Starting phenix.real_space_refine on Sat Aug 23 16:47:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hoy_34927/08_2025/8hoy_34927.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hoy_34927/08_2025/8hoy_34927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hoy_34927/08_2025/8hoy_34927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hoy_34927/08_2025/8hoy_34927.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hoy_34927/08_2025/8hoy_34927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hoy_34927/08_2025/8hoy_34927.map" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 8624 2.51 5 N 2229 2.21 5 O 2529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13454 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 8215 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 37, 'TRANS': 968} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3467 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 10, 'TRANS': 415} Chain: "B" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1772 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 13, 'TRANS': 204} Time building chain proxies: 2.79, per 1000 atoms: 0.21 Number of scatterers: 13454 At special positions: 0 Unit cell: (107.52, 125.16, 139.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2529 8.00 N 2229 7.00 C 8624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 427.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3158 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 16 sheets defined 38.2% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.507A pdb=" N ASN A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 281 Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.551A pdb=" N ASP A 377 " --> pdb=" O ASP A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 448 through 474 removed outlier: 3.774A pdb=" N CYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.726A pdb=" N VAL A 493 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 502 through 514 removed outlier: 3.702A pdb=" N LEU A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU A 512 " --> pdb=" O LYS A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 576 through 591 Processing helix chain 'A' and resid 621 through 643 removed outlier: 3.865A pdb=" N LYS A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN A 643 " --> pdb=" O LYS A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 665 Processing helix chain 'A' and resid 666 through 672 removed outlier: 3.654A pdb=" N GLY A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 702 Processing helix chain 'A' and resid 764 through 781 Processing helix chain 'A' and resid 836 through 854 removed outlier: 3.942A pdb=" N GLU A 852 " --> pdb=" O THR A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 882 Processing helix chain 'A' and resid 908 through 915 removed outlier: 3.838A pdb=" N THR A 912 " --> pdb=" O MET A 908 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR A 914 " --> pdb=" O LEU A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 942 Processing helix chain 'A' and resid 970 through 983 Processing helix chain 'A' and resid 986 through 997 removed outlier: 4.181A pdb=" N GLN A 994 " --> pdb=" O ILE A 990 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 997 " --> pdb=" O PHE A 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 18 removed outlier: 5.958A pdb=" N GLU C 12 " --> pdb=" O THR C 8 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU C 13 " --> pdb=" O ASN C 9 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 36 removed outlier: 3.713A pdb=" N ASN C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER C 33 " --> pdb=" O GLU C 29 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU C 36 " --> pdb=" O ASN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.606A pdb=" N ASP C 59 " --> pdb=" O SER C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 177 through 188 removed outlier: 3.632A pdb=" N TYR C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 257 removed outlier: 3.782A pdb=" N LYS C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 298 removed outlier: 3.580A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 324 Processing helix chain 'C' and resid 330 through 341 Processing helix chain 'C' and resid 341 through 350 removed outlier: 3.606A pdb=" N LYS C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN C 350 " --> pdb=" O ARG C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 362 Processing helix chain 'C' and resid 367 through 374 Processing helix chain 'C' and resid 392 through 396 removed outlier: 3.951A pdb=" N ASN C 396 " --> pdb=" O ASN C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 406 removed outlier: 3.645A pdb=" N GLU C 401 " --> pdb=" O ASN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 425 removed outlier: 3.631A pdb=" N PHE C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 19 through 31 removed outlier: 4.316A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 39 removed outlier: 3.599A pdb=" N LEU B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.614A pdb=" N PHE B 49 " --> pdb=" O PRO B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 137 through 