Starting phenix.real_space_refine on Mon Jun 9 04:54:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wlj_32585/06_2025/7wlj_32585.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wlj_32585/06_2025/7wlj_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wlj_32585/06_2025/7wlj_32585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wlj_32585/06_2025/7wlj_32585.map" model { file = "/net/cci-nas-00/data/ceres_data/7wlj_32585/06_2025/7wlj_32585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wlj_32585/06_2025/7wlj_32585.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'ARG:plan': 3, 'TRP:plan': 1} 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: {'ARG:plan': 3, 'TRP:plan': 1} 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: 199 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'Y01:plan-2': 1, '3PE:plan-1': 4, '3PE:plan-2': 4, 'Y01:plan-1': 3} 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: 9.60, per 1000 atoms: 1.02 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: 2.34 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 0.90 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: 2.75 Time building geometry restraints manager: 2.74 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 - 35.67: 5893 35.67 - 71.34: 149 71.34 - 107.01: 18 107.01 - 142.68: 3 142.68 - 178.35: 3 Dihedral angle restraints: 6066 sinusoidal: 2747 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 6063 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: 0.010 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.730 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 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 : 16.923 178.349 3901 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.002 TRP A 231 HIS 0.014 0.001 HIS A1440 PHE 0.029 0.002 PHE A 772 TYR 0.014 0.002 TYR A1473 ARG 0.009 0.001 ARG A1278 Details of bonding type rmsd link_NAG-ASN : bond 0.00651 ( 2) link_NAG-ASN : angle 4.01906 ( 6) hydrogen bonds : bond 0.14507 ( 596) hydrogen bonds : angle 6.12922 ( 1725) SS BOND : bond 0.00145 ( 5) SS BOND : angle 0.77660 ( 10) covalent geometry : bond 0.00884 ( 9669) covalent geometry : angle 1.01173 (13119) *********************** 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 : 1.205 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: 0.1627 time to fit residues: 62.8508 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 : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.122623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.088721 restraints weight = 24274.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.091748 restraints weight = 11686.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.093598 restraints weight = 7942.119| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9676 Z= 0.168 Angle : 0.811 12.700 13135 Z= 0.399 Chirality : 0.046 0.231 1537 Planarity : 0.005 0.042 1580 Dihedral : 13.001 140.969 1781 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.79 % Allowed : 13.42 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.25), residues: 1130 helix: 0.88 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -1.94 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1382 HIS 0.013 0.002 HIS A1440 PHE 0.024 0.002 PHE A1434 TYR 0.032 0.002 TYR A1473 ARG 0.005 0.001 ARG A1355 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 2) link_NAG-ASN : angle 3.46872 ( 6) hydrogen bonds : bond 0.04493 ( 596) hydrogen bonds : angle 5.09281 ( 1725) SS BOND : bond 0.00133 ( 5) SS BOND : angle 1.00890 ( 10) covalent geometry : bond 0.00377 ( 9669) covalent geometry : angle 0.80736 (13119) *********************** 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 234 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 1.075 Fit side-chains 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. revert: symmetry clash TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8990 (tp) cc_final: 0.8753 (tt) REVERT: A 208 MET cc_start: 0.7464 (mtm) cc_final: 0.6449 (mtm) REVERT: A 373 TYR cc_start: 0.8279 (m-80) cc_final: 0.8073 (m-10) REVERT: A 387 PHE cc_start: 0.8801 (t80) cc_final: 0.8529 (t80) REVERT: A 400 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8268 (mm-40) REVERT: A 694 PHE cc_start: 0.8031 (m-80) cc_final: 0.7718 (m-80) REVERT: A 717 TRP cc_start: 0.8715 (m100) cc_final: 0.8496 (t60) REVERT: A 759 MET cc_start: 0.8697 (ppp) cc_final: 0.8293 (tmm) REVERT: A 767 MET cc_start: 0.6865 (mtt) cc_final: 0.6426 (mmt) REVERT: A 778 ILE cc_start: 0.9396 (mm) cc_final: 0.9085 (tt) REVERT: A 1181 PHE cc_start: 0.8496 (t80) cc_final: 