Starting phenix.real_space_refine on Mon Jun 9 05:01:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wlk_32586/06_2025/7wlk_32586.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wlk_32586/06_2025/7wlk_32586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wlk_32586/06_2025/7wlk_32586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wlk_32586/06_2025/7wlk_32586.map" model { file = "/net/cci-nas-00/data/ceres_data/7wlk_32586/06_2025/7wlk_32586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wlk_32586/06_2025/7wlk_32586.cif" } resolution = 3.6 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 1 5.49 5 S 78 5.16 5 C 6283 2.51 5 N 1503 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9461 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: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 350 Unusual residues: {' CA': 2, '3PE': 6, '7TB': 1, 'NAG': 2, 'Y01': 6} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'Y01:plan-2': 1, '3PE:plan-1': 5, '3PE:plan-2': 5, 'Y01:plan-1': 3} Unresolved non-hydrogen planarities: 50 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: 11.16, per 1000 atoms: 1.18 Number of scatterers: 9461 At special positions: 0 Unit cell: (112.32, 124.8, 109.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 78 16.00 P 1 15.00 O 1594 8.00 N 1503 7.00 C 6283 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=1, symmetry=0 Links applied NAG-ASN " NAG A2311 " - " ASN A1345 " " NAG A2313 " - " ASN A1342 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 2.4 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: 53 helices and 2 sheets defined 76.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 66 through 77 removed outlier: 3.879A pdb=" N CYS A 72 " --> pdb=" O PRO A 68 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N MET A 75 " --> pdb=" O TRP A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 98 removed outlier: 3.691A pdb=" N GLU A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 138 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 148 through 170 Processing helix chain 'A' and resid 177 through 190 Proline residue: A 185 - end of helix removed outlier: 3.563A pdb=" N ILE A 189 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 206 Processing helix chain 'A' and resid 209 through 232 removed outlier: 3.600A pdb=" N PHE A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 232 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.522A pdb=" N ASN A 237 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.555A 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 343 through 355 Processing helix chain 'A' and resid 358 through 370 removed outlier: 3.590A pdb=" N ILE A 362 " --> pdb=" O GLY A 358 " (cutoff:3.500A) 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 removed outlier: 3.832A pdb=" N MET A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 638 removed outlier: 3.924A pdb=" N LYS A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 634 " --> pdb=" O ARG A 630 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 660 removed outlier: 4.232A pdb=" N GLU A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.512A pdb=" N LEU A 691 " --> pdb=" O MET A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 702 removed outlier: 4.431A pdb=" N ASN A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 721 removed outlier: 3.723A pdb=" N ILE A 706 " --> pdb=" O ASN A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 731 through 744 removed outlier: 3.641A pdb=" N LEU A 735 " --> pdb=" O THR A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 785 removed outlier: 3.531A pdb=" N ARG A 749 " --> pdb=" O MET A 745 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASN A 761 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 763 " --> pdb=" O MET A 759 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N THR A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.842A 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: 3.678A 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: 4.032A pdb=" N PHE A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 866 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: 3.733A 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 1289 through 1304 removed outlier: 3.684A 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 1366 through 1378 Processing helix chain 'A' and resid 1381 through 1392 removed outlier: 3.619A pdb=" N ILE A1385 " --> pdb=" O GLY A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1406 No H-bonds generated for 'chain 'A' and resid 1404 through 1406' Processing helix chain 'A' and resid 1407 through 1462 removed outlier: 3.718A pdb=" N LEU A1415 " --> pdb=" O PHE A1411 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A1440 " --> pdb=" O LYS A1436 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA A1443 " --> pdb=" O GLN A1439 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A1444 " --> pdb=" O HIS A1440 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A1451 " --> pdb=" O ARG A1447 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A1454 " --> pdb=" O