10) REVERT: A 387 PHE cc_start: 0.8873 (t80) cc_final: 0.8655 (t80) REVERT: A 400 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8465 (mm-40) REVERT: A 694 PHE cc_start: 0.8407 (m-80) cc_final: 0.7991 (m-10) REVERT: A 767 MET cc_start: 0.7189 (mtt) cc_final: 0.6484 (mmt) REVERT: A 839 SER cc_start: 0.9509 (p) cc_final: 0.9303 (p) REVERT: A 1181 PHE cc_start: 0.8662 (t80) cc_final: 0.8422 (t80) REVERT: A 1244 ASP cc_start: 0.9079 (m-30) cc_final: 0.8856 (m-30) REVERT: A 1386 MET cc_start: 0.8989 (ttp) cc_final: 0.8569 (ttp) REVERT: A 1501 VAL cc_start: 0.9655 (t) cc_final: 0.9396 (t) REVERT: A 1504 MET cc_start: 0.8741 (mpp) cc_final: 0.8251 (mpp) REVERT: A 1522 CYS cc_start: 0.9503 (m) cc_final: 0.9214 (p) REVERT: A 1662 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7964 (mm-30) outliers start: 1 outliers final: 0 residues processed: 256 average time/residue: 0.0700 time to fit residues: 27.5017 Evaluate side-chains 190 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.0370 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 GLN A 229 GLN ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 HIS A 653 ASN A 820 GLN A 855 ASN A1241 ASN A1362 ASN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1510 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.123757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.090537 restraints weight = 24202.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.093631 restraints weight = 11464.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.095517 restraints weight = 7715.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.096327 restraints weight = 6342.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.096948 restraints weight = 5841.512| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9676 Z= 0.154 Angle : 0.799 12.915 13135 Z= 0.395 Chirality : 0.045 0.244 1537 Planarity : 0.005 0.043 1580 Dihedral : 10.184 114.572 1359 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.69 % Allowed : 13.22 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.25), residues: 1130 helix: 0.88 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -1.94 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1355 TYR 0.031 0.002 TYR A1473 PHE 0.025 0.002 PHE A1546 TRP 0.015 0.002 TRP A 319 HIS 0.015 0.002 HIS A1440 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 9669) covalent geometry : angle 0.79562 / 0.39 (13119) SS BOND : bond 0.00114 / 0.06 ( 5) SS BOND : angle 0.98301 / 0.57 ( 10) hydrogen bonds : bond 0.04464 / 2.92 ( 596) hydrogen bonds : angle 5.02964 / 3.66 ( 1725) link_NAG-ASN : bond 0.00397 / 0.21 ( 2) link_NAG-ASN : angle 3.36410 / 2.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 219 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8890 (tp) cc_final: 0.8654 (tt) REVERT: A 208 MET cc_start: 0.7432 (mtm) cc_final: 0.6819 (mtp) REVERT: A 387 PHE cc_start: 0.8810 (t80) cc_final: 0.8543 (t80) REVERT: A 694 PHE cc_start: 0.7941 (m-80) cc_final: 0.7638 (m-80) REVERT: A 717 TRP cc_start: 0.8672 (m100) cc_final: 0.8469 (t60) REVERT: A 759 MET cc_start: 0.8670 (ppp) cc_final: 0.8258 (tmm) REVERT: A 767 MET cc_start: 0.6743 (mtt) cc_final: 0.6336 (mmt) REVERT: A 778 ILE cc_start: 0.9343 (mm) cc_final: 0.9067 (tt) REVERT: A 1181 PHE cc_start: 0.8435 (t80) cc_final: 0.8177 (t80) REVERT: A 1364 ASP cc_start: 0.8182 (m-30) cc_final: 0.7937 (t0) REVERT: A 1488 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.6831 (m-80) REVERT: A 1519 LEU cc_start: 0.9570 (mp) cc_final: 0.8842 (pp) REVERT: A 1662 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7578 (mm-30) REVERT: A 1704 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7592 (t80) outliers start: 17 outliers final: 10 residues processed: 228 average time/residue: 0.0739 time to fit residues: 25.5848 Evaluate side-chains 202 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 761 ASN Chi-restraints excluded: chain A residue 1203 PHE Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1362 ASN Chi-restraints excluded: chain A residue 1488 TYR Chi-restraints excluded: chain A residue 1704 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 71 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 29 optimal weight: 0.0030 chunk 105 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 ASN A1362 ASN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1552 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.123973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.091102 restraints weight = 39234.