0.8232 (t80) REVERT: A 1364 ASP cc_start: 0.8200 (m-30) cc_final: 0.7959 (t0) REVERT: A 1488 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.6895 (m-80) REVERT: A 1501 VAL cc_start: 0.9679 (t) cc_final: 0.9337 (t) REVERT: A 1519 LEU cc_start: 0.9533 (mp) cc_final: 0.8812 (pp) REVERT: A 1662 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7658 (mm-30) REVERT: A 1704 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7618 (t80) outliers start: 18 outliers final: 9 residues processed: 227 average time/residue: 0.1867 time to fit residues: 63.3924 Evaluate side-chains 196 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 111 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 0.0020 chunk 47 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1362 ASN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1552 ASN A1650 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.124195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.089712 restraints weight = 27121.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.092933 restraints weight = 12429.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.094918 restraints weight = 8258.125| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9676 Z= 0.144 Angle : 0.773 13.624 13135 Z= 0.383 Chirality : 0.045 0.238 1537 Planarity : 0.004 0.047 1580 Dihedral : 12.015 134.568 1781 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.09 % Allowed : 15.81 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.25), residues: 1130 helix: 0.88 (0.19), residues: 779 sheet: None (None), residues: 0 loop : -2.08 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 319 HIS 0.004 0.001 HIS A1481 PHE 0.025 0.002 PHE A1246 TYR 0.025 0.002 TYR A1473 ARG 0.005 0.001 ARG A1355 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 2) link_NAG-ASN : angle 3.03846 ( 6) hydrogen bonds : bond 0.04148 ( 596) hydrogen bonds : angle 4.81401 ( 1725) SS BOND : bond 0.00085 ( 5) SS BOND : angle 0.81555 ( 10) covalent geometry : bond 0.00310 ( 9669) covalent geometry : angle 0.77023 (13119) *********************** 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 233 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 212 time to evaluate : 1.048 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 TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 125 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8567 (t80) REVERT: A 133 LYS cc_start: 0.9120 (ttpp) cc_final: 0.8913 (tptp) REVERT: A 167 LEU cc_start: 0.8941 (tp) cc_final: 0.8690 (tt) REVERT: A 208 MET cc_start: 0.7534 (mtm) cc_final: 0.6655 (mtm) REVERT: A 387 PHE cc_start: 0.8769 (t80) cc_final: 0.8455 (t80) REVERT: A 400 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8113 (mm110) REVERT: A 694 PHE cc_start: 0.8080 (m-80) cc_final: 0.7816 (m-80) REVERT: A 717 TRP cc_start: 0.8731 (m100) cc_final: 0.8506 (t60) REVERT: A 759 MET cc_start: 0.8627 (ppp) cc_final: 0.8257 (tmm) REVERT: A 767 MET cc_start: 0.6770 (mtt) cc_final: 0.6346 (mmt) REVERT: A 778 ILE cc_start: 0.9349 (mm) cc_final: 0.9141 (tt) REVERT: A 1364 ASP cc_start: 0.8161 (m-30) cc_final: 0.7807 (t0) REVERT: A 1483 MET cc_start: 0.8003 (tpp) cc_final: 0.7688 (tpp) REVERT: A 1488 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.6809 (m-80) REVERT: A 1598 LEU cc_start: 0.9563 (mp) cc_final: 0.8915 (mm) REVERT: A 1704 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7582 (t80) outliers start: 21 outliers final: 4 residues processed: 221 average time/residue: 0.1723 time to fit residues: 57.1276 Evaluate side-chains 199 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 192 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 707 PHE 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 1488 TYR 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 38 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 107 optimal weight: 0.0770 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 339 ASN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.124695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.090206 restraints weight = 29734.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.093521 restraints weight = 13373.