150 Processing helix chain 'B' and resid 165 through 170 removed outlier: 3.508A pdb=" N LYS B 169 " --> pdb=" O ASN B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 removed outlier: 3.507A pdb=" N ILE B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126 removed outlier: 5.670A pdb=" N CYS A 5 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ARG A 23 " --> pdb=" O CYS A 5 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 7 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N HIS A 141 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LYS A 134 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 5.149A pdb=" N MET A 88 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 Processing sheet with id=AA4, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.412A pdb=" N SER A 73 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU A 611 " --> pdb=" O CYS A 601 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.258A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N VAL A 237 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N THR A 201 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N CYS A 239 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 163 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA7, first strand: chain 'A' and resid 298 through 303 removed outlier: 4.333A pdb=" N CYS A 298 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 355 through 360 removed outlier: 4.743A pdb=" N VAL A 417 " --> pdb=" O PHE A 370 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLY A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE A 410 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS A 416 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS A 408 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A 418 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 732 through 734 removed outlier: 5.552A pdb=" N ASN A 703 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N SER A 747 " --> pdb=" O ASN A 703 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE A 756 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA A 793 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASP A 549 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N PHE A 791 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASN A 797 " --> pdb=" O MET A 809 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N MET A 809 " --> pdb=" O ASN A 797 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LYS A 805 " --> pdb=" O GLN A 801 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 166 through 168 removed outlier: 4.143A pdb=" N ILE C 197 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL C 210 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR C 199 " --> pdb=" O GLN C 208 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN C 208 " --> pdb=" O TYR C 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 124 through 132 removed outlier: 6.734A pdb=" N ILE C 124 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER C 143 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE C 126 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA C 141 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG C 128 " --> pdb=" O GLU C 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 222 through 223 removed outlier: 3.910A pdb=" N SER C 222 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR C 239 " --> pdb=" O LYS C 243 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 267 through 268 Processing sheet with id=AB5, first strand: chain 'C' and resid 375 through 380 removed outlier: 6.357A pdb=" N GLU C 380 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N VAL C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.523A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU B 155 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 107 through 108 525 hydrogen bonds defined for protein. 1491 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4297 1.34 - 1.46: 2920 1.46 - 1.58: 6419 1.58 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 13746 Sorted by residual: bond pdb=" CB ASN C 9 " pdb=" CG ASN C 9 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.02e-01 bond pdb=" CA ASN C 9 " pdb=" CB ASN C 9 " ideal model delta sigma weight residual 1.529 1.544 -0.015 1.62e-02 3.81e+03 8.95e-01 bond pdb=" C CYS A 934 " pdb=" O CYS A 934 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 8.29e-01 bond pdb=" C ILE B 13 " pdb=" N THR B 14 " ideal model delta sigma weight residual 1.328 1.339 -0.011 1.30e-02 5.92e+03 7.72e-01 bond pdb=" C VAL A 938 " pdb=" N PRO A 939 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.64e-01 ... (remaining 13741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 18186 1.32 - 2.63: 306 2.63 - 3.95: 62 3.95 - 5.27: 20 5.27 - 6.59: 2 Bond angle restraints: 18576 Sorted by residual: angle pdb=" N ILE C 228 " pdb=" CA ILE C 228 " pdb=" C ILE C 228 " ideal model delta sigma weight residual 113.71 108.95 4.76 9.50e-01 1.11e+00 2.51e+01 angle pdb=" N GLU A 969 " pdb=" CA GLU A 969 " pdb=" C GLU A 969 " ideal model delta sigma weight residual 108.34 113.48 -5.14 1.31e+00 5.83e-01 1.54e+01 angle pdb=" N ILE