Starting phenix.real_space_refine on Thu Jun 12 01:11:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hoy_34927/06_2025/8hoy_34927.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hoy_34927/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hoy_34927/06_2025/8hoy_34927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hoy_34927/06_2025/8hoy_34927.map" model { file = "/net/cci-nas-00/data/ceres_data/8hoy_34927/06_2025/8hoy_34927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hoy_34927/06_2025/8hoy_34927.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.34, per 1000 atoms: 0.62 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: 2.96 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.41 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: 4.74 Time building geometry restraints manager: 3.63 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 32.430 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.050 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (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 TRP 0.007 0.001 TRP A 470 HIS 0.002 0.000 HIS A 170 PHE 0.012 0.001 PHE A 433 TYR 0.013 0.001 TYR A 190 ARG 0.003 0.000 ARG B 193 Details of bonding type rmsd hydrogen bonds : bond 0.14870 ( 525) hydrogen bonds : angle 6.51536 ( 1491) covalent geometry : bond 0.00185 (13746) covalent geometry : angle 0.46327 (18576) *********************** 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 : 1.363 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: 0.4585 (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: 0.5377 (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: 1.1593 time to fit residues: 349.7700 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 : 1.346 ------------------------------------------------------------------------------- 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 137 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 148 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A 825 ASN A 915 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5125 r_free = 0.5125 target = 0.290870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.245825 restraints weight = 16048.546| |-----------------------------------------------------------------------------| r_work (start): 0.4761 rms_B_bonded: 1.80 r_work: 0.4507 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4417 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 13746 Z= 0.308 Angle : 0.830 12.018 18576 Z= 0.443 Chirality : 0.054 0.241 2054 Planarity : 0.008 0.125 2366 Dihedral : 5.343 27.073 1826 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.04 % Favored : 89.90 % Rotamer: Outliers : 4.20 % Allowed : 12.87 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.20), residues: 1644 helix: -0.13 (0.21), residues: 580 sheet: -0.92 (0.33), residues: 219 loop : -2.29 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 8 HIS 0.014 0.002 HIS A 170 PHE 0.032 0.003 PHE A 107 TYR 0.040 0.003 TYR A 190 ARG 0.009 0.001 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.06612 ( 525) hydrogen bonds : angle 6.20777 ( 1491) covalent geometry : bond 0.00731 (13746) covalent geometry : angle 0.82969 (18576) *********************** 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 224 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 160 time to evaluate : 1.893 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: 0.6485 (OUTLIER) cc_final: 0.5568 (m-10) REVERT: A 146 ARG cc_start: 0.7177 (tmt170) cc_final: 0.6946 (mmt180) REVERT: A 278 LEU cc_start: 0.5713 (OUTLIER) cc_final: 0.5440 (mt) REVERT: A 357 MET cc_start: 0.6218 (mmm) cc_final: 0.5306 (mmt) REVERT: A 566 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6849 (pp20) REVERT: A 625 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6738 (tpt170) REVERT: A 722 PHE cc_start: 0.6064 (OUTLIER) cc_final: 0.4643 (p90) REVERT: C 160 LEU cc_start: 0.2314 (tt) cc_final: 0.1525 (tm) REVERT: B 48 LYS cc_start: 0.4159 (mttt) cc_final: 0.3889 (mttt) REVERT: B 49 PHE cc_start: 0.4341 (m-10) cc_final: 0.3916 (m-10) REVERT: B 54 LYS cc_start: 0.4190 (OUTLIER) cc_final: 0.3870 (mmmm) REVERT: B 72 LYS cc_start: 0.6688 (mttt) cc_final: 0.6432 (tppp) REVERT: B 164 SER cc_start: 0.7793 (p) cc_final: 0.7398 (m) outliers start: 64 outliers final: 24 residues processed: 196 average time/residue: 1.3539 time to fit residues: 296.2072 Evaluate side-chains 164 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 2.738 ------------------------------------------------------------------------------- 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 