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.095563 restraints weight = 8711.085| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9676 Z= 0.141 Angle : 0.774 14.081 13135 Z= 0.381 Chirality : 0.046 0.238 1537 Planarity : 0.004 0.045 1580 Dihedral : 11.265 145.988 1781 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.79 % Allowed : 18.39 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.25), residues: 1130 helix: 0.84 (0.19), residues: 785 sheet: None (None), residues: 0 loop : -2.15 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 319 HIS 0.005 0.001 HIS A1358 PHE 0.024 0.001 PHE A1246 TYR 0.017 0.001 TYR A 345 ARG 0.004 0.001 ARG A1191 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 2) link_NAG-ASN : angle 2.81978 ( 6) hydrogen bonds : bond 0.03965 ( 596) hydrogen bonds : angle 4.79360 ( 1725) SS BOND : bond 0.00093 ( 5) SS BOND : angle 0.69263 ( 10) covalent geometry : bond 0.00306 ( 9669) covalent geometry : angle 0.77218 (13119) *********************** 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 228 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.978 Fit side-chains 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 TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 125 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8573 (t80) REVERT: A 133 LYS cc_start: 0.9135 (ttpp) cc_final: 0.8917 (tptp) REVERT: A 208 MET cc_start: 0.7469 (mtm) cc_final: 0.6537 (mtm) REVERT: A 345 TYR cc_start: 0.8419 (m-80) cc_final: 0.8132 (m-80) REVERT: A 363 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.7776 (tmm) REVERT: A 387 PHE cc_start: 0.8777 (t80) cc_final: 0.8455 (t80) REVERT: A 400 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8034 (mm110) REVERT: A 694 PHE cc_start: 0.8090 (m-80) cc_final: 0.7857 (m-80) REVERT: A 717 TRP cc_start: 0.8740 (m100) cc_final: 0.8506 (t60) REVERT: A 759 MET cc_start: 0.8555 (ppp) cc_final: 0.8130 (tmm) REVERT: A 767 MET cc_start: 0.6758 (mtt) cc_final: 0.6393 (mmt) REVERT: A 778 ILE cc_start: 0.9419 (mm) cc_final: 0.9109 (tt) REVERT: A 1364 ASP cc_start: 0.8080 (m-30) cc_final: 0.7741 (t0) REVERT: A 1488 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.6843 (m-80) REVERT: A 1601 MET cc_start: 0.8022 (pmm) cc_final: 0.7811 (tpt) REVERT: A 1609 LEU cc_start: 0.8982 (mm) cc_final: 0.8383 (pp) REVERT: A 1662 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7543 (mm-30) REVERT: A 1704 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7555 (t80) outliers start: 18 outliers final: 7 residues processed: 218 average time/residue: 0.1775 time to fit residues: 58.3242 Evaluate side-chains 199 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 188 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 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 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 39 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** 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 = 0.3872 r_free = 0.3872 target = 0.123362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.088654 restraints weight = 28944.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.091843 restraints weight = 13209.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.093831 restraints weight = 8560.778| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 9676 Z= 0.146 Angle : 0.782 13.979 13135 Z= 0.389 Chirality : 0.046 0.262 1537 Planarity : 0.004 0.049 1580 Dihedral : 10.914 151.926 1781 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.99 % Allowed : 20.18 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.25), residues: 1130 helix: 0.84 (0.19), residues: 786 sheet: None (None), residues: 0 loop : -2.20 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 319 HIS 0.006 0.001 HIS A1403 PHE 0.025 0.002 PHE A1631 TYR 0.024 0.001 TYR A1473 ARG 0.004 0.000 ARG A1191 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 2) link_NAG-ASN : angle 2.58648 ( 6) hydrogen bonds : bond 0.03973 ( 596) hydrogen bonds : angle 4.82663 ( 1725) SS BOND : bond 0.00111 ( 5) SS BOND : angle 0.66340 ( 10) covalent geometry : bond 0.00330 ( 9669) covalent geometry : angle 0.78056 (13119) *********************** 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 215 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 1.074 Fit side-chains 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. revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8508 (t80) REVERT: A 218 PHE cc_start: 0.8691 (t80) cc_final: 0.8473 (t80) REVERT: A 363 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.7867 (tmm) REVERT: A 387 PHE cc_start: 0.8844 (t80) cc_final: 0.8465 (t80) REVERT: A 694 PHE cc_start: 0.8067 (m-80) cc_final: 0.7811 (m-80) REVERT: A 717 TRP cc_start: 0.8723 (m100) cc_final: 0.8485 (t60) REVERT: A 759 MET cc_start: 0.8598 (ppp) cc_final: 0.8177 (tmm) REVERT: A 767 MET cc_start: 0.6858 (mtt) cc_final: 0.6422 (mmt) REVERT: A 778 ILE cc_start: 0.9360 (mm) cc_final: 0.9147 (tt) REVERT: A 822 ASP cc_start: 0.8355 (t0) cc_final: 0.8073 (t70) REVERT: A 1364 ASP cc_start: 0.8086 (m-30) cc_final: 0.7718 (t0) REVERT: A 1488 TYR cc_start: 0.7490 (OUTLIER) cc_final: 0.6940 (m-80) REVERT: A 1609 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8283 (pp) REVERT: A 1662 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7497 (mm-30) REVERT: A 1704 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7563 (t80) outliers start: 20 outliers final: 10 residues processed: 203 average time/residue: 0.2067 time to fit residues: 63.5443 Evaluate side-chains 201 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 390 ILE Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 762 VAL 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 1609 LEU Chi-restraints excluded: chain A residue 1684 MET 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 40 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 7 optimal weight: 0.0570 chunk 5 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3869 r_free = 0.3869 target = 0.122821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.086847 restraints weight = 42284.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.090507 restraints weight = 16204.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.092804 restraints weight = 9599.786| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9676 Z= 0.172 Angle : 0.799 13.903 13135 Z= 0.394 Chirality : 0.046 0.235 1537 Planarity : 0.004 0.046 1580 Dihedral : 10.675 155.555 1781 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.29 % Allowed : 20.97 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1130 helix: 0.88 (0.19), residues: 786 sheet: None (None), residues: 0 loop : -2.09 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1382 HIS 0.007 0.001 HIS A1358 PHE 0.026 0.002 PHE A1246 TYR 0.015 0.001 TYR A 345 ARG 0.005 0.000 ARG A1191 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 2) link_NAG-ASN : angle 2.47306 ( 6) hydrogen bonds : bond 0.03945 ( 596) hydrogen bonds : angle 4.83728 ( 1725) SS BOND : bond 0.00110 ( 5) SS BOND : angle 0.70569 ( 10) covalent geometry : bond 0.00400 ( 9669) covalent geometry : angle 0.79766 (13119) *********************** 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: 23 poor density : 202 time to evaluate : 1.013 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: A 124 ILE cc_start: 0.9558 (mt) cc_final: 0.9268 (tp) REVERT: A 125 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8671 (t80) REVERT: A 133 LYS cc_start: 0.9128 (tptp) cc_final: 0.8900 (tttt) REVERT: A 363 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8027 (tmm) REVERT: A 387 PHE cc_start: 0.8751 (t80) cc_final: 0.8389 (t80) REVERT: A 694 PHE cc_start: 0.8025 (m-80) cc_final: 0.7734 (m-80) REVERT: A 717 TRP cc_start: 0.8707 (m100) cc_final: 0.8479 (t60) REVERT: A 759 MET cc_start: 0.8553 (ppp) cc_final: 0.8127 (tmm) REVERT: A 767 MET cc_start: 0.6925 (mtt) cc_final: 0.6498 (mmt) REVERT: A 778 ILE cc_start: 0.9336 (mm) cc_final: 0.9080 (tt) REVERT: A 822 ASP cc_start: 0.8389 (t0) cc_final: 0.8101 (t70) REVERT: A 1364 ASP cc_start: 0.8054 (m-30) cc_final: 0.7717 (t0) REVERT: A 1407 MET cc_start: 0.8645 (mmp) cc_final: 0.8358 (mmt) REVERT: A 1488 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.6855 (m-80) REVERT: A 1609 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8298 (pp) REVERT: A 1662 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7544 (mm-30) REVERT: A 1704 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7531 (t80) outliers start: 23 outliers final: 14 residues processed: 213 average time/residue: 0.1923 time to fit residues: 63.4463 Evaluate side-chains 209 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 839 SER 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 1546 PHE Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1684 MET 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 37 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3822 r_free = 0.3822 target = 0.120567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.083913 restraints weight = 39895.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.087382 restraints weight = 15973.