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.093688 restraints weight = 16113.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.093926 restraints weight = 9657.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.094631 restraints weight = 8966.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.094694 restraints weight = 8343.437| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9676 Z= 0.143 Angle : 0.770 13.230 13135 Z= 0.380 Chirality : 0.045 0.246 1537 Planarity : 0.004 0.047 1580 Dihedral : 9.784 112.262 1359 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.29 % Allowed : 16.30 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.25), residues: 1130 helix: 0.82 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -2.10 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1355 TYR 0.025 0.001 TYR A1473 PHE 0.024 0.002 PHE A1246 TRP 0.013 0.001 TRP A 319 HIS 0.005 0.001 HIS A1358 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 9669) covalent geometry : angle 0.76718 / 0.38 (13119) SS BOND : bond 0.00080 / 0.04 ( 5) SS BOND : angle 0.80162 / 0.47 ( 10) hydrogen bonds : bond 0.04145 / 2.72 ( 596) hydrogen bonds : angle 4.87170 / 3.53 ( 1725) link_NAG-ASN : bond 0.00420 / 0.22 ( 2) link_NAG-ASN : angle 3.07475 / 1.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8655 (t80) REVERT: A 167 LEU cc_start: 0.9124 (tp) cc_final: 0.8889 (tt) REVERT: A 387 PHE cc_start: 0.8786 (t80) cc_final: 0.8502 (t80) REVERT: A 694 PHE cc_start: 0.8265 (m-80) cc_final: 0.8018 (m-80) REVERT: A 717 TRP cc_start: 0.8773 (m100) cc_final: 0.8534 (t60) REVERT: A 759 MET cc_start: 0.8656 (ppp) cc_final: 0.8367 (tmm) REVERT: A 767 MET cc_start: 0.6868 (mtt) cc_final: 0.6457 (mmt) REVERT: A 778 ILE cc_start: 0.9362 (mm) cc_final: 0.9151 (tt) REVERT: A 1364 ASP cc_start: 0.8083 (m-30) cc_final: 0.7754 (t0) REVERT: A 1483 MET cc_start: 0.8146 (tpp) cc_final: 0.7937 (tpp) REVERT: A 1488 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.6978 (m-80) REVERT: A 1598 LEU cc_start: 0.9562 (mp) cc_final: 0.8886 (mm) REVERT: A 1662 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7621 (mm-30) REVERT: A 1704 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7678 (t80) outliers start: 23 outliers final: 10 residues processed: 222 average time/residue: 0.0628 time to fit residues: 21.3697 Evaluate side-chains 202 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1203 PHE Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1362 ASN Chi-restraints excluded: chain A residue 1488 TYR Chi-restraints excluded: chain A residue 1489 LEU Chi-restraints excluded: chain A residue 1704 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 87 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 GLN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.123801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.087599 restraints weight = 49075.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.092803 restraints weight = 18372.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.094367 restraints weight = 9170.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.094016 restraints weight = 7601.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.094520 restraints weight = 8005.789| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3384 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9676 Z= 0.151 Angle : 0.768 14.342 13135 Z= 0.376 Chirality : 0.045 0.245 1537 Planarity : 0.004 0.046 1580 Dihedral : 9.539 111.488 1359 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.59 % Allowed : 19.09 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.25), residues: 1130 helix: 0.84 (0.19), residues: 785 sheet: None (None), residues: 0 loop : -2.14 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1191 TYR 0.014 0.001 TYR A 364 PHE 0.024 0.002 PHE A1246 TRP 0.011 0.001 TRP A1382 HIS 0.008 0.001 HIS A1358 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 9669) covalent geometry : angle 0.76538 / 0.38 (13119) SS BOND : bond 0.00106 / 0.06 ( 5) SS BOND : angle 0.74491 / 0.43 ( 10) hydrogen bonds : bond 0.03981 / 2.62 ( 596) hydrogen bonds : angle 4.86094 / 3.53 ( 1725) link_NAG-ASN : bond 0.00378 / 0.20 ( 2) link_NAG-ASN : angle 2.91629 / 1.