A 729 " pdb=" CA ILE A 729 " pdb=" C ILE A 729 " ideal model delta sigma weight residual 113.20 109.72 3.48 9.60e-01 1.09e+00 1.32e+01 angle pdb=" N THR A 949 " pdb=" CA THR A 949 " pdb=" C THR A 949 " ideal model delta sigma weight residual 110.97 113.74 -2.77 1.09e+00 8.42e-01 6.44e+00 angle pdb=" N ILE C 162 " pdb=" CA ILE C 162 " pdb=" C ILE C 162 " ideal model delta sigma weight residual 108.05 110.91 -2.86 1.18e+00 7.18e-01 5.89e+00 ... (remaining 18571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 7477 17.11 - 34.22: 709 34.22 - 51.33: 117 51.33 - 68.43: 17 68.43 - 85.54: 4 Dihedral angle restraints: 8324 sinusoidal: 3427 harmonic: 4897 Sorted by residual: dihedral pdb=" CA ALA B 9 " pdb=" C ALA B 9 " pdb=" N PRO B 10 " pdb=" CA PRO B 10 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA SER B 43 " pdb=" C SER B 43 " pdb=" N PRO B 44 " pdb=" CA PRO B 44 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ASP A 654 " pdb=" CB ASP A 654 " pdb=" CG ASP A 654 " pdb=" OD1 ASP A 654 " ideal model delta sinusoidal sigma weight residual -30.00 -86.91 56.91 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 8321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1384 0.035 - 0.071: 480 0.071 - 0.106: 139 0.106 - 0.141: 48 0.141 - 0.177: 3 Chirality restraints: 2054 Sorted by residual: chirality pdb=" CB ILE C 313 " pdb=" CA ILE C 313 " pdb=" CG1 ILE C 313 " pdb=" CG2 ILE C 313 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CB THR A 949 " pdb=" CA THR A 949 " pdb=" OG1 THR A 949 " pdb=" CG2 THR A 949 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ILE C 77 " pdb=" N ILE C 77 " pdb=" C ILE C 77 " pdb=" CB ILE C 77 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 2051 not shown) Planarity restraints: 2366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 168 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ILE C 168 " 0.059 2.00e-02 2.50e+03 pdb=" O ILE C 168 " -0.022 2.00e-02 2.50e+03 pdb=" N GLU C 169 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 593 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.19e+00 pdb=" N PRO A 594 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 594 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 594 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 9 " -0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO B 10 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 10 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 10 " -0.028 5.00e-02 4.00e+02 ... (remaining 2363 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 651 2.73 - 3.27: 13527 3.27 - 3.82: 22212 3.82 - 4.36: 26919 4.36 - 4.90: 44830 Nonbonded interactions: 108139 Sorted by model distance: nonbonded pdb=" OH TYR C 363 " pdb=" OD1 ASN C 406 " model vdw 2.189 3.040 nonbonded pdb=" O LEU A 988 " pdb=" OG SER A 991 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR A 391 " pdb=" OH TYR A 468 " model vdw 2.204 3.040 nonbonded pdb=" O PRO A 527 " pdb=" OH TYR A 681 " model vdw 2.219 3.040 nonbonded pdb=" OG SER A 564 " pdb=" OE1 GLU A 566 " model vdw 2.223 3.040 ... (remaining 108134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.390 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5276 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 : 0.002 0.029 13746 Z= 0.093 Angle : 0.463 6.586 18576 Z= 0.257 Chirality : 0.041 0.177 2054 Planarity : 0.004 0.051 2366 Dihedral : 13.252 85.543 5166 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.36 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.21), residues: 1644 helix: 1.35 (0.23), residues: 565 sheet: -0.20 (0.35), residues: 234 loop : -1.82 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 193 TYR 0.013 0.001 TYR A 190 PHE 0.012 0.001 PHE A 433 TRP 0.007 0.001 TRP A 470 HIS 0.002 0.000 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00185 (13746) covalent geometry : angle 0.46327 (18576) hydrogen bonds : bond 0.14870 ( 525) hydrogen bonds : angle 6.51536 ( 1491) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.5799 (ttt180) cc_final: 0.5561 (tpt-90) REVERT: A 211 GLN cc_start: 0.4798 (pm20) cc_final: 0.4586 (mp10) REVERT: A 357 MET cc_start: 0.5718 (mmm) cc_final: 0.5242 (mmt) REVERT: A 516 ILE cc_start: 0.5145 (mt) cc_final: 0.4920 (mt) REVERT: C 98 LEU cc_start: 0.5734 (mt) cc_final: 0.5376 (tt) REVERT: B 164 SER cc_start: 0.7617 (p) cc_final: 0.7337 (m) outliers start: 0 outliers final: 2 residues processed: 274 average time/residue: 0.5118 time to fit residues: 154.3104 Evaluate side-chains 160 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 233 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 101 ASN A 296 HIS A 461 HIS A 551 ASN A 556 ASN ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN A 607 ASN A 709 ASN A 825 ASN A 915 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN C 339 ASN C 374 ASN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5145 r_free = 0.5145 target = 0.293338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.250616 restraints weight = 16146.375| |-----------------------------------------------------------------------------| r_work (start): 0.4800 rms_B_bonded: 1.97 r_work: 0.4518 