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.089562 restraints weight = 9742.236| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3334 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= 0.152 Angle : 0.811 15.167 13135 Z= 0.396 Chirality : 0.046 0.235 1537 Planarity : 0.004 0.049 1580 Dihedral : 10.244 154.735 1781 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.25), residues: 1130 helix: 0.89 (0.19), residues: 787 sheet: None (None), residues: 0 loop : -2.09 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1382 HIS 0.006 0.001 HIS A1358 PHE 0.027 0.001 PHE A1246 TYR 0.023 0.001 TYR A1473 ARG 0.005 0.000 ARG A1191 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 2) link_NAG-ASN : angle 2.24736 ( 6) hydrogen bonds : bond 0.03806 ( 596) hydrogen bonds : angle 4.80602 ( 1725) SS BOND : bond 0.00113 ( 5) SS BOND : angle 0.65279 ( 10) covalent geometry : bond 0.00347 ( 9669) covalent geometry : angle 0.80957 (13119) *********************** 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 220 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 1.646 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: A 124 ILE cc_start: 0.9547 (mt) cc_final: 0.9261 (tp) REVERT: A 125 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8656 (t80) REVERT: A 218 PHE cc_start: 0.8672 (t80) cc_final: 0.8446 (t80) REVERT: A 363 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8230 (tmm) REVERT: A 387 PHE cc_start: 0.8780 (t80) cc_final: 0.8394 (t80) REVERT: A 694 PHE cc_start: 0.8094 (m-80) cc_final: 0.7822 (m-80) REVERT: A 717 TRP cc_start: 0.8750 (m100) cc_final: 0.8508 (t60) REVERT: A 759 MET cc_start: 0.8533 (ppp) cc_final: 0.8115 (tmm) REVERT: A 767 MET cc_start: 0.7004 (mtt) cc_final: 0.6491 (mmt) REVERT: A 778 ILE cc_start: 0.9309 (mm) cc_final: 0.9044 (tt) REVERT: A 822 ASP cc_start: 0.8388 (t0) cc_final: 0.8081 (t70) REVERT: A 855 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8086 (t0) REVERT: A 1364 ASP cc_start: 0.8092 (m-30) cc_final: 0.7761 (t0) REVERT: A 1483 MET cc_start: 0.8016 (tpp) cc_final: 0.7811 (tpp) REVERT: A 1488 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.6905 (m-80) REVERT: A 1609 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8207 (pp) REVERT: A 1662 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7552 (mm-30) REVERT: A 1704 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7594 (t80) outliers start: 23 outliers final: 13 residues processed: 210 average time/residue: 0.2060 time to fit residues: 66.4414 Evaluate side-chains 209 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 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 855 ASN 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 1488 TYR Chi-restraints excluded: chain A residue 1546 PHE Chi-restraints excluded: chain A residue 1609 LEU 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 96 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3812 r_free = 0.3812 target = 0.120108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.084750 restraints weight = 40768.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.088735 restraints weight = 15988.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.090123 restraints weight = 8583.619| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9676 Z= 0.159 Angle : 0.824 16.768 13135 Z= 0.399 Chirality : 0.046 0.235 1537 Planarity : 0.004 0.046 1580 Dihedral : 9.861 144.769 1781 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.19 % Allowed : 21.77 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1130 helix: 0.88 (0.19), residues: 786 sheet: None (None), residues: 0 loop : -2.08 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1382 HIS 0.006 0.001 HIS A1358 PHE 0.029 0.002 PHE A1246 TYR 0.013 0.001 TYR A 345 ARG 0.004 0.000 ARG A1191 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 2) link_NAG-ASN : angle 2.13525 ( 6) hydrogen bonds : bond 0.03831 ( 596) hydrogen bonds : angle 4.80351 ( 1725) SS BOND : bond 0.00114 ( 5) SS BOND : angle 0.66271 ( 10) covalent geometry : bond 0.00364 ( 9669) covalent geometry : angle 0.82292 (13119) *********************** 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 219 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 0.948 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: A 124 ILE cc_start: 0.9570 (mt) cc_final: 0.9301 (tp) REVERT: A 125 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8713 (t80) REVERT: A 363 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8298 (tmm) REVERT: A 387 PHE cc_start: 0.8824 (t80) cc_final: 0.8585 (t80) REVERT: A 694 PHE cc_start: 0.8203 (m-80) cc_final: 0.7917 (m-80) REVERT: A 717 TRP cc_start: 0.8821 (m100) cc_final: 0.8550 (t60) REVERT: A 759 MET cc_start: 0.8505 (ppp) cc_final: 0.8085 (tmm) REVERT: A 767 MET cc_start: 0.7028 (mtt) cc_final: 0.6528 (mmt) REVERT: A 778 ILE cc_start: 0.9309 (mm) cc_final: 0.9046 (tt) REVERT: A 822 ASP cc_start: 0.8414 (t0) cc_final: 0.8072 (t70) REVERT: A 855 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8148 (t0) REVERT: A 1364 ASP cc_start: 0.8166 (m-30) cc_final: 0.7860 (t0) REVERT: A 1483 MET cc_start: 0.8083 (tpp) cc_final: 0.7863 (tpp) REVERT: A 1488 TYR cc_start: 0.7601 (OUTLIER) cc_final: 0.6979 (m-80) REVERT: A 1609 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8222 (pp) REVERT: A 1662 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7618 (mm-30) REVERT: A 1704 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7678 (t80) outliers start: 22 outliers final: 14 residues processed: 208 average time/residue: 0.1701 time to fit residues: 53.8295 Evaluate side-chains 211 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 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 839 SER Chi-restraints excluded: chain A residue 855 ASN 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 1357 VAL Chi-restraints excluded: chain A residue 1488 TYR Chi-restraints excluded: chain A residue 1609 LEU 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 108 optimal weight: 0.0030 chunk 89 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 86 optimal weight: 0.0060 chunk 48 optimal weight: 0.0370 chunk 9 optimal weight: 0.9980 overall best weight: 0.2884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3832 r_free = 0.3832 target = 0.121551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.087827 restraints weight = 23901.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.090691 restraints weight = 11946.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.092440 restraints weight = 8200.280| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 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 = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9676 Z= 0.134 Angle : 0.815 15.386 13135 Z= 0.394 Chirality : 0.046 0.282 1537 Planarity : 0.004 0.050 1580 Dihedral : 9.223 121.360 1781 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.79 % Allowed : 22.37 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.25), residues: 1130 helix: 0.88 (0.19), residues: 787 sheet: None (None), residues: 0 loop : -2.11 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 823 HIS 0.004 0.001 HIS A1440 PHE 0.030 0.001 PHE A1246 TYR 0.020 0.001 TYR A1473 ARG 0.004 0.000 ARG A1585 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 2) link_NAG-ASN : angle 1.82649 ( 6) hydrogen bonds : bond 0.03748 ( 596) hydrogen bonds : angle 4.74677 ( 1725) SS BOND : bond 0.00095 ( 5) SS BOND : angle 0.59978 ( 10) covalent geometry : bond 0.00282 ( 9669) covalent geometry : angle 0.81403 (13119) *********************** 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 229 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 1.054 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: 0.9523 (mt) cc_final: 0.9231 (tp) REVERT: A 125 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8618 (t80) REVERT: A 363 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8359 (tmm) REVERT: A 387 PHE cc_start: 0.8679 (t80) cc_final: 0.8280 (t80) REVERT: A 694 PHE cc_start: 0.8037 (m-80) cc_final: 0.7796 (m-80) REVERT: A 717 TRP cc_start: 0.8784 (m100) cc_final: 0.8538 (t60) REVERT: A 759 MET cc_start: 0.8504 (ppp) cc_final: 0.8023 (tmm) REVERT: A 767 MET cc_start: 0.6891 (mtt) cc_final: 0.6417 (mmt) REVERT: A 778 ILE cc_start: 0.9246 (mm) cc_final: 0.9019 (tt) REVERT: A 822 ASP cc_start: 0.8297 (t0) cc_final: 0.7824 (t70) REVERT: A 1185 ILE cc_start: 0.9428 (mt) cc_final: 0.9228 (mt) REVERT: A 1364 ASP cc_start: 0.8104 (m-30) cc_final: 0.7765 (t0) REVERT: A 1488 TYR cc_start: 0.7507 (OUTLIER) cc_final: 0.6863 (m-80) REVERT: A 1533 GLU cc_start: 0.8777 (pp20) cc_final: 0.8571 (pp20) REVERT: A 1662 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7458 (mm-30) REVERT: A 1704 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7587 (t80) outliers start: 18 outliers final: 9 residues processed: 219 average time/residue: 0.1761 time to fit residues: 57.1381 Evaluate side-chains 210 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 409 HIS Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1357 VAL 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 40 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN A 761 ASN A 820 GLN A 850 ASN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.120395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.084859 restraints weight = 37352.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.088278 restraints weight = 15330.