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8582 (t80) REVERT: A 387 PHE cc_start: 0.8835 (t80) cc_final: 0.8560 (t80) REVERT: A 400 GLN cc_start: 0.8409 (mm-40) cc_final: 0.8093 (mm-40) REVERT: A 694 PHE cc_start: 0.8154 (m-80) cc_final: 0.7881 (m-80) REVERT: A 717 TRP cc_start: 0.8803 (m100) cc_final: 0.8551 (t60) REVERT: A 759 MET cc_start: 0.8577 (ppp) cc_final: 0.8140 (tmm) REVERT: A 767 MET cc_start: 0.6801 (mtt) cc_final: 0.6430 (mmt) REVERT: A 778 ILE cc_start: 0.9436 (mm) cc_final: 0.9080 (tt) REVERT: A 1364 ASP cc_start: 0.8084 (m-30) cc_final: 0.7826 (t0) REVERT: A 1483 MET cc_start: 0.8147 (tpp) cc_final: 0.7920 (tpp) REVERT: A 1488 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.6987 (m-80) REVERT: A 1568 LEU cc_start: 0.9433 (mt) cc_final: 0.9190 (mt) REVERT: A 1609 LEU cc_start: 0.9138 (mm) cc_final: 0.8389 (pp) REVERT: A 1662 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7496 (mm-30) REVERT: A 1704 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7674 (t80) outliers start: 16 outliers final: 9 residues processed: 211 average time/residue: 0.0698 time to fit residues: 22.4266 Evaluate side-chains 204 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1488 TYR Chi-restraints excluded: chain A residue 1704 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 6 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1723 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.120785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.087488 restraints weight = 42434.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.089369 restraints weight = 17020.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.090678 restraints weight = 10918.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.090893 restraints weight = 9454.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.090913 restraints weight = 8845.305| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 9676 Z= 0.209 Angle : 0.807 15.249 13135 Z= 0.397 Chirality : 0.047 0.309 1537 Planarity : 0.004 0.050 1580 Dihedral : 9.481 109.389 1359 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.19 % Allowed : 20.97 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.25), residues: 1130 helix: 0.77 (0.19), residues: 784 sheet: None (None), residues: 0 loop : -2.22 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1191 TYR 0.026 0.002 TYR A 364 PHE 0.027 0.002 PHE A 218 TRP 0.013 0.001 TRP A1382 HIS 0.008 0.001 HIS A1358 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 ( 9669) covalent geometry : angle 0.80504 / 0.40 (13119) SS BOND : bond 0.00160 / 0.10 ( 5) SS BOND : angle 0.80030 / 0.45 ( 10) hydrogen bonds : bond 0.04130 / 2.71 ( 596) hydrogen bonds : angle 4.92414 / 3.55 ( 1725) link_NAG-ASN : bond 0.00269 / 0.14 ( 2) link_NAG-ASN : angle 2.83936 / 1.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.368 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8702 (t80) REVERT: A 387 PHE cc_start: 0.8902 (t80) cc_final: 0.8526 (t80) REVERT: A 400 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8205 (mm-40) REVERT: A 687 MET cc_start: 0.8840 (mtm) cc_final: 0.8594 (mpp) REVERT: A 694 PHE cc_start: 0.8180 (m-80) cc_final: 0.7880 (m-80) REVERT: A 717 TRP cc_start: 0.8782 (m100) cc_final: 0.8517 (t60) REVERT: A 759 MET cc_start: 0.8623 (ppp) cc_final: 0.8141 (tmm) REVERT: A 767 MET cc_start: 0.7095 (mtt) cc_final: 0.6704 (mmt) REVERT: A 778 ILE cc_start: 0.9366 (mm) cc_final: 0.9003 (tt) REVERT: A 822 ASP cc_start: 0.8474 (t0) cc_final: 0.8022 (t70) REVERT: A 1184 CYS cc_start: 0.9283 (m) cc_final: 0.9083 (m) REVERT: A 1364 ASP cc_start: 0.8112 (m-30) cc_final: 0.7805 (t0) REVERT: A 1407 MET cc_start: 0.8705 (mmp) cc_final: 0.8430 (mmt) REVERT: A 1483 MET cc_start: 0.8143 (tpp) cc_final: 0.7932 (tpp) REVERT: A 1598 LEU cc_start: 0.9469 (mm) cc_final: 0.8911 (mp) REVERT: A 1704 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7651 (t80) outliers start: 22 outliers final: 16 residues processed: 214 average time/residue: 0.0689 time to fit residues: 22.8670 Evaluate side-chains 218 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 761 ASN Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1693 HIS Chi-restraints excluded: chain A residue 1704 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1362 ASN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.121998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.088984 restraints weight = 42804.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.090861 restraints weight = 16468.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.091820 restraints weight = 10405.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.092239 restraints weight = 9066.