477 THR Chi-restraints excluded: chain A residue 515 THR 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 722 PHE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain B residue 54 LYS 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 40 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 chunk 112 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 73 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 607 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN C 406 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5145 r_free = 0.5145 target = 0.293441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.252308 restraints weight = 16188.691| |-----------------------------------------------------------------------------| r_work (start): 0.4809 rms_B_bonded: 1.72 r_work: 0.4507 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4373 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13746 Z= 0.136 Angle : 0.602 9.199 18576 Z= 0.317 Chirality : 0.045 0.193 2054 Planarity : 0.005 0.071 2366 Dihedral : 4.635 23.625 1822 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.54 % Favored : 92.40 % Rotamer: Outliers : 3.81 % Allowed : 15.50 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.20), residues: 1644 helix: 0.14 (0.21), residues: 582 sheet: -0.84 (0.34), residues: 205 loop : -2.26 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 212 HIS 0.004 0.001 HIS B 181 PHE 0.014 0.001 PHE A 722 TYR 0.049 0.001 TYR C 158 ARG 0.005 0.000 ARG C 286 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 525) hydrogen bonds : angle 5.51432 ( 1491) covalent geometry : bond 0.00305 (13746) covalent geometry : angle 0.60155 (18576) *********************** 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 207 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 149 time to evaluate : 1.363 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 146 ARG cc_start: 0.7188 (tmt170) cc_final: 0.6980 (mmt180) REVERT: A 278 LEU cc_start: 0.5543 (OUTLIER) cc_final: 0.5258 (mt) REVERT: A 285 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7387 (mm) REVERT: A 357 MET cc_start: 0.6179 (mmm) cc_final: 0.5267 (mmt) REVERT: A 407 ARG cc_start: 0.6720 (ppt90) cc_final: 0.6161 (mtm-85) REVERT: A 724 MET cc_start: 0.4553 (OUTLIER) cc_final: 0.4247 (mmm) REVERT: A 859 MET cc_start: -0.0067 (pp-130) cc_final: -0.1245 (ppp) REVERT: B 17 ASP cc_start: 0.8012 (m-30) cc_final: 0.7535 (m-30) REVERT: B 20 GLU cc_start: 0.7827 (tp30) cc_final: 0.7241 (mt-10) REVERT: B 48 LYS cc_start: 0.4084 (mttt) cc_final: 0.3879 (mttt) REVERT: B 164 SER cc_start: 0.7609 (p) cc_final: 0.7276 (m) REVERT: B 212 TRP cc_start: 0.6801 (m100) cc_final: 0.6362 (m100) outliers start: 58 outliers final: 19 residues processed: 187 average time/residue: 1.1422 time to fit residues: 239.6594 Evaluate side-chains 151 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 76 LEU 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 619 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 724 MET 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 311 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 49 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 64 optimal weight: 0.0060 chunk 128 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 101 optimal weight: 0.3980 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5137 r_free = 0.5137 target = 0.293274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.252997 restraints weight = 15971.281| |-----------------------------------------------------------------------------| r_work (start): 0.4811 rms_B_bonded: 1.81 r_work: 0.4497 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.4383 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 moved from start: 0.3306 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= 0.140 Angle : 0.591 8.058 18576 Z= 0.312 Chirality : 0.044 0.210 2054 Planarity : 0.005 0.071 2366 Dihedral : 4.580 23.398 1822 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.58 % Favored : 91.36 % Rotamer: Outliers : 4.20 % Allowed : 17.60 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.20), residues: 1644 helix: 0.24 (0.21), residues: 578 sheet: -1.20 (0.34), residues: 213 loop : -2.15 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 470 HIS 0.006 0.001 HIS B 181 PHE 0.013 0.002 PHE A 526 TYR 0.030 0.001 TYR C 158 ARG 0.005 0.000 ARG A 33 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 525) hydrogen bonds : angle 5.31065 ( 1491) covalent geometry : bond 0.00316 (13746) covalent geometry : angle 0.59124 (18576) *********************** 