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.090326 restraints weight = 9398.765| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9676 Z= 0.148 Angle : 0.872 15.672 13135 Z= 0.423 Chirality : 0.046 0.282 1537 Planarity : 0.004 0.048 1580 Dihedral : 8.988 104.270 1781 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.25), residues: 1130 helix: 0.78 (0.19), residues: 787 sheet: None (None), residues: 0 loop : -2.10 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1382 HIS 0.004 0.001 HIS A1358 PHE 0.032 0.002 PHE A1246 TYR 0.012 0.001 TYR A 345 ARG 0.003 0.000 ARG A1191 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 2) link_NAG-ASN : angle 1.85325 ( 6) hydrogen bonds : bond 0.03886 ( 596) hydrogen bonds : angle 4.81376 ( 1725) SS BOND : bond 0.00104 ( 5) SS BOND : angle 0.58467 ( 10) covalent geometry : bond 0.00326 ( 9669) covalent geometry : angle 0.87193 (13119) ********************** 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 219 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 1.161 Fit side-chains 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. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.9536 (mt) cc_final: 0.9249 (tp) REVERT: A 125 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8643 (t80) REVERT: A 363 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8405 (tmm) REVERT: A 387 PHE cc_start: 0.8727 (t80) cc_final: 0.8362 (t80) REVERT: A 400 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8008 (mm-40) REVERT: A 694 PHE cc_start: 0.8119 (m-80) cc_final: 0.7852 (m-80) REVERT: A 717 TRP cc_start: 0.8817 (m100) cc_final: 0.8550 (t60) REVERT: A 759 MET cc_start: 0.8506 (ppp) cc_final: 0.8028 (tmm) REVERT: A 767 MET cc_start: 0.6871 (mtt) cc_final: 0.6456 (mmt) REVERT: A 778 ILE cc_start: 0.9295 (mm) cc_final: 0.9023 (tt) REVERT: A 822 ASP cc_start: 0.8327 (t0) cc_final: 0.7972 (t70) REVERT: A 855 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8174 (t0) REVERT: A 1185 ILE cc_start: 0.9449 (mt) cc_final: 0.9153 (mt) REVERT: A 1364 ASP cc_start: 0.8136 (m-30) cc_final: 0.7796 (t0) REVERT: A 1386 MET cc_start: 0.9066 (ttp) cc_final: 0.8850 (ttp) REVERT: A 1407 MET cc_start: 0.8920 (mmt) cc_final: 0.8709 (mmp) REVERT: A 1488 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.6898 (m-80) REVERT: A 1601 MET cc_start: 0.8198 (pmm) cc_final: 0.7721 (tpt) REVERT: A 1609 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.7971 (tt) REVERT: A 1662 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7497 (mm-30) REVERT: A 1704 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7561 (t80) outliers start: 18 outliers final: 9 residues processed: 209 average time/residue: 0.1924 time to fit residues: 60.2656 Evaluate side-chains 211 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 707 PHE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1357 VAL Chi-restraints excluded: chain A residue 1488 TYR Chi-restraints excluded: chain A residue 1609 LEU 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 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 11 optimal weight: 0.0970 chunk 105 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 chunk 12 optimal weight: 0.0980 chunk 37 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 ASN A 820 GLN A 850 ASN ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.121211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.086415 restraints weight = 31207.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.089660 restraints weight = 13884.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.091627 restraints weight = 8903.865| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 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 = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9676 Z= 0.143 Angle : 0.855 15.306 13135 Z= 0.415 Chirality : 0.046 0.272 1537 Planarity : 0.004 0.050 1580 Dihedral : 8.691 83.660 1781 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.59 % Allowed : 23.36 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1130 helix: 0.77 (0.19), residues: 787 sheet: None (None), residues: 0 loop : -2.10 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 823 HIS 0.004 0.001 HIS A1440 PHE 0.033 0.001 PHE A1246 TYR 0.019 0.001 TYR A1473 ARG 0.004 0.000 ARG A 184 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 2) link_NAG-ASN : angle 1.78915 ( 6) hydrogen bonds : bond 0.03847 ( 596) hydrogen bonds : angle 4.79723 ( 1725) SS BOND : bond 0.00088 ( 5) SS BOND : angle 0.59515 ( 10) covalent geometry : bond 0.00311 ( 9669) covalent geometry : angle 0.85500 (13119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3901.13 seconds wall clock time: 70 minutes 8.85 seconds (4208.85 seconds total)