GLU A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1505 removed outlier: 4.109A pdb=" N ASP A1490 " --> pdb=" O SER A1486 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A1491 " --> pdb=" O HIS A1487 " (cutoff:3.500A) removed outlier: 4.434A 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: 3.951A pdb=" N PHE A1546 " --> pdb=" O GLY A1542 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A1547 " --> pdb=" O LEU A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1575 removed outlier: 3.700A pdb=" N ASN A1574 " --> pdb=" O GLU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1591 removed outlier: 3.966A pdb=" N ILE A1584 " --> pdb=" O ASN A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1600 removed outlier: 3.648A pdb=" N LYS A1597 " --> pdb=" O ARG A1594 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A1600 " --> 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 1676 removed outlier: 3.963A pdb=" N THR A1670 " --> pdb=" O MET A1666 " (cutoff:3.500A) Processing helix chain 'A' and resid 1679 through 1688 Processing helix chain 'A' and resid 1696 through 1700 Processing helix chain 'A' and resid 1701 through 1738 Proline residue: A1707 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 238 through 239 removed outlier: 3.705A pdb=" N ARG A 238 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 3.659A 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 1334 612 hydrogen bonds defined for protein. 1752 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: 2.91 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1432 1.31 - 1.43: 2565 1.43 - 1.56: 5473 1.56 - 1.69: 79 1.69 - 1.81: 127 Bond restraints: 9676 Sorted by residual: bond pdb=" C21 3PE A2302 " pdb=" O21 3PE A2302 " ideal model delta sigma weight residual 1.316 1.461 -0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" C31 3PE A2302 " pdb=" O31 3PE A2302 " ideal model delta sigma weight residual 1.331 1.467 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" C32 7TB A2301 " pdb=" N07 7TB A2301 " ideal model delta sigma weight residual 1.366 1.494 -0.128 2.00e-02 2.50e+03 4.11e+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 A2305 " pdb=" C32 3PE A2305 " ideal model delta sigma weight residual 1.504 1.603 -0.099 2.00e-02 2.50e+03 2.47e+01 ... (remaining 9671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 12779 2.87 - 5.75: 301 5.75 - 8.62: 31 8.62 - 11.50: 7 11.50 - 14.37: 1 Bond angle restraints: 13119 Sorted by residual: angle pdb=" N ALA A 176 " pdb=" CA ALA A 176 " pdb=" C ALA A 176 " ideal model delta sigma weight residual 114.39 106.32 8.07 1.45e+00 4.76e-01 3.10e+01 angle pdb=" N ILE A 177 " pdb=" CA ILE A 177 " pdb=" C ILE A 177 " ideal model delta sigma weight residual 113.39 106.33 7.06 1.47e+00 4.63e-01 2.31e+01 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 2.29e+01 angle pdb=" N ILE A1412 " pdb=" CA ILE A1412 " pdb=" C ILE A1412 " ideal model delta sigma weight residual 111.81 108.64 3.17 8.60e-01 1.35e+00 1.35e+01 angle pdb=" C TYR A1354 " pdb=" N ARG A1355 " pdb=" CA ARG A1355 " ideal model delta sigma weight residual 121.54 128.47 -6.93 1.91e+00 2.74e-01 1.32e+01 ... (remaining 13114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.02: 5616 24.02 - 48.04: 381 48.04 - 72.06: 62 72.06 - 96.09: 10 96.09 - 120.11: 1 Dihedral angle restraints: 6070 sinusoidal: 2751 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 93.00 175.52 -82.52 1 1.00e+01 1.00e-02 8.35e+01 dihedral pdb=" CA ASN A 332 " pdb=" C ASN A 332 " pdb=" N PRO A 333 " pdb=" CA PRO A 333 " ideal model delta harmonic sigma weight residual -180.00 -151.17 -28.83 0 5.00e+00 4.00e-02 3.32e+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 -41.98 -44.02 1 1.00e+01 1.00e-02 2.70e+01 ... (remaining 6067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1452 0.106 - 0.212: 63 0.212 - 0.318: 11 0.318 - 0.424: 3 0.424 - 0.531: 6 Chirality restraints: 1535 Sorted by residual: chirality pdb=" CBG Y01 A2312 " pdb=" CAQ Y01 A2312 " pdb=" CBD Y01 A2312 " pdb=" CBI Y01 A2312 " both_signs ideal model delta sigma weight residual False -2.33 -2.86 0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" CBG Y01 A2314 " pdb=" CAQ Y01 A2314 " pdb=" CBD Y01 A2314 " pdb=" CBI Y01 A2314 " both_signs ideal model delta sigma weight residual False -2.33 -2.84 0.50 2.00e-01 2.50e+01 6.35e+00 chirality pdb=" CBG Y01 A2309 " pdb=" CAQ Y01 A2309 " pdb=" CBD Y01 A2309 " pdb=" CBI Y01 A2309 " both_signs ideal model delta sigma weight residual False -2.33 -2.83 0.50 2.00e-01 2.50e+01 6.20e+00 ... (remaining 1532 not shown) Planarity restraints: 1583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1626 " -0.026 2.00e-02 2.50e+03 2.02e-02 7.13e+00 pdb=" CG PHE A1626 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A1626 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A1626 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A1626 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A1626 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A1626 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1616 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO A1617 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A1617 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1617 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 702 " 0.033 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO A 703 " -0.088 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 ... (remaining 1580 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 39 2.46 - 3.07: 6950 3.07 - 3.68: 14079 3.68 - 4.29: 20647 4.29 - 4.90: 33706 Nonbonded interactions: 75421 Sorted by model distance: nonbonded pdb=" CD1 LEU A 861 " pdb=" CD2 LEU A1423 " model vdw 1.853 3.880 nonbonded pdb=" OG SER A1238 " pdb=" OD1 ASN A1241 " model vdw 2.170 3.040 nonbonded pdb=" O HIS A1481 " pdb=" OG1 THR A1485 " model vdw 2.182 3.040 nonbonded pdb=" N GLN A1164 " pdb=" O VAL A1224 " model vdw 2.215 3.120 nonbonded pdb=" OE2 GLU A 660 " pdb=" NE2 GLN A1326 " model vdw 2.221 3.120 ... (remaining 75416 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 39.360 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: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 32.810 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.010 0.145 9684 Z= 0.490 Angle : 0.991 14.370 13135 Z= 0.482 Chirality : 0.064 0.531 1535 Planarity : 0.004 0.052 1581 Dihedral : 15.420 120.107 3905 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % 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: 0.27 (0.25), residues: 1130 helix: 0.91 (0.18), residues: 761 sheet: None (None), residues: 0 loop : -1.31 (0.35), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 359 HIS 0.006 0.001 HIS A1358 PHE 0.045 0.002 PHE A1626 TYR 0.011 0.002 TYR A1333 ARG 0.008 0.001 ARG A 238 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 2) link_NAG-ASN : angle 3.26184 ( 6) hydrogen bonds : bond 0.14779 ( 612) hydrogen bonds : angle 5.91027 ( 1752) SS BOND : bond 0.00173 ( 5) SS BOND : angle 0.94902 ( 10) covalent geometry : bond 0.01021 ( 9676) covalent geometry : angle 0.98873 (13119) Misc. bond : bond 0.00148 ( 1) *********************** 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 205 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 1.042 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 648 MET cc_start: 0.6302 (mmm) cc_final: 0.5671 (ppp) REVERT: A 756 MET cc_start: 0.7099 (tmm) cc_final: 0.6755 (tmm) REVERT: A 1441 GLN cc_start: 0.7746 (tp-100) cc_final: 0.7315 (tp-100) REVERT: A 1487 HIS cc_start: 0.7671 (m90) cc_final: 0.7388 (m90) REVERT: A 1497 ILE cc_start: 0.9012 (mm) cc_final: 0.8745 (mm) REVERT: A 1592 ILE cc_start: 0.9159 (tp) cc_final: 0.8883 (tp) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.1768 time to fit residues: 54.2986 Evaluate side-chains 154 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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: 1.9990 chunk 85 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 0.0270 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 ASN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1523 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.149571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115170 restraints weight = 21423.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118740 restraints weight = 9936.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.120957 restraints weight = 6456.181| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9684 Z= 0.146 Angle : 0.659 9.734 13135 Z= 0.338 Chirality : 0.042 0.247 1535 Planarity : 0.004 0.042 1581 Dihedral : 10.677 59.426 1785 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.49 % Allowed : 9.34 % Favored : 89.17 % 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: 0.61 (0.25), residues: 1130 helix: 1.19 (0.18), residues: 785 sheet: None (None), residues: 0 loop : -1.41 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1680 HIS 0.005 0.001 HIS A1358 PHE 0.040 0.002 PHE A1626 TYR 0.014 0.001 TYR A 364 ARG 0.005 0.001 ARG A 238 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 2) link_NAG-ASN : angle 2.70301 ( 6) hydrogen bonds : bond 0.04431 ( 612) hydrogen bonds : angle 4.68923 ( 1752) SS BOND : bond 0.00267 ( 5) SS BOND : angle 0.96659 ( 10) covalent geometry : bond 0.00322 ( 9676) covalent geometry : angle 0.65583 (13119) Misc. bond : bond 0.00017 ( 1) *********************** 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 197 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 1.019 Fit side-chains TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 159 MET cc_start: 0.7907 (mmm) cc_final: 0.7496 (mmp) REVERT: A 364 TYR cc_start: 0.8548 (m-80) cc_final: 0.8226 (m-80) REVERT: A 386 SER cc_start: 0.8896 (p) cc_final: 0.8475 (t) REVERT: A 648 MET cc_start: 0.6265 (mmm) cc_final: 0.5465 (tmm) REVERT: A 683 PHE cc_start: 0.7645 (m-80) cc_final: 0.7218 (m-80) REVERT: A 756 MET cc_start: 0.7024 (tmm) cc_final: 0.6669 (tmm) REVERT: A 1249 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7655 (t80) REVERT: A 1497 ILE cc_start: 0.9033 (mm) cc_final: 0.8724 (mm) REVERT: A 1592 ILE cc_start: 0.9042 (tp) cc_final: 0.8769 (tp) outliers start: 15 outliers final: 8 residues processed: 185 average time/residue: 0.1839 time to fit residues: 50.2019 Evaluate side-chains 166 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 359 TRP Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 1249 PHE Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1567 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 20 optimal weight: 0.0670 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 GLN ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.150403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.118637 restraints weight = 27835.