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.092335 restraints weight = 8512.136| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9676 Z= 0.157 Angle : 0.783 14.609 13135 Z= 0.379 Chirality : 0.045 0.279 1537 Planarity : 0.004 0.047 1580 Dihedral : 9.275 109.354 1359 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.49 % Allowed : 20.58 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.25), residues: 1130 helix: 0.88 (0.19), residues: 785 sheet: None (None), residues: 0 loop : -2.23 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1191 TYR 0.013 0.001 TYR A1470 PHE 0.024 0.002 PHE A1246 TRP 0.012 0.001 TRP A1382 HIS 0.006 0.001 HIS A1358 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 9669) covalent geometry : angle 0.78095 / 0.38 (13119) SS BOND : bond 0.00121 / 0.06 ( 5) SS BOND : angle 0.71324 / 0.40 ( 10) hydrogen bonds : bond 0.03993 / 2.59 ( 596) hydrogen bonds : angle 4.76638 / 3.44 ( 1725) link_NAG-ASN : bond 0.00326 / 0.17 ( 2) link_NAG-ASN : angle 2.54865 / 1.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.379 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.9172 (mmt) cc_final: 0.8616 (mmt) REVERT: A 125 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8590 (t80) REVERT: A 218 PHE cc_start: 0.8803 (t80) cc_final: 0.8548 (t80) REVERT: A 363 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.7979 (tmm) REVERT: A 387 PHE cc_start: 0.8820 (t80) cc_final: 0.8521 (t80) REVERT: A 694 PHE cc_start: 0.8077 (m-80) cc_final: 0.7726 (m-80) REVERT: A 717 TRP cc_start: 0.8703 (m100) cc_final: 0.8466 (t60) REVERT: A 759 MET cc_start: 0.8513 (ppp) cc_final: 0.8087 (tmm) REVERT: A 767 MET cc_start: 0.7124 (mtt) cc_final: 0.6751 (mmt) REVERT: A 778 ILE cc_start: 0.9384 (mm) cc_final: 0.9112 (tt) REVERT: A 822 ASP cc_start: 0.8417 (t0) cc_final: 0.8089 (t70) REVERT: A 1184 CYS cc_start: 0.9239 (m) cc_final: 0.9027 (m) REVERT: A 1364 ASP cc_start: 0.8031 (m-30) cc_final: 0.7729 (t0) REVERT: A 1407 MET cc_start: 0.8690 (mmp) cc_final: 0.8441 (mmt) REVERT: A 1488 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.6786 (m-80) REVERT: A 1662 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7541 (mm-30) REVERT: A 1704 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7601 (t80) outliers start: 25 outliers final: 15 residues processed: 213 average time/residue: 0.0663 time to fit residues: 21.8445 Evaluate side-chains 215 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1362 ASN Chi-restraints excluded: chain A residue 1441 GLN Chi-restraints excluded: chain A residue 1488 TYR Chi-restraints excluded: chain A residue 1704 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 45 optimal weight: 0.3980 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 86 optimal weight: 0.0770 chunk 56 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 GLN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.120428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.084738 restraints weight = 29132.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.087829 restraints weight = 13517.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.089755 restraints weight = 8919.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.090786 restraints weight = 7245.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.091228 restraints weight = 6542.866| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9676 Z= 0.164 Angle : 0.798 12.576 13135 Z= 0.389 Chirality : 0.046 0.297 1537 Planarity : 0.004 0.050 1580 Dihedral : 9.075 109.019 1359 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.29 % Allowed : 21.37 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.25), residues: 1130 helix: 0.87 (0.19), residues: 786 sheet: None (None), residues: 0 loop : -2.18 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 191 TYR 0.024 0.001 TYR A1473 PHE 0.027 0.002 PHE A 765 TRP 0.011 0.001 TRP A1382 HIS 0.005 0.001 HIS A1358 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 9669) covalent geometry : angle 0.79655 / 0.39 (13119) SS BOND : bond 0.00121 / 0.07 ( 5) SS BOND : angle 0.69713 / 0.39 ( 10) hydrogen bonds : bond 0.03985 / 2.57 ( 596) hydrogen bonds : angle 4.75946 / 3.43 ( 1725) link_NAG-ASN : bond 0.00309 / 0.16 ( 2) link_NAG-ASN : angle 2.35227 / 1.