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.4416 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6077 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 13746 Z= 0.267 Angle : 0.754 10.359 18576 Z= 0.403 Chirality : 0.051 0.224 2054 Planarity : 0.007 0.107 2366 Dihedral : 5.028 27.354 1826 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.55 % Favored : 90.39 % Rotamer: Outliers : 4.01 % Allowed : 12.21 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.20), residues: 1644 helix: 0.16 (0.21), residues: 580 sheet: -0.81 (0.34), residues: 220 loop : -2.17 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 713 TYR 0.036 0.002 TYR A 190 PHE 0.028 0.003 PHE A 107 TRP 0.019 0.003 TRP A 8 HIS 0.012 0.002 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00624 (13746) covalent geometry : angle 0.75426 (18576) hydrogen bonds : bond 0.06193 ( 525) hydrogen bonds : angle 6.00690 ( 1491) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 156 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.6539 (OUTLIER) cc_final: 0.5522 (m-80) REVERT: A 175 PHE cc_start: 0.7377 (t80) cc_final: 0.7173 (t80) REVERT: A 278 LEU cc_start: 0.5586 (OUTLIER) cc_final: 0.5285 (mt) REVERT: A 357 MET cc_start: 0.6093 (mmm) cc_final: 0.5260 (mmt) REVERT: A 559 ILE cc_start: 0.7092 (tp) cc_final: 0.6876 (tp) REVERT: A 566 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6783 (pp20) REVERT: A 625 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6760 (tpt170) REVERT: A 722 PHE cc_start: 0.5812 (OUTLIER) cc_final: 0.4326 (p90) REVERT: A 800 MET cc_start: 0.0397 (mpp) cc_final: 0.0155 (mpp) REVERT: C 160 LEU cc_start: 0.2239 (tt) cc_final: 0.1595 (tm) REVERT: C 299 ARG cc_start: 0.6299 (ppt170) cc_final: 0.6037 (mtp180) REVERT: B 48 LYS cc_start: 0.4090 (mttt) cc_final: 0.3814 (mttt) REVERT: B 49 PHE cc_start: 0.4277 (m-10) cc_final: 0.3898 (m-10) REVERT: B 54 LYS cc_start: 0.3873 (OUTLIER) cc_final: 0.3663 (mmmt) REVERT: B 164 SER cc_start: 0.7818 (p) cc_final: 0.7423 (m) outliers start: 61 outliers final: 23 residues processed: 192 average time/residue: 0.4300 time to fit residues: 92.3366 Evaluate side-chains 160 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 181 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 77 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 139 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 185 HIS ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 HIS ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5128 r_free = 0.5128 target = 0.291210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.4754 r_free = 0.4754 target = 0.237431 restraints weight = 16188.535| |-----------------------------------------------------------------------------| r_work (start): 0.4675 rms_B_bonded: 2.73 r_work: 0.4483 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4388 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 13746 Z= 0.224 Angle : 0.714 12.436 18576 Z= 0.377 Chirality : 0.049 0.201 2054 Planarity : 0.006 0.086 2366 Dihedral : 5.085 24.391 1822 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.31 % Favored : 90.63 % Rotamer: Outliers : 4.79 % Allowed : 15.50 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.20), residues: 1644 helix: -0.24 (0.21), residues: 582 sheet: -1.17 (0.34), residues: 215 loop : -2.36 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 33 TYR 0.045 0.002 TYR C 158 PHE 0.025 0.002 PHE A 526 TRP 0.022 0.003 TRP B 212 HIS 0.009 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00524 (13746) covalent geometry : angle 0.71402 (18576) hydrogen bonds : bond 0.05611 ( 525) hydrogen bonds : angle 5.88920 ( 1491) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 149 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.5938 (mmm) cc_final: 0.5719 (mmm) REVERT: A 140 TYR cc_start: 0.6609 (OUTLIER) cc_final: 0.5529 (m-10) REVERT: A 278 LEU cc_start: 0.5664 (OUTLIER) cc_final: 0.5327 (mt) REVERT: A 285 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7495 (mm) REVERT: A 357 MET cc_start: 0.6209 (mmm) cc_final: 0.5248 (mmt) REVERT: A 407 ARG cc_start: 0.6443 (ttp80) cc_final: 0.6161 (ppt90) REVERT: A 559 ILE cc_start: 0.6922 (tp) cc_final: 0.6698 (tp) REVERT: A 566 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6735 (pp20) REVERT: A 722 PHE cc_start: 0.5803 (OUTLIER) cc_final: 0.4350 (p90) REVERT: A 859 MET cc_start: 0.0046 (pp-130) cc_final: -0.1310 (ppp) REVERT: C 410 PHE cc_start: 0.6271 (t80) cc_final: 0.5751 (t80) REVERT: B 20 GLU cc_start: 0.7869 (tp30) cc_final: 0.7259 (mt-10) REVERT: B 164 SER cc_start: 0.7668 (p) cc_final: 0.7324 (m) outliers start: 73 outliers final: 28 residues processed: 200 average time/residue: 0.4709 time to fit residues: 105.2226 Evaluate side-chains 167 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 181 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 148 optimal weight: 0.5980 chunk 158 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 296 HIS A 589 GLN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN C 351 GLN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5137 r_free = 0.5137 target = 0.293126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.251932 