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 205 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 141 time to evaluate : 1.369 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 146 ARG cc_start: 0.7288 (tmt170) cc_final: 0.6975 (mmt180) REVERT: A 285 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7354 (mm) REVERT: A 357 MET cc_start: 0.6139 (mmm) cc_final: 0.5397 (mmt) REVERT: A 566 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6545 (pp20) REVERT: A 722 PHE cc_start: 0.5864 (OUTLIER) cc_final: 0.4479 (p90) REVERT: A 859 MET cc_start: 0.0233 (pp-130) cc_final: -0.0723 (ppp) REVERT: C 160 LEU cc_start: 0.1852 (OUTLIER) cc_final: 0.1233 (tt) REVERT: C 179 GLU cc_start: 0.7286 (tm-30) cc_final: 0.7039 (mm-30) REVERT: B 20 GLU cc_start: 0.7840 (tp30) cc_final: 0.7261 (mt-10) REVERT: B 164 SER cc_start: 0.7749 (p) cc_final: 0.7438 (m) outliers start: 64 outliers final: 29 residues processed: 187 average time/residue: 0.9262 time to fit residues: 196.3306 Evaluate side-chains 164 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 1.652 ------------------------------------------------------------------------------- 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 72 ILE Chi-restraints excluded: chain A residue 76 LEU 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 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 518 VAL Chi-restraints excluded: chain A residue 566 GLU 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 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 311 VAL Chi-restraints excluded: chain C residue 369 ILE 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 181 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 102 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 156 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 551 ASN A 600 HIS ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 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 = 0.5086 r_free = 0.5086 target = 0.286606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.237631 restraints weight = 16131.046| |-----------------------------------------------------------------------------| r_work (start): 0.4640 rms_B_bonded: 1.92 r_work: 0.4409 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4311 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.109 13746 Z= 0.344 Angle : 0.903 17.813 18576 Z= 0.477 Chirality : 0.054 0.272 2054 Planarity : 0.008 0.116 2366 Dihedral : 5.879 27.114 1822 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.95 % Favored : 88.99 % Rotamer: Outliers : 5.38 % Allowed : 18.84 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.19), residues: 1644 helix: -0.69 (0.20), residues: 570 sheet: -1.35 (0.32), residues: 242 loop : -2.57 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP B 212 HIS 0.013 0.002 HIS A 170 PHE 0.069 0.004 PHE A 526 TYR 0.033 0.003 TYR C 158 ARG 0.010 0.001 ARG C 227 Details of bonding type rmsd hydrogen bonds : bond 0.06946 ( 525) hydrogen bonds : angle 6.31081 ( 1491) covalent geometry : bond 0.00813 (13746) covalent geometry : angle 0.90327 (18576) *********************** 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 224 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 142 time to evaluate : 1.473 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: A 122 ASP cc_start: 0.6647 (OUTLIER) cc_final: 0.6253 (p0) REVERT: A 140 TYR cc_start: 0.6584 (OUTLIER) cc_final: 0.5671 (m-10) REVERT: A 146 ARG cc_start: 0.7502 (tmt170) cc_final: 0.7192 (tmm-80) REVERT: A 285 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7335 (mm) REVERT: A 357 MET cc_start: 0.5786 (mmm) cc_final: 0.5548 (mmt) REVERT: A 526 PHE cc_start: 0.5371 (OUTLIER) cc_final: 0.2586 (p90) REVERT: A 566 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6884 (pp20) REVERT: A 670 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7073 (mp) REVERT: A 722 PHE cc_start: 0.6221 (OUTLIER) cc_final: 0.5010 (p90) REVERT: A 787 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.5615 (m-80) REVERT: A 859 MET cc_start: 0.0387 (pp-130) cc_final: -0.0635 (ppp) REVERT: C 111 ARG cc_start: 0.4887 (mtp180) cc_final: 0.4564 (mtt180) REVERT: C 160 LEU cc_start: 0.2060 (OUTLIER) cc_final: 0.1558 (tt) REVERT: C 179 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7196 (mm-30) REVERT: C 218 MET cc_start: 0.5432 (OUTLIER) cc_final: 0.5008 (mtt) REVERT: C 410 PHE cc_start: 0.6509 (t80) cc_final: 0.6169 (t80) REVERT: B 138 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7291 (t0) REVERT: B 207 LYS cc_start: 0.5885 (OUTLIER) cc_final: 0.5257 (mtmm) outliers start: 