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.364 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.9531 (mt) cc_final: 0.9257 (tp) REVERT: A 125 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.8655 (t80) REVERT: A 187 LYS cc_start: 0.8804 (mtpt) cc_final: 0.8059 (mtpp) REVERT: A 191 ARG cc_start: 0.8101 (mtm-85) cc_final: 0.7865 (mtm-85) REVERT: A 363 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8046 (tmm) REVERT: A 387 PHE cc_start: 0.8847 (t80) cc_final: 0.8510 (t80) REVERT: A 694 PHE cc_start: 0.8043 (m-80) cc_final: 0.7678 (m-80) REVERT: A 717 TRP cc_start: 0.8737 (m100) cc_final: 0.8485 (t60) REVERT: A 759 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8026 (tmm) REVERT: A 767 MET cc_start: 0.7159 (mtt) cc_final: 0.6746 (mmt) REVERT: A 778 ILE cc_start: 0.9390 (mm) cc_final: 0.9038 (tt) REVERT: A 822 ASP cc_start: 0.8409 (t0) cc_final: 0.8109 (t70) REVERT: A 1364 ASP cc_start: 0.8082 (m-30) cc_final: 0.7729 (t0) REVERT: A 1407 MET cc_start: 0.8711 (mmp) cc_final: 0.8453 (mmt) REVERT: A 1488 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.6787 (m-80) REVERT: A 1497 ILE cc_start: 0.9580 (mm) cc_final: 0.9171 (tt) REVERT: A 1662 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7510 (mm-30) REVERT: A 1704 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7593 (t80) outliers start: 23 outliers final: 17 residues processed: 212 average time/residue: 0.0726 time to fit residues: 23.7405 Evaluate side-chains 217 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 759 MET Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1441 GLN Chi-restraints excluded: chain A residue 1488 TYR Chi-restraints excluded: chain A residue 1684 MET Chi-restraints excluded: chain A residue 1704 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.121748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.086260 restraints weight = 29421.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.089413 restraints weight = 13496.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.091345 restraints weight = 8844.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.092184 restraints weight = 7180.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.092779 restraints weight = 6561.759| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9676 Z= 0.142 Angle : 0.800 11.729 13135 Z= 0.387 Chirality : 0.045 0.259 1537 Planarity : 0.004 0.047 1580 Dihedral : 8.877 109.078 1359 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.99 % Allowed : 22.27 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.25), residues: 1130 helix: 0.88 (0.19), residues: 787 sheet: None (None), residues: 0 loop : -2.10 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 191 TYR 0.014 0.001 TYR A1469 PHE 0.031 0.002 PHE A 218 TRP 0.011 0.001 TRP A1382 HIS 0.004 0.001 HIS A1358 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 9669) covalent geometry : angle 0.79860 / 0.39 (13119) SS BOND : bond 0.00101 / 0.05 ( 5) SS BOND : angle 0.65094 / 0.36 ( 10) hydrogen bonds : bond 0.03871 / 2.50 ( 596) hydrogen bonds : angle 4.72989 / 3.42 ( 1725) link_NAG-ASN : bond 0.00360 / 0.19 ( 2) link_NAG-ASN : angle 2.16509 / 1.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.400 Fit side-chains TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.9531 (mt) cc_final: 0.9254 (tp) REVERT: A 125 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8633 (t80) REVERT: A 133 LYS cc_start: 0.9040 (ttpt) cc_final: 0.8673 (tttt) REVERT: A 187 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8142 (mtpp) REVERT: A 363 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8352 (tmm) REVERT: A 387 PHE cc_start: 0.8756 (t80) cc_final: 0.8447 (t80) REVERT: A 391 ASN cc_start: 0.8507 (m-40) cc_final: 0.8223 (m110) REVERT: A 694 PHE cc_start: 0.8080 (m-80) cc_final: 0.7761 (m-80) REVERT: A 717 TRP cc_start: 0.8751 (m100) cc_final: 0.8495 (t60) REVERT: A 759 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7982 (tmm) REVERT: A 767 MET cc_start: 0.7136 (mtt) cc_final: 0.6652 (mmt) REVERT: A 778 ILE cc_start: 0.9304 (mm) cc_final: 0.9027 (tt) REVERT: A 781 MET cc_start: 0.8513 (mmm) cc_final: 0.8299 (mtt) REVERT: A 822 ASP cc_start: 0.8346 (t0) cc_final: 0.8056 (t70) REVERT: A 1364 ASP cc_start: 0.8022 (m-30) cc_final: 0.7678 (t0) REVERT: A 1407 MET cc_start: 0.8665 (mmp) cc_final: 0.8401 (mmt) REVERT: A 1488 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.6765 (m-80) REVERT: A 1497 ILE cc_start: 0.9608 (mm) cc_final: 0.9205 (tt) REVERT: A 1662 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7438 (mm-30) REVERT: A 1704 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7579 (t80) outliers start: 20 outliers final: 11 residues processed: 216 average time/residue: 0.0749 time to fit residues: 24.9192 Evaluate side-chains 214 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 759 MET Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1441 GLN Chi-restraints excluded: chain A residue 1488 TYR Chi-restraints excluded: chain A residue 1684 MET Chi-restraints excluded: chain A residue 1704 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 102 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 14 optimal weight: 0.0770 chunk 60 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 GLN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.121308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.085087 restraints weight = 42131.