restraints weight = 15878.078| |-----------------------------------------------------------------------------| r_work (start): 0.4807 rms_B_bonded: 1.70 r_work: 0.4497 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4359 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13746 Z= 0.130 Angle : 0.593 9.819 18576 Z= 0.311 Chirality : 0.044 0.218 2054 Planarity : 0.005 0.072 2366 Dihedral : 4.662 24.079 1822 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.70 % Favored : 91.24 % Rotamer: Outliers : 3.74 % Allowed : 18.25 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.20), residues: 1644 helix: 0.23 (0.21), residues: 574 sheet: -1.05 (0.34), residues: 209 loop : -2.26 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 577 TYR 0.031 0.001 TYR C 158 PHE 0.015 0.001 PHE A 722 TRP 0.023 0.002 TRP B 212 HIS 0.005 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00289 (13746) covalent geometry : angle 0.59318 (18576) hydrogen bonds : bond 0.04190 ( 525) hydrogen bonds : angle 5.39547 ( 1491) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 143 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7335 (mm) REVERT: A 357 MET cc_start: 0.6134 (mmm) cc_final: 0.5363 (mmt) REVERT: A 393 ASN cc_start: 0.4875 (m110) cc_final: 0.4609 (t0) REVERT: A 859 MET cc_start: 0.0325 (pp-130) cc_final: -0.0832 (ppp) REVERT: C 160 LEU cc_start: 0.1787 (OUTLIER) cc_final: 0.1259 (tt) REVERT: C 179 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7151 (mm-30) REVERT: B 17 ASP cc_start: 0.7830 (m-30) cc_final: 0.7290 (m-30) REVERT: B 20 GLU cc_start: 0.7834 (tp30) cc_final: 0.7245 (mt-10) REVERT: B 164 SER cc_start: 0.7614 (p) cc_final: 0.7275 (m) REVERT: B 212 TRP cc_start: 0.6681 (m100) cc_final: 0.6193 (m100) outliers start: 57 outliers final: 23 residues processed: 183 average time/residue: 0.3968 time to fit residues: 81.4575 Evaluate side-chains 156 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 181 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 103 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 121 optimal weight: 30.0000 chunk 153 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 296 HIS A 551 ASN A 703 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5120 r_free = 0.5120 target = 0.290355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.249792 restraints weight = 16079.141| |-----------------------------------------------------------------------------| r_work (start): 0.4779 rms_B_bonded: 1.89 r_work: 0.4444 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4320 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 13746 Z= 0.206 Angle : 0.694 14.167 18576 Z= 0.362 Chirality : 0.047 0.199 2054 Planarity : 0.006 0.079 2366 Dihedral : 5.040 25.406 1822 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.04 % Favored : 89.84 % Rotamer: Outliers : 4.73 % Allowed : 19.44 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.12 (0.20), residues: 1644 helix: -0.14 (0.21), residues: 581 sheet: -1.37 (0.34), residues: 217 loop : -2.41 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 604 TYR 0.031 0.002 TYR C 158 PHE 0.030 0.002 PHE A 526 TRP 0.016 0.003 TRP A 470 HIS 0.009 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00483 (13746) covalent geometry : angle 0.69424 (18576) hydrogen bonds : bond 0.05243 ( 525) hydrogen bonds : angle 5.69022 ( 1491) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 140 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7310 (mm) REVERT: A 357 MET cc_start: 0.5857 (mmm) cc_final: 0.5128 (mmt) REVERT: A 559 ILE cc_start: 0.6809 (tp) cc_final: 0.6594 (tp) REVERT: A 625 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.6244 (tpm-80) REVERT: A 722 PHE cc_start: 0.6075 (OUTLIER) cc_final: 0.4591 (p90) REVERT: A 859 MET cc_start: 0.0320 (pp-130) cc_final: -0.0694 (ppp) REVERT: A 996 MET cc_start: 0.1734 (ttt) cc_final: 0.0617 (ppp) REVERT: C 160 LEU cc_start: 0.2063 (OUTLIER) cc_final: 0.1561 (tt) REVERT: C 179 GLU cc_start: 0.7353 (tm-30) cc_final: 0.7040 (mm-30) REVERT: C 299 ARG cc_start: 0.6244 (ppt170) cc_final: 0.5965 (mtp180) REVERT: C 410 PHE cc_start: 0.6236 (t80) cc_final: 0.5806 (t80) REVERT: B 20 GLU cc_start: 0.7818 (tp30) cc_final: 0.7252 (mt-10) REVERT: B 164 SER cc_start: 0.7701 (p) cc_final: 0.7358 (m) outliers start: 72 outliers final: 40 residues processed: 193 average time/residue: 0.4771 time to fit residues: 103.6341 Evaluate side-chains 176 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 181 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 126 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 336 GLN A 551 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 214 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5067 r_free = 0.5067 target = 0.285313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.237514 restraints weight = 16221.266| |-----------------------------------------------------------------------------| r_work (start): 0.4660 rms_B_bonded: 1.84 r_work: 0.4414 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4315 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.107 13746 Z= 0.329 Angle : 0.890 20.675 18576 Z= 0.466 Chirality : 0.054 0.255 2054 Planarity : 0.008 0.123 2366 Dihedral : 5.955 29.985 1822 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.19 % Favored : 88.75 % Rotamer: Outliers : 6.04 % Allowed : 20.09 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.19), residues: 1644 helix: -0.72 (0.20), residues: 565 sheet: -1.47 (0.33), residues: 233 loop : -2.65 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 604 TYR 0.028 0.003 TYR C 158 PHE 0.073 0.003 PHE A 526 TRP 0.024 0.004 TRP B 212 HIS 0.013 0.002 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00774 (13746) covalent geometry : angle 0.88994 (18576) hydrogen bonds : bond 0.06769 ( 525) hydrogen bonds : angle 6.35955 ( 1491) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 141 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLN cc_start: 0.5630 (mm-40) cc_final: 0.5427 (mt0) REVERT: A 92 GLU cc_start: 0.5712 (OUTLIER) cc_final: 0.5390 (mt-10) REVERT: A 122 ASP cc_start: 0.6722 (OUTLIER) cc_final: 0.6273 (p0) REVERT: A 140 TYR cc_start: 0.6682 (OUTLIER) cc_final: 0.5729 (m-10) REVERT: A 190 TYR cc_start: 0.6818 (OUTLIER) cc_final: 0.6518 (t80) REVERT: A 285 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7367 (mm) REVERT: A 526 PHE cc_start: 0.5516 (OUTLIER) cc_final: 0.2548 (p90) REVERT: A 625 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.6339 (tpm-80) REVERT: A 722 PHE cc_start: 0.6138 (OUTLIER) cc_final: 0.4975 (p90) REVERT: A 787 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.5628 (m-80) REVERT: A 799 ILE cc_start: 0.2038 (OUTLIER) cc_final: 0.1369 (pp) REVERT: A 859 MET cc_start: 0.0224 (pp-130) cc_final: -0.0858 (ppp) REVERT: C 111 ARG cc_start: 0.4984 (mtp180) cc_final: 0.4712 (mtt180) REVERT: C 160 LEU cc_start: 0.2018 (OUTLIER) cc_final: 0.1547 (tt) REVERT: C 179 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7192 (mm-30) REVERT: C 186 ARG cc_start: 0.5938 (mtm180) cc_final: 0.5649 (mpt180) REVERT: C 410 PHE cc_start: 0.6522 (t80) cc_final: 0.6280 (t80) REVERT: B 63 CYS cc_start: 0.4643 (t) cc_final: 0.4256 (t) REVERT: B 136 TYR cc_start: 0.5853 (OUTLIER) cc_final: 0.4361 (m-80) REVERT: B 138 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7274 (t0) outliers start: 92 outliers final: 55 residues processed: 214 average time/residue: 0.4396 time to fit residues: 106.7153 Evaluate side-chains 202 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 134 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 210 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 75 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 ASN C 397 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5132 r_free = 0.5132 target = 0.292736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.239550 restraints weight = 16193.079| |-----------------------------------------------------------------------------| r_work (start): 0.4665 rms_B_bonded: 2.96 r_work: 0.4483 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4377 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.4377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13746 Z= 0.139 Angle : 0.651 12.977 18576 Z= 0.335 Chirality : 0.045 0.185 2054 Planarity : 0.005 0.082 2366 Dihedral : 5.039 28.058 1822 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.70 % Favored : 91.24 % Rotamer: Outliers : 4.27 % Allowed : 22.65 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.20), residues: 1644 helix: -0.06 (0.21), residues: 570 sheet: -1.12 (0.34), residues: 222 loop : -2.49 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 286 TYR 0.033 0.001 TYR C 31 PHE 0.041 0.002 PHE C 233 TRP 0.021 0.002 TRP B 212 HIS 0.007 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00311 (13746) covalent geometry : angle 0.65116 (18576) hydrogen bonds : bond 0.04322 ( 525) hydrogen bonds : angle 5.53988 ( 1491) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 148 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLN cc_start: 0.5571 (mm-40) cc_final: 0.5341 (mt0) REVERT: A 285 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7256 (mm) REVERT: A 301 GLU cc_start: 0.7168 (mp0) cc_final: 0.6945 (mp0) REVERT: A 357 MET cc_start: 0.5468 (mmt) cc_final: 0.4950 (mmt) REVERT: A 399 GLU cc_start: 0.7478 (tp30) cc_final: 0.7262 (mm-30) REVERT: A 522 THR cc_start: 0.7271 (OUTLIER) cc_final: 0.7062 (t) REVERT: A 722 PHE cc_start: 0.5750 (OUTLIER) cc_final: 0.4491 (p90) REVERT: A 787 PHE cc_start: 0.7131 (OUTLIER) cc_final: 0.5378 (m-80) REVERT: A 791 PHE cc_start: 0.5286 (t80) cc_final: 0.4905 (t80) REVERT: A 799 ILE cc_start: 0.2098 (OUTLIER) cc_final: 0.1470 (pp) REVERT: A 859 MET cc_start: 0.0315 (pp-130) cc_final: -0.0805 (ppp) REVERT: C 160 LEU cc_start: 0.2048 (OUTLIER) cc_final: 0.1670 (tt) REVERT: C 179 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7198 (mm-30) REVERT: C 299 ARG cc_start: 0.6286 (ppt170) cc_final: 0.5710 (mtp180) REVERT: C 399 SER cc_start: 0.7632 (t) cc_final: 0.7238 (p) REVERT: B 49 PHE cc_start: 0.4312 (m-10) cc_final: 0.3946 (m-80) REVERT: B 207 LYS cc_start: 0.5610 (OUTLIER) cc_final: 0.5150 (mtmm) outliers start: 65 outliers final: 28 residues processed: 196 average time/residue: 0.4680 time to fit residues: 