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122937 restraints weight = 12677.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122731 restraints weight = 8511.628| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9684 Z= 0.136 Angle : 0.630 9.649 13135 Z= 0.318 Chirality : 0.041 0.247 1535 Planarity : 0.004 0.038 1581 Dihedral : 10.038 59.844 1785 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.79 % Allowed : 11.23 % Favored : 86.98 % 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: 0.81 (0.25), residues: 1130 helix: 1.36 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -1.32 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 359 HIS 0.004 0.001 HIS A1358 PHE 0.034 0.001 PHE A1626 TYR 0.010 0.001 TYR A 364 ARG 0.008 0.001 ARG A1275 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 2) link_NAG-ASN : angle 3.05526 ( 6) hydrogen bonds : bond 0.03936 ( 612) hydrogen bonds : angle 4.49157 ( 1752) SS BOND : bond 0.00153 ( 5) SS BOND : angle 0.67155 ( 10) covalent geometry : bond 0.00304 ( 9676) covalent geometry : angle 0.62700 (13119) Misc. bond : bond 0.00028 ( 1) *********************** 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 191 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 1.176 Fit side-chains TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 364 TYR cc_start: 0.8670 (m-80) cc_final: 0.8291 (m-80) REVERT: A 386 SER cc_start: 0.8911 (p) cc_final: 0.8468 (t) REVERT: A 648 MET cc_start: 0.6401 (mmm) cc_final: 0.5507 (tmm) REVERT: A 683 PHE cc_start: 0.7595 (m-80) cc_final: 0.7295 (m-80) REVERT: A 756 MET cc_start: 0.7006 (tmm) cc_final: 0.6628 (tmm) REVERT: A 1237 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7448 (ttm110) REVERT: A 1249 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7743 (t80) REVERT: A 1497 ILE cc_start: 0.9017 (mm) cc_final: 0.8747 (mm) REVERT: A 1550 ARG cc_start: 0.7047 (ttm170) cc_final: 0.4834 (ptt90) REVERT: A 1592 ILE cc_start: 0.9087 (tp) cc_final: 0.8809 (tp) outliers start: 18 outliers final: 14 residues processed: 178 average time/residue: 0.1887 time to fit residues: 49.4231 Evaluate side-chains 169 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 359 TRP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 1237 ARG Chi-restraints excluded: chain A residue 1249 PHE Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1487 HIS Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1671 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.149396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118817 restraints weight = 33010.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.120827 restraints weight = 15412.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121314 restraints weight = 12112.759| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9684 Z= 0.148 Angle : 0.636 9.687 13135 Z= 0.320 Chirality : 0.042 0.288 1535 Planarity : 0.004 0.036 1581 Dihedral : 9.798 59.502 1785 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.29 % Allowed : 11.13 % Favored : 86.58 % 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: 0.83 (0.25), residues: 1130 helix: 1.40 (0.18), residues: 780 sheet: None (None), residues: 0 loop : -1.39 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 359 HIS 0.007 0.001 HIS A1481 PHE 0.039 0.002 PHE A1713 TYR 0.014 0.001 TYR A1633 ARG 0.007 0.000 ARG A1275 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 2) link_NAG-ASN : angle 2.94733 ( 6) hydrogen bonds : bond 0.03823 ( 612) hydrogen bonds : angle 4.41617 ( 1752) SS BOND : bond 0.00124 ( 5) SS BOND : angle 0.60532 ( 10) covalent geometry : bond 0.00341 ( 9676) covalent geometry : angle 0.63268 (13119) Misc. bond : bond 0.00050 ( 1) *********************** 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 192 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 1.296 Fit side-chains TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 128 MET cc_start: 0.8363 (mmm) cc_final: 0.7964 (mmm) REVERT: A 364 TYR cc_start: 0.8593 (m-80) cc_final: 0.8225 (m-80) REVERT: A 386 SER cc_start: 0.8871 (p) cc_final: 0.8543 (t) REVERT: A 648 MET cc_start: 0.6533 (mmm) cc_final: 0.5579 (tmm) REVERT: A 683 PHE cc_start: 0.7637 (m-80) cc_final: 0.7402 (m-80) REVERT: A 756 MET cc_start: 0.7002 (tmm) cc_final: 0.6605 (tmm) REVERT: A 1237 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7450 (ttm110) REVERT: A 1249 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7662 (t80) REVERT: A 1497 ILE cc_start: 0.9023 (mm) cc_final: 0.8766 (mm) REVERT: A 1550 ARG cc_start: 0.7057 (ttm170) cc_final: 