82 outliers final: 38 residues processed: 202 average time/residue: 0.8768 time to fit residues: 202.7098 Evaluate side-chains 184 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 134 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 76 LEU 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 178 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 285 ILE 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 477 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 670 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 787 PHE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 218 MET 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 123 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 210 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 50 optimal weight: 0.6980 chunk 96 optimal weight: 20.0000 chunk 11 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 158 optimal weight: 6.9990 chunk 63 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 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 = 0.5136 r_free = 0.5136 target = 0.293123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.240951 restraints weight = 16318.709| |-----------------------------------------------------------------------------| r_work (start): 0.4684 rms_B_bonded: 2.85 r_work: 0.4488 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4384 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13746 Z= 0.129 Angle : 0.612 9.364 18576 Z= 0.320 Chirality : 0.044 0.183 2054 Planarity : 0.005 0.078 2366 Dihedral : 4.858 25.510 1822 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.85 % Favored : 92.09 % Rotamer: Outliers : 3.94 % Allowed : 21.34 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.20), residues: 1644 helix: 0.05 (0.21), residues: 575 sheet: -1.34 (0.34), residues: 203 loop : -2.29 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 212 HIS 0.006 0.001 HIS B 181 PHE 0.017 0.001 PHE C 407 TYR 0.032 0.001 TYR C 158 ARG 0.004 0.000 ARG C 286 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 525) hydrogen bonds : angle 5.34199 ( 1491) covalent geometry : bond 0.00281 (13746) covalent geometry : angle 0.61230 (18576) *********************** 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 204 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 144 time to evaluate : 1.422 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 146 ARG cc_start: 0.7385 (tmt170) cc_final: 0.7097 (tmm-80) REVERT: A 285 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7283 (mm) REVERT: A 302 ARG cc_start: 0.5864 (OUTLIER) cc_final: 0.5525 (mmm-85) REVERT: A 357 MET cc_start: 0.5687 (mmm) cc_final: 0.4957 (mmt) REVERT: A 399 GLU cc_start: 0.7503 (tp30) cc_final: 0.7303 (mm-30) REVERT: A 625 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.6530 (tpm170) REVERT: A 711 MET cc_start: 0.4543 (mmt) cc_final: 0.4328 (mmp) REVERT: A 722 PHE cc_start: 0.5746 (OUTLIER) cc_final: 0.4248 (p90) REVERT: A 791 PHE cc_start: 0.5321 (t80) cc_final: 0.4967 (t80) REVERT: A 799 ILE cc_start: 0.1850 (OUTLIER) cc_final: 0.1233 (pp) REVERT: A 859 MET cc_start: 0.0448 (pp-130) cc_final: -0.0603 (ppp) REVERT: C 160 LEU cc_start: 0.2085 (OUTLIER) cc_final: 0.1633 (tt) REVERT: C 179 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7240 (mm-30) REVERT: B 20 GLU cc_start: 0.7815 (tp30) cc_final: 0.7476 (tp30) REVERT: B 127 LEU cc_start: 0.6150 (mt) cc_final: 0.5847 (mm) REVERT: B 164 SER cc_start: 0.7546 (p) cc_final: 0.7129 (m) REVERT: B 207 LYS cc_start: 0.5447 (OUTLIER) cc_final: 0.4916 (mtmm) outliers start: 60 outliers final: 24 residues processed: 185 average time/residue: 0.9863 time to fit residues: 205.3377 Evaluate side-chains 155 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 76 LEU 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 302 ARG Chi-restraints excluded: chain A residue 310 VAL 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 567 THR Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 799 ILE 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 246 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 369 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5129 r_free = 0.5129 target = 0.292214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.243775 restraints weight = 16213.110| |-----------------------------------------------------------------------------| r_work (start): 0.4711 rms_B_bonded: 2.70 r_work: 0.4444 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.4336 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6033 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13746 