103.9031 Evaluate side-chains 164 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 207 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 47 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 56 optimal weight: 0.0270 chunk 76 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 55 optimal weight: 0.0470 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN B 31 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5125 r_free = 0.5125 target = 0.291964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.237805 restraints weight = 16095.660| |-----------------------------------------------------------------------------| r_work (start): 0.4658 rms_B_bonded: 2.77 r_work: 0.4479 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4376 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13746 Z= 0.142 Angle : 0.642 12.080 18576 Z= 0.331 Chirality : 0.045 0.194 2054 Planarity : 0.005 0.078 2366 Dihedral : 4.889 26.950 1822 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.31 % Favored : 90.63 % Rotamer: Outliers : 3.74 % Allowed : 23.64 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.20), residues: 1644 helix: 0.16 (0.21), residues: 570 sheet: -1.29 (0.34), residues: 219 loop : -2.39 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 577 TYR 0.024 0.001 TYR C 31 PHE 0.022 0.002 PHE A 526 TRP 0.021 0.002 TRP B 212 HIS 0.008 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00322 (13746) covalent geometry : angle 0.64215 (18576) hydrogen bonds : bond 0.04366 ( 525) hydrogen bonds : angle 5.43387 ( 1491) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 133 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7239 (mm) REVERT: A 357 MET cc_start: 0.5416 (mmt) cc_final: 0.4898 (mmt) REVERT: A 522 THR cc_start: 0.7281 (OUTLIER) cc_final: 0.7070 (t) REVERT: A 694 MET cc_start: 0.6556 (OUTLIER) cc_final: 0.4954 (mpp) REVERT: A 722 PHE cc_start: 0.5657 (OUTLIER) cc_final: 0.4193 (p90) REVERT: A 787 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.5441 (m-80) REVERT: A 799 ILE cc_start: 0.2114 (OUTLIER) cc_final: 0.1477 (pp) REVERT: A 859 MET cc_start: 0.0297 (pp-130) cc_final: -0.0822 (ppp) REVERT: C 160 LEU cc_start: 0.1876 (OUTLIER) cc_final: 0.1239 (tt) REVERT: C 179 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7234 (mm-30) REVERT: C 224 LYS cc_start: 0.7746 (mppt) cc_final: 0.7489 (mmmt) REVERT: C 299 ARG cc_start: 0.6251 (ppt170) cc_final: 0.5670 (mtp180) REVERT: B 48 LYS cc_start: 0.3851 (mttt) cc_final: 0.3366 (tttt) REVERT: B 49 PHE cc_start: 0.4422 (m-10) cc_final: 0.3777 (m-10) REVERT: B 207 LYS cc_start: 0.5529 (OUTLIER) cc_final: 0.5065 (mtmm) REVERT: B 214 GLN cc_start: 0.5381 (OUTLIER) cc_final: 0.5016 (mp10) outliers start: 57 outliers final: 32 residues processed: 177 average time/residue: 0.4131 time to fit residues: 82.5698 Evaluate side-chains 166 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 214 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 117 optimal weight: 0.0370 chunk 2 optimal weight: 0.6980 chunk 85 optimal weight: 0.0070 chunk 94 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 overall best weight: 0.9478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN B 55 GLN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5128 r_free = 0.5128 target = 0.292481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.240379 restraints weight = 16290.909| |-----------------------------------------------------------------------------| r_work (start): 0.4681 rms_B_bonded: 2.76 r_work: 0.4482 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4380 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13746 Z= 0.137 Angle : 0.644 12.440 18576 Z= 0.329 Chirality : 0.045 0.188 2054 Planarity : 0.005 0.074 2366 Dihedral : 4.796 26.116 1822 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.70 % Favored : 91.24 % Rotamer: Outliers : 3.48 % Allowed : 24.16 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.20), residues: 1644 helix: 0.35 (0.22), residues: 559 sheet: -1.10 (0.33), residues: 236 loop : -2.36 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 577 TYR 0.029 0.001 TYR C 158 PHE 0.015 0.002 PHE A 526 TRP 0.025 0.002 TRP B 212 HIS 0.008 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00308 (13746) covalent geometry : angle 0.64374 (18576) hydrogen bonds : bond 0.04246 ( 525) hydrogen bonds : angle 5.34609 ( 1491) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 136 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7258 (mm) REVERT: A 357 MET cc_start: 0.5527 (mmt) cc_final: 0.5130 (mmt) REVERT: A 458 TYR cc_start: 0.6628 (t80) cc_final: 0.6316 (t80) REVERT: A 522 THR cc_start: 0.7292 (OUTLIER) cc_final: 0.7057 (t) REVERT: A 526 PHE cc_start: 0.4817 (OUTLIER) cc_final: 0.3018 (p90) REVERT: A 722 PHE cc_start: 0.5738 (OUTLIER) cc_final: 0.4430 (p90) REVERT: A 787 PHE cc_start: 0.7129 (OUTLIER) cc_final: 0.5357 (m-80) REVERT: A 799 ILE cc_start: 0.2111 (OUTLIER) cc_final: 0.1485 (pp) REVERT: A 859 MET cc_start: 0.0182 (pp-130) cc_final: -0.0907 (ppp) REVERT: C 95 MET cc_start: 0.3279 (tpp) cc_final: 0.2627 (tpt) REVERT: C 160 LEU cc_start: 0.1663 (OUTLIER) cc_final: 0.1125 (tt) REVERT: C 