0.4837 (ptt90) REVERT: A 1592 ILE cc_start: 0.9108 (tp) cc_final: 0.8763 (tp) outliers start: 23 outliers final: 15 residues processed: 177 average time/residue: 0.1986 time to fit residues: 53.0548 Evaluate side-chains 176 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 359 TRP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 1237 ARG Chi-restraints excluded: chain A residue 1249 PHE Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1487 HIS Chi-restraints excluded: chain A residue 1494 THR Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1644 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 14 optimal weight: 0.0040 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 66 optimal weight: 0.1980 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 HIS A 761 ASN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN A1208 ASN ** A1500 ASN ** 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 = 0.3900 r_free = 0.3900 target = 0.151595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120944 restraints weight = 23624.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.122138 restraints weight = 13966.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.122805 restraints weight = 8863.602| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9684 Z= 0.125 Angle : 0.613 9.653 13135 Z= 0.308 Chirality : 0.041 0.279 1535 Planarity : 0.004 0.038 1581 Dihedral : 9.384 59.671 1785 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.39 % Allowed : 12.72 % Favored : 84.89 % 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: 0.97 (0.25), residues: 1130 helix: 1.53 (0.18), residues: 777 sheet: None (None), residues: 0 loop : -1.38 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 359 HIS 0.004 0.001 HIS A1358 PHE 0.037 0.001 PHE A1713 TYR 0.013 0.001 TYR A1633 ARG 0.006 0.000 ARG A1275 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 2) link_NAG-ASN : angle 2.60102 ( 6) hydrogen bonds : bond 0.03566 ( 612) hydrogen bonds : angle 4.27003 ( 1752) SS BOND : bond 0.00101 ( 5) SS BOND : angle 0.55509 ( 10) covalent geometry : bond 0.00272 ( 9676) covalent geometry : angle 0.61078 (13119) Misc. bond : bond 0.00045 ( 1) *********************** 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 205 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 1.031 Fit side-chains TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 75 MET cc_start: 0.5945 (mpp) cc_final: 0.3839 (tpp) REVERT: A 159 MET cc_start: 0.7851 (mmm) cc_final: 0.7413 (mmp) REVERT: A 364 TYR cc_start: 0.8624 (m-80) cc_final: 0.8269 (m-80) REVERT: A 386 SER cc_start: 0.8943 (p) cc_final: 0.8494 (t) REVERT: A 648 MET cc_start: 0.6430 (mmm) cc_final: 0.5624 (tmm) REVERT: A 756 MET cc_start: 0.6971 (tmm) cc_final: 0.6557 (tmm) REVERT: A 1237 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7351 (ttm110) REVERT: A 1497 ILE cc_start: 0.9009 (mm) cc_final: 0.8727 (mm) REVERT: A 1550 ARG cc_start: 0.7020 (ttm170) cc_final: 0.4823 (ptt90) REVERT: A 1592 ILE cc_start: 0.9099 (tp) cc_final: 0.8764 (tp) outliers start: 24 outliers final: 16 residues processed: 190 average time/residue: 0.1755 time to fit residues: 50.4500 Evaluate side-chains 179 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 1221 LEU Chi-restraints excluded: chain A residue 1237 ARG Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1487 HIS Chi-restraints excluded: chain A residue 1494 THR Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1644 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 104 optimal weight: 0.0570 chunk 39 optimal weight: 5.9990 chunk 110 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 14 optimal weight: 0.0470 chunk 50 optimal weight: 1.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 ASN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1552 ASN A1614 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.153785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122184 restraints weight = 23314.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.123597 restraints weight = 14283.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.124258 restraints weight = 8732.208| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9684 Z= 0.120 Angle : 0.608 9.572 13135 Z= 0.305 Chirality : 0.040 0.278 1535 Planarity : 0.004 0.039 1581 Dihedral : 9.098 59.979 1785 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.58 % Allowed : 13.92 % Favored : 83.50 % 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: 1.08 (0.25), residues: 1130 helix: 1.60 (0.18), residues: 778 sheet: None (None), residues: 0 loop : -1.32 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1680 HIS 0.004 0.001 HIS A1358 PHE 0.035 0.001 PHE A1713 TYR 0.015 0.001 TYR A1633 ARG 0.006 0.000 ARG A1275 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 2) link_NAG-ASN : angle 2.44415 ( 6) hydrogen bonds : bond 0.03444 ( 612) hydrogen bonds : angle 4.16467 ( 1752) SS BOND : bond 0.00077 ( 5) SS BOND : angle 0.50749 ( 10) covalent geometry : bond 0.00261 ( 9676) covalent geometry : angle 0.60644 (13119) Misc. bond : bond 0.00022 ( 1) *********************** 