Z= 0.150 Angle : 0.639 11.877 18576 Z= 0.334 Chirality : 0.045 0.192 2054 Planarity : 0.005 0.077 2366 Dihedral : 4.837 26.094 1822 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.85 % Favored : 90.09 % Rotamer: Outliers : 3.87 % Allowed : 22.32 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.20), residues: 1644 helix: 0.17 (0.21), residues: 570 sheet: -1.36 (0.34), residues: 204 loop : -2.23 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 212 HIS 0.007 0.001 HIS B 181 PHE 0.015 0.002 PHE A 526 TYR 0.029 0.001 TYR C 158 ARG 0.006 0.000 ARG A 577 Details of bonding type rmsd hydrogen bonds : bond 0.04512 ( 525) hydrogen bonds : angle 5.35180 ( 1491) covalent geometry : bond 0.00343 (13746) covalent geometry : angle 0.63943 (18576) *********************** 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 187 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 128 time to evaluate : 2.229 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 92 GLU cc_start: 0.5738 (OUTLIER) cc_final: 0.5363 (mt-10) REVERT: A 146 ARG cc_start: 0.7494 (tmt170) cc_final: 0.7151 (tmm-80) REVERT: A 215 GLU cc_start: 0.6200 (mp0) cc_final: 0.5959 (mp0) REVERT: A 285 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7384 (mm) REVERT: A 302 ARG cc_start: 0.5914 (OUTLIER) cc_final: 0.5618 (mmm-85) REVERT: A 357 MET cc_start: 0.5695 (mmm) cc_final: 0.4978 (mmt) REVERT: A 522 THR cc_start: 0.7174 (OUTLIER) cc_final: 0.6970 (t) REVERT: A 625 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6666 (tpm170) REVERT: A 711 MET cc_start: 0.4609 (mmt) cc_final: 0.4340 (mmp) REVERT: A 712 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6855 (mm) REVERT: A 722 PHE cc_start: 0.5667 (OUTLIER) cc_final: 0.4190 (p90) REVERT: A 799 ILE cc_start: 0.1911 (OUTLIER) cc_final: 0.1292 (pp) REVERT: A 859 MET cc_start: 0.0326 (pp-130) cc_final: -0.0752 (ppp) REVERT: C 1 MET cc_start: 0.3144 (ppp) cc_final: 0.2935 (tmm) REVERT: C 160 LEU cc_start: 0.1989 (OUTLIER) cc_final: 0.1631 (tt) REVERT: C 179 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7219 (mm-30) REVERT: B 20 GLU cc_start: 0.7778 (tp30) cc_final: 0.7205 (mt-10) REVERT: B 127 LEU cc_start: 0.6192 (mt) cc_final: 0.5922 (mm) REVERT: B 207 LYS cc_start: 0.5564 (OUTLIER) cc_final: 0.5041 (mtmm) REVERT: B 214 GLN cc_start: 0.5388 (OUTLIER) cc_final: 0.4975 (mp10) outliers start: 59 outliers final: 32 residues processed: 174 average time/residue: 1.2568 time to fit residues: 246.2320 Evaluate side-chains 164 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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 72 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 92 GLU 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 302 ARG 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 477 THR 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 625 ARG Chi-restraints excluded: chain A residue 701 VAL 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 799 ILE Chi-restraints excluded: chain A residue 892 LEU 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 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 149 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 161 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5115 r_free = 0.5115 target = 0.290647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.241195 restraints weight = 16215.969| |-----------------------------------------------------------------------------| r_work (start): 0.4688 rms_B_bonded: 2.26 r_work: 0.4475 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4377 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.4377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13746 Z= 0.183 Angle : 0.678 13.477 18576 Z= 0.353 Chirality : 0.046 0.214 2054 Planarity : 0.006 0.080 2366 Dihedral : 4.979 26.203 1822 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.79 % Favored : 90.15 % Rotamer: Outliers : 4.33 % Allowed : 22.