179 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7195 (mm-30) REVERT: C 224 LYS cc_start: 0.7721 (mppt) cc_final: 0.7496 (mmmt) REVERT: C 299 ARG cc_start: 0.6239 (ppt170) cc_final: 0.5674 (mtp180) REVERT: B 20 GLU cc_start: 0.7798 (tp30) cc_final: 0.7306 (mt-10) REVERT: B 48 LYS cc_start: 0.3692 (mttt) cc_final: 0.3462 (tttt) REVERT: B 207 LYS cc_start: 0.5443 (OUTLIER) cc_final: 0.5001 (mtmm) REVERT: B 214 GLN cc_start: 0.5396 (OUTLIER) cc_final: 0.5090 (mp10) outliers start: 53 outliers final: 34 residues processed: 173 average time/residue: 0.4140 time to fit residues: 81.5179 Evaluate side-chains 172 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 214 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 156 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 ASN C 9 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5136 r_free = 0.5136 target = 0.293238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.241619 restraints weight = 16142.967| |-----------------------------------------------------------------------------| r_work (start): 0.4682 rms_B_bonded: 2.68 r_work: 0.4490 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4387 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5935 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13746 Z= 0.134 Angle : 0.655 15.950 18576 Z= 0.331 Chirality : 0.045 0.187 2054 Planarity : 0.005 0.072 2366 Dihedral : 4.699 25.716 1822 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.27 % Favored : 91.67 % Rotamer: Outliers : 3.22 % Allowed : 24.56 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.20), residues: 1644 helix: 0.43 (0.22), residues: 559 sheet: -1.31 (0.32), residues: 240 loop : -2.30 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 577 TYR 0.028 0.001 TYR C 158 PHE 0.012 0.001 PHE A 494 TRP 0.025 0.002 TRP B 212 HIS 0.009 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00299 (13746) covalent geometry : angle 0.65504 (18576) hydrogen bonds : bond 0.04166 ( 525) hydrogen bonds : angle 5.29598 ( 1491) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 135 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7229 (mm) REVERT: A 357 MET cc_start: 0.5480 (mmt) cc_final: 0.5070 (mmt) REVERT: A 458 TYR cc_start: 0.6575 (t80) cc_final: 0.6261 (t80) REVERT: A 522 THR cc_start: 0.7233 (OUTLIER) cc_final: 0.7014 (t) REVERT: A 526 PHE cc_start: 0.4971 (OUTLIER) cc_final: 0.3016 (p90) REVERT: A 722 PHE cc_start: 0.5783 (OUTLIER) cc_final: 0.4488 (p90) REVERT: A 787 PHE cc_start: 0.7177 (OUTLIER) cc_final: 0.5413 (m-80) REVERT: A 799 ILE cc_start: 0.2067 (OUTLIER) cc_final: 0.1436 (pp) REVERT: A 859 MET cc_start: 0.0190 (pp-130) cc_final: -0.0872 (ppp) REVERT: C 1 MET cc_start: 0.2851 (ppp) cc_final: 0.1656 (ppp) REVERT: C 95 MET cc_start: 0.3330 (tpp) cc_final: 0.2770 (tpt) REVERT: C 111 ARG cc_start: 0.5000 (mtp180) cc_final: 0.4755 (mtt-85) REVERT: C 160 LEU cc_start: 0.1417 (OUTLIER) cc_final: 0.0994 (tp) REVERT: C 179 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7148 (mm-30) REVERT: C 299 ARG cc_start: 0.6257 (ppt170) cc_final: 0.5710 (mtp180) REVERT: B 20 GLU cc_start: 0.7782 (tp30) cc_final: 0.7283 (mt-10) REVERT: B 48 LYS cc_start: 0.3752 (mttt) cc_final: 0.3493 (tttt) REVERT: B 125 CYS cc_start: 0.5241 (m) cc_final: 0.4230 (p) REVERT: B 164 SER cc_start: 0.7627 (p) cc_final: 0.7355 (p) REVERT: B 207 LYS cc_start: 0.5553 (OUTLIER) cc_final: 0.5109 (mtmm) REVERT: B 214 GLN cc_start: 0.5334 (OUTLIER) cc_final: 0.5121 (mp10) outliers start: 49 outliers final: 30 residues processed: 172 average time/residue: 0.3903 time to fit residues: 75.7385 Evaluate side-chains 168 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 58 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 118 optimal weight: 20.0000 chunk 44 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN A 589 GLN A 607 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5080 r_free = 0.5080 target = 0.287118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.235080 restraints weight = 16273.730| |-----------------------------------------------------------------------------| r_work (start): 0.4655 rms_B_bonded: 2.81 r_work: 0.4435 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4336 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 13746 Z= 0.243 Angle : 0.782 17.676 18576 Z= 0.399 Chirality : 0.050 0.194 2054 Planarity : 0.006 0.081 2366 Dihedral : 5.285 26.454 1822 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.22 % Favored : 89.72 % Rotamer: Outliers : 3.48 % Allowed : 24.49 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.20 (0.20), residues: 1644 helix: -0.12 (0.21), residues: 563 sheet: -1.66 (0.33), residues: 223 loop : -2.40 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 33 TYR 0.027 0.002 TYR C 158 PHE 0.035 0.003 PHE A 526 TRP 0.032 0.003 TRP B 212 HIS 0.010 0.002 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00570 (13746) covalent geometry : angle 0.78241 (18576) hydrogen bonds : bond 0.05589 ( 525) hydrogen bonds : angle 5.76813 ( 1491) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7117.70 seconds wall clock time: 121 minutes 42.59 seconds (7302.59 seconds total)