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 210 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 1.233 Fit side-chains TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 75 MET cc_start: 0.5919 (mpp) cc_final: 0.3988 (tpp) REVERT: A 128 MET cc_start: 0.8267 (mmm) cc_final: 0.7904 (mmm) REVERT: A 364 TYR cc_start: 0.8501 (m-80) cc_final: 0.8177 (m-80) REVERT: A 386 SER cc_start: 0.8916 (p) cc_final: 0.8409 (t) REVERT: A 648 MET cc_start: 0.6330 (mmm) cc_final: 0.5555 (tmm) REVERT: A 683 PHE cc_start: 0.7426 (m-80) cc_final: 0.7219 (m-80) REVERT: A 756 MET cc_start: 0.6910 (tmm) cc_final: 0.6478 (tmm) REVERT: A 1237 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7312 (ttm110) REVERT: A 1249 PHE cc_start: 0.7999 (t80) cc_final: 0.7683 (t80) REVERT: A 1497 ILE cc_start: 0.8991 (mm) cc_final: 0.8708 (mm) REVERT: A 1550 ARG cc_start: 0.7042 (ttm170) cc_final: 0.4887 (ptt90) REVERT: A 1592 ILE cc_start: 0.9026 (tp) cc_final: 0.8679 (tp) outliers start: 26 outliers final: 16 residues processed: 195 average time/residue: 0.2553 time to fit residues: 74.0410 Evaluate side-chains 184 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 1221 LEU Chi-restraints excluded: chain A residue 1237 ARG Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1494 THR Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1644 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 80 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.0040 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1614 GLN A1621 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.150386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120203 restraints weight = 23328.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.121585 restraints weight = 14055.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122161 restraints weight = 8955.397| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9684 Z= 0.145 Angle : 0.638 10.365 13135 Z= 0.318 Chirality : 0.041 0.280 1535 Planarity : 0.004 0.037 1581 Dihedral : 9.084 59.291 1785 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.88 % Allowed : 14.71 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.10 (0.26), residues: 1130 helix: 1.62 (0.18), residues: 777 sheet: None (None), residues: 0 loop : -1.30 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1382 HIS 0.003 0.001 HIS A1358 PHE 0.037 0.002 PHE A1713 TYR 0.015 0.001 TYR A1633 ARG 0.005 0.000 ARG A1275 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 2) link_NAG-ASN : angle 2.60991 ( 6) hydrogen bonds : bond 0.03581 ( 612) hydrogen bonds : angle 4.22720 ( 1752) SS BOND : bond 0.00122 ( 5) SS BOND : angle 0.55217 ( 10) covalent geometry : bond 0.00334 ( 9676) covalent geometry : angle 0.63620 (13119) Misc. bond : bond 0.00033 ( 1) *********************** 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 199 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 1.016 Fit side-chains TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 75 MET cc_start: 0.6068 (mpp) cc_final: 0.4016 (tpp) REVERT: A 159 MET cc_start: 0.7777 (mmm) cc_final: 0.7369 (mmp) REVERT: A 237 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8647 (p0) REVERT: A 364 TYR cc_start: 0.8469 (m-80) cc_final: 0.8116 (m-80) REVERT: A 386 SER cc_start: 0.8901 (p) cc_final: 0.8393 (t) REVERT: A 648 MET cc_start: 0.6432 (mmm) cc_final: 0.5644 (tmm) REVERT: A 683 PHE cc_start: 0.7444 (m-80) cc_final: 0.7179 (m-80) REVERT: A 756 MET cc_start: 0.6983 (tmm) cc_final: 0.6551 (tmm) REVERT: A 1237 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7338 (ttm110) REVERT: A 1249 PHE cc_start: 0.7932 (t80) cc_final: 0.7504 (t80) REVERT: A 1497 ILE cc_start: 0.9049 (mm) cc_final: 0.8590 (mm) REVERT: A 1550 ARG cc_start: 0.7063 (ttm170) cc_final: 0.4911 (ptt90) REVERT: A 1592 ILE cc_start: 0.9095 (tp) cc_final: 0.8738 (tp) outliers start: 29 outliers final: 24 residues processed: 187 average time/residue: 0.1882 time to fit residues: 52.4432 Evaluate side-chains 195 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 761 ASN Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 1221 LEU Chi-restraints excluded: chain A residue 1237 ARG Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1487 HIS Chi-restraints excluded: chain A residue 1494 THR Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1562 SER Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1601 MET Chi-restraints excluded: chain A residue 1644 LEU Chi-restraints excluded: chain A residue 1662 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 112 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 86 optimal weight: 0.1980 chunk 21 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1621 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.150591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.120097 restraints weight = 29656.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.121502 restraints weight = 14380.