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.088706 restraints weight = 16291.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.090971 restraints weight = 9666.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.092313 restraints weight = 7374.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.092957 restraints weight = 6451.875| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9676 Z= 0.144 Angle : 0.835 14.179 13135 Z= 0.406 Chirality : 0.046 0.289 1537 Planarity : 0.004 0.050 1580 Dihedral : 8.790 109.023 1359 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.09 % Allowed : 22.66 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.25), residues: 1130 helix: 0.87 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -2.06 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.022 0.001 TYR A1473 PHE 0.028 0.002 PHE A1246 TRP 0.011 0.001 TRP A 319 HIS 0.004 0.001 HIS A1358 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 9669) covalent geometry : angle 0.83441 / 0.41 (13119) SS BOND : bond 0.00083 / 0.04 ( 5) SS BOND : angle 0.62649 / 0.35 ( 10) hydrogen bonds : bond 0.03962 / 2.53 ( 596) hydrogen bonds : angle 4.74966 / 3.43 ( 1725) link_NAG-ASN : bond 0.00355 / 0.19 ( 2) link_NAG-ASN : angle 2.04557 / 1.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 0.356 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.9521 (mt) cc_final: 0.9244 (tp) REVERT: A 125 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8601 (t80) REVERT: A 363 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8384 (tmm) REVERT: A 387 PHE cc_start: 0.8825 (t80) cc_final: 0.8362 (t80) REVERT: A 400 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8279 (mm-40) REVERT: A 694 PHE cc_start: 0.8058 (m-80) cc_final: 0.7733 (m-80) REVERT: A 717 TRP cc_start: 0.8758 (m100) cc_final: 0.8495 (t60) REVERT: A 759 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7981 (tmm) REVERT: A 767 MET cc_start: 0.7060 (mtt) cc_final: 0.6638 (mmt) REVERT: A 778 ILE cc_start: 0.9276 (mm) cc_final: 0.8998 (tt) REVERT: A 822 ASP cc_start: 0.8332 (t0) cc_final: 0.7991 (t70) REVERT: A 855 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.7807 (t0) REVERT: A 1185 ILE cc_start: 0.9478 (mt) cc_final: 0.9211 (mt) REVERT: A 1364 ASP cc_start: 0.8065 (m-30) cc_final: 0.7712 (t0) REVERT: A 1407 MET cc_start: 0.8669 (mmp) cc_final: 0.8400 (mmt) REVERT: A 1488 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.6736 (m-80) REVERT: A 1497 ILE cc_start: 0.9577 (mm) cc_final: 0.9142 (tt) REVERT: A 1662 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7364 (mm-30) REVERT: A 1704 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7607 (t80) outliers start: 21 outliers final: 14 residues processed: 210 average time/residue: 0.0739 time to fit residues: 23.7645 Evaluate side-chains 215 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 759 MET Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1441 GLN Chi-restraints excluded: chain A residue 1488 TYR Chi-restraints excluded: chain A residue 1684 MET Chi-restraints excluded: chain A residue 1704 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 59 optimal weight: 8.9990 chunk 17 optimal weight: 0.0980 chunk 8 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** 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 = 0.3802 r_free = 0.3802 target = 0.119523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.084461 restraints weight = 33059.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.087657 restraints weight = 14318.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.089626 restraints weight = 9062.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.090741 restraints weight = 7183.