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.122232 restraints weight = 11065.689| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9684 Z= 0.141 Angle : 0.644 12.078 13135 Z= 0.320 Chirality : 0.041 0.276 1535 Planarity : 0.004 0.037 1581 Dihedral : 9.030 59.339 1785 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.88 % Allowed : 14.81 % Favored : 82.31 % 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: 1.14 (0.26), residues: 1130 helix: 1.64 (0.19), residues: 772 sheet: None (None), residues: 0 loop : -1.24 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1382 HIS 0.003 0.001 HIS A1358 PHE 0.040 0.002 PHE A1713 TYR 0.014 0.001 TYR A1633 ARG 0.005 0.000 ARG A1275 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 2) link_NAG-ASN : angle 2.53088 ( 6) hydrogen bonds : bond 0.03565 ( 612) hydrogen bonds : angle 4.23536 ( 1752) SS BOND : bond 0.00107 ( 5) SS BOND : angle 0.45467 ( 10) covalent geometry : bond 0.00324 ( 9676) covalent geometry : angle 0.64150 (13119) Misc. bond : bond 0.00027 ( 1) *********************** 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 202 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 1.138 Fit side-chains TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 75 MET cc_start: 0.6115 (mpp) cc_final: 0.4155 (mmt) REVERT: A 159 MET cc_start: 0.7826 (mmm) cc_final: 0.7389 (mmp) REVERT: A 237 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8455 (p0) REVERT: A 364 TYR cc_start: 0.8446 (m-80) cc_final: 0.8163 (m-80) REVERT: A 386 SER cc_start: 0.8808 (p) cc_final: 0.8390 (t) REVERT: A 648 MET cc_start: 0.6349 (mmm) cc_final: 0.5483 (tmm) REVERT: A 683 PHE cc_start: 0.7407 (m-80) cc_final: 0.7155 (m-80) REVERT: A 756 MET cc_start: 0.7035 (tmm) cc_final: 0.6551 (tmm) REVERT: A 1237 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7352 (ttm110) REVERT: A 1249 PHE cc_start: 0.7976 (t80) cc_final: 0.7483 (t80) REVERT: A 1489 LEU cc_start: 0.7806 (tp) cc_final: 0.7587 (tp) REVERT: A 1550 ARG cc_start: 0.7022 (ttm170) cc_final: 0.4814 (ptt90) REVERT: A 1592 ILE cc_start: 0.9091 (tp) cc_final: 0.8748 (tp) outliers start: 29 outliers final: 21 residues processed: 191 average time/residue: 0.1996 time to fit residues: 56.4186 Evaluate side-chains 190 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 1221 LEU Chi-restraints excluded: chain A residue 1237 ARG Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1487 HIS Chi-restraints excluded: chain A residue 1494 THR Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1562 SER Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1644 LEU Chi-restraints excluded: chain A residue 1662 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 105 optimal weight: 4.9990 chunk 20 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 0.0370 chunk 21 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1621 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.151849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.116839 restraints weight = 27956.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.120753 restraints weight = 11618.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.123219 restraints weight = 7068.311| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9684 Z= 0.130 Angle : 0.638 12.582 13135 Z= 0.317 Chirality : 0.041 0.273 1535 Planarity : 0.004 0.057 1581 Dihedral : 8.906 59.703 1785 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.39 % Allowed : 15.41 % Favored : 82.21 % 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: 1.11 (0.26), residues: 1130 helix: 1.60 (0.19), residues: 779 sheet: None (None), residues: 0 loop : -1.24 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1680 HIS 0.006 0.001 HIS A1481 PHE 0.038 0.001 PHE A1713 TYR 0.014 0.001 TYR A1633 ARG 0.005 0.000 ARG A1275 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 2) link_NAG-ASN : angle 2.40062 ( 6) hydrogen bonds : bond 0.03509 ( 612) hydrogen bonds : angle 4.23175 ( 1752) SS BOND : bond 0.00115 ( 5) SS BOND : angle 0.49786 ( 10) covalent geometry : bond 0.00292 ( 9676) covalent geometry : angle 0.63603 (13119) Misc. bond : bond 0.00022 ( 1) *********************** 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 201 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 1.146 Fit side-chains TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 75 MET cc_start: 0.6056 (mpp) cc_final: 0.4168 (mmt) REVERT: A 128 MET cc_start: 0.8260 (mmm) cc_final: 0.7904 (mmm) REVERT: A 237 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8474 (p0) REVERT: A 364 TYR cc_start: 0.8395 (m-80) cc_final: 0.8064 (m-80) REVERT: A 648 MET cc_start: 0.6171 (mmm) cc_final: 0.5482 (tmm) REVERT: A 683 PHE cc_start: 0.7433 (m-80) cc_final: 0.7204 (m-80) REVERT: A 756 MET cc_start: 0.7039 (tmm) cc_final: 0.6554 (tmm) REVERT: A 1237 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7498 (tpp-160) REVERT: A 1489 LEU cc_start: 0.7763 (tp) cc_final: 0.7539 (tp) REVERT: A 1550 ARG cc_start: 0.7034 (ttm170) cc_final: 0.4910 (ptt90) REVERT: A 1592 ILE cc_start: 0.9061 (tp) cc_final: 0.8731 (tp) outliers start: 24 outliers final: 21 residues processed: 192 average time/residue: 0.1911 time to fit residues: 55.0910 Evaluate side-chains 191 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 1221 LEU Chi-restraints excluded: chain A residue 1237 ARG Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1494 THR Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1562 SER Chi-restraints excluded: chain A residue 1601 MET Chi-restraints excluded: chain A residue 1621 ASN Chi-restraints excluded: chain A residue 1644 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 89 optimal weight: 0.6980 chunk 58 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 33 optimal weight: 0.1980 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN A1326 GLN A1500 ASN A1621 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.151652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122852 restraints weight = 34762.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.125555 restraints weight = 17007.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.125910 restraints weight = 12116.984| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9684 Z= 0.133 Angle : 0.654 13.198 13135 Z= 0.324 Chirality : 0.041 0.272 1535 Planarity : 0.004 0.068 1581 Dihedral : 8.868 59.384 1785 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.19 % Allowed : 16.00 % Favored : 81.81 % 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: 1.12 (0.26), residues: 1130 helix: 1.59 (0.19), residues: 779 sheet: None (None), residues: 0 loop : -1.20 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1680 HIS 0.007 0.001 HIS A1481 PHE 0.037 0.001 PHE A1713 TYR 0.014 0.001 TYR A1633 ARG 0.005 0.000 ARG A1275 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 2) link_NAG-ASN : angle 2.37195 ( 6) hydrogen bonds : bond 0.03525 ( 612) hydrogen bonds : angle 4.22447 ( 1752) SS BOND : bond 0.00112 ( 5) SS BOND : angle 0.53169 ( 10) covalent geometry : bond 0.00299 ( 9676) covalent geometry : angle 0.65226 (13119) Misc. bond : bond 0.00022 ( 1) ********************** 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 193 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 1.005 Fit side-chains TARDY: cannot create tardy model for: "LEU A 730 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 766 " (corrupted residue). Skipping it. REVERT: A 75 MET cc_start: 0.6070 (mpp) cc_final: 0.4188 (mmt) REVERT: A 128 MET cc_start: 0.8222 (mmm) cc_final: 0.7824 (mmm) REVERT: A 159 MET cc_start: 0.7755 (mmm) cc_final: 0.7351 (mmp) REVERT: A 364 TYR cc_start: 0.8362 (m-80) cc_final: 0.8096 (m-80) REVERT: A 648 MET cc_start: 0.6200 (mmm) cc_final: 0.5515 (tmm) REVERT: A 756 MET cc_start: 0.7043 (tmm) cc_final: 0.6576 (tmm) REVERT: A 1237 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7548 (tpp-160) REVERT: A 1489 LEU cc_start: 0.7817 (tp) cc_final: 0.7603 (tp) REVERT: A 1550 ARG cc_start: 0.7054 (ttm170) cc_final: 0.4874 (ptt90) REVERT: A 1592 ILE cc_start: 0.9100 (tp) cc_final: 0.8755 (tp) outliers start: 22 outliers final: 20 residues processed: 184 average time/residue: 0.1785 time to fit residues: 48.7679 Evaluate side-chains 186 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 1221 LEU Chi-restraints excluded: chain A residue 1237 ARG Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1285 VAL Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1432 GLU Chi-restraints excluded: chain A residue 1476 THR Chi-restraints excluded: chain A residue 1494 THR Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1562 SER Chi-restraints excluded: chain A residue 1601 MET Chi-restraints excluded: chain A residue 1621 ASN Chi-restraints excluded: chain A residue 1644 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 8 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 0.0370 chunk 84 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 HIS ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN ** A1621 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 = 0.3894 r_free = 0.3894 target = 0.151459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121962 restraints weight = 30469.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.123039 restraints weight = 14777.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123411 restraints weight = 11795.245| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9684 Z= 0.140 Angle : 0.656 13.255 13135 Z= 0.325 Chirality : 0.041 0.272 1535 Planarity : 0.004 0.070 1581 Dihedral : 8.865 59.125 1785 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.19 % Allowed : 16.00 % Favored : 81.81 % 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: 1.11 (0.26), residues: 1130 helix: 1.59 (0.19), residues: 778 sheet: None (None), residues: 0 loop : -1.21 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1680 HIS 0.007 0.001 HIS A1481 PHE 0.047 0.002 PHE A 683 TYR 0.014 0.001 TYR A1633 ARG 0.005 0.000 ARG A1275 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 2) link_NAG-ASN : angle 2.43085 ( 6) hydrogen bonds : bond 0.03550 ( 612) hydrogen bonds : angle 4.25116 ( 1752) SS BOND : bond 0.00111 ( 5) SS BOND : angle 0.45183 ( 10) covalent geometry : bond 0.00320 ( 9676) covalent geometry : angle 0.65372 (13119) Misc. bond : bond 0.00027 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3913.66 seconds wall clock time: 69 minutes 29.33 seconds (4169.33 seconds total)