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.091109 restraints weight = 6402.709| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9676 Z= 0.145 Angle : 0.855 18.402 13135 Z= 0.413 Chirality : 0.045 0.277 1537 Planarity : 0.004 0.048 1580 Dihedral : 8.742 108.876 1359 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.99 % Allowed : 22.66 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.25), residues: 1130 helix: 0.88 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -2.04 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 191 TYR 0.016 0.001 TYR A 145 PHE 0.036 0.002 PHE A 218 TRP 0.010 0.001 TRP A 319 HIS 0.004 0.001 HIS A1358 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 9669) covalent geometry : angle 0.85386 / 0.41 (13119) SS BOND : bond 0.00095 / 0.05 ( 5) SS BOND : angle 0.61196 / 0.34 ( 10) hydrogen bonds : bond 0.03934 / 2.52 ( 596) hydrogen bonds : angle 4.72722 / 3.42 ( 1725) link_NAG-ASN : bond 0.00355 / 0.19 ( 2) link_NAG-ASN : angle 1.94785 / 1.22 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.396 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 383 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.9509 (mt) cc_final: 0.9236 (tp) REVERT: A 125 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8605 (t80) REVERT: A 363 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8459 (tmm) REVERT: A 387 PHE cc_start: 0.8766 (t80) cc_final: 0.8342 (t80) REVERT: A 694 PHE cc_start: 0.8096 (m-80) cc_final: 0.7757 (m-80) REVERT: A 717 TRP cc_start: 0.8761 (m100) cc_final: 0.8500 (t60) REVERT: A 759 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8002 (tmm) REVERT: A 767 MET cc_start: 0.7080 (mtt) cc_final: 0.6630 (mmt) REVERT: A 778 ILE cc_start: 0.9301 (mm) cc_final: 0.8984 (tt) REVERT: A 822 ASP cc_start: 0.8346 (t0) cc_final: 0.8004 (t70) REVERT: A 855 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.7842 (t0) REVERT: A 1185 ILE cc_start: 0.9490 (mt) cc_final: 0.9201 (mt) REVERT: A 1364 ASP cc_start: 0.8086 (m-30) cc_final: 0.7747 (t0) REVERT: A 1407 MET cc_start: 0.8689 (mmp) cc_final: 0.8424 (mmt) REVERT: A 1488 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.6752 (m-80) REVERT: A 1497 ILE cc_start: 0.9612 (mm) cc_final: 0.9193 (tt) REVERT: A 1662 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7271 (mm-30) REVERT: A 1704 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7627 (t80) outliers start: 20 outliers final: 14 residues processed: 209 average time/residue: 0.0735 time to fit residues: 23.7971 Evaluate side-chains 215 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 759 MET Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1208 ASN Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1441 GLN Chi-restraints excluded: chain A residue 1488 TYR Chi-restraints excluded: chain A residue 1684 MET Chi-restraints excluded: chain A residue 1704 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 36 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 33 optimal weight: 6.9990 chunk 48 optimal weight: 0.1980 chunk 50 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** 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 = 0.3818 r_free = 0.3818 target = 0.120499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.085724 restraints weight = 30876.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.088880 restraints weight = 13731.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.090803 restraints weight = 8837.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.091942 restraints weight = 7053.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.092345 restraints weight = 6302.264| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9676 Z= 0.143 Angle : 0.855 17.328 13135 Z= 0.412 Chirality : 0.045 0.284 1537 Planarity : 0.004 0.050 1580 Dihedral : 8.653 108.638 1359 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.79 % Allowed : 23.36 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.25), residues: 1130 helix: 0.88 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -2.03 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 191 TYR 0.020 0.001 TYR A1473 PHE 0.031 0.002 PHE A1246 TRP 0.012 0.001 TRP A 823 HIS 0.004 0.001 HIS A1358 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 9669) covalent geometry : angle 0.85402 / 0.41 (13119) SS BOND : bond 0.00086 / 0.04 ( 5) SS BOND : angle 0.60076 / 0.33 ( 10) hydrogen bonds : bond 0.03914 / 2.50 ( 596) hydrogen bonds : angle 4.73759 / 3.44 ( 1725) link_NAG-ASN : bond 0.00353 / 0.18 ( 2) link_NAG-ASN : angle 1.87113 / 1.17 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1878.95 seconds wall clock time: 33 minutes 10.93 seconds (1990.93 seconds total)