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.20), residues: 1644 helix: 0.05 (0.21), residues: 572 sheet: -1.42 (0.34), residues: 204 loop : -2.25 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 212 HIS 0.008 0.001 HIS B 181 PHE 0.020 0.002 PHE A 526 TYR 0.027 0.002 TYR C 158 ARG 0.004 0.000 ARG A 519 Details of bonding type rmsd hydrogen bonds : bond 0.04928 ( 525) hydrogen bonds : angle 5.44167 ( 1491) covalent geometry : bond 0.00427 (13746) covalent geometry : angle 0.67842 (18576) *********************** 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 192 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 126 time to evaluate : 2.617 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 92 GLU cc_start: 0.5710 (OUTLIER) cc_final: 0.5409 (mt-10) REVERT: A 146 ARG cc_start: 0.7469 (tmt170) cc_final: 0.7117 (tmm-80) REVERT: A 215 GLU cc_start: 0.6203 (mp0) cc_final: 0.5968 (mp0) REVERT: A 285 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7296 (mm) REVERT: A 302 ARG cc_start: 0.5938 (OUTLIER) cc_final: 0.5667 (mmm-85) REVERT: A 357 MET cc_start: 0.5765 (mmm) cc_final: 0.5037 (mmt) REVERT: A 522 THR cc_start: 0.7259 (OUTLIER) cc_final: 0.7035 (t) REVERT: A 625 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6582 (tpm170) REVERT: A 711 MET cc_start: 0.4646 (mmt) cc_final: 0.4376 (mmp) REVERT: A 712 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6839 (mm) REVERT: A 722 PHE cc_start: 0.5735 (OUTLIER) cc_final: 0.4262 (p90) REVERT: A 799 ILE cc_start: 0.2124 (OUTLIER) cc_final: 0.1490 (pp) REVERT: A 859 MET cc_start: 0.0365 (pp-130) cc_final: -0.0714 (ppp) REVERT: C 45 ILE cc_start: 0.5331 (OUTLIER) cc_final: 0.5104 (pp) REVERT: C 160 LEU cc_start: 0.1976 (OUTLIER) cc_final: 0.1401 (tt) REVERT: C 179 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7209 (mm-30) REVERT: C 410 PHE cc_start: 0.6266 (t80) cc_final: 0.5888 (t80) REVERT: B 20 GLU cc_start: 0.7743 (tp30) cc_final: 0.7396 (tp30) REVERT: B 127 LEU cc_start: 0.6427 (mt) cc_final: 0.6166 (mm) REVERT: B 207 LYS cc_start: 0.5618 (OUTLIER) cc_final: 0.5094 (mtmm) REVERT: B 214 GLN cc_start: 0.5513 (OUTLIER) cc_final: 0.5254 (mp10) outliers start: 66 outliers final: 44 residues processed: 178 average time/residue: 1.6450 time to fit residues: 337.8414 Evaluate side-chains 181 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 125 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 92 GLU 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 302 ARG Chi-restraints excluded: chain A residue 310 VAL 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 477 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 625 ARG Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 701 VAL 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 799 ILE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 47 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 124 ILE 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 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 149 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 92 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5100 r_free = 0.5100 target = 0.288454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.234417 restraints weight = 16035.054| |-----------------------------------------------------------------------------| r_work (start): 0.4627 rms_B_bonded: 2.71 r_work: 0.4433 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4334 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 13746 Z= 0.273 Angle : 0.817 20.105 18576 Z= 0.422 Chirality : 0.051 0.216 2054 Planarity : 0.007 0.086 2366 Dihedral : 5.576 28.773 1822 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.89 % Favored : 89.05 % Rotamer: Outliers : 4.53 % Allowed : 22.98 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.20), residues: 1644 helix: -0.43 (0.21), residues: 574 sheet: -1.52 (0.32), residues: 234 loop : -2.49 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 212 HIS 0.012 0.002 HIS A 170 PHE 0.037 0.003 PHE A 526 TYR 0.024 0.002 TYR B 136 ARG 0.006 0.001 ARG A 519 Details of bonding type rmsd hydrogen bonds : bond 0.06088 ( 525) hydrogen bonds : angle 5.94227 ( 1491) covalent geometry : bond 0.00643 (13746) covalent geometry : angle 0.81656 (18576) *********************** 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 202 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 133 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.5592 (OUTLIER) cc_final: 0.5275 (mt-10) REVERT: A 122 ASP cc_start: 0.6478 (OUTLIER) cc_final: 0.6170 (p0) REVERT: A 146 ARG cc_start: 0.7592 (tmt170) cc_final: 0.7116 (tmm-80) REVERT: A 215 GLU cc_start: 0.6270 (mp0) cc_final: 0.6019 (mp0) REVERT: A 285 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7265 (mm) REVERT: A 302 ARG cc_start: 0.6001 (OUTLIER) cc_final: 0.5746 (mmm-85) REVERT: A 522 THR cc_start: 0.7237 (OUTLIER) cc_final: 0.6990 (t) REVERT: A 711 MET cc_start: 0.4632 (mmt) cc_final: 0.4344 (mmp) REVERT: A 722 PHE cc_start: 0.6073 (OUTLIER) cc_final: 0.4648 (p90) REVERT: A 787 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.5526 (m-80) REVERT: A 799 ILE cc_start: 0.2144 (OUTLIER) cc_final: 0.1474 (pp) REVERT: A 859 MET cc_start: 0.0410 (pp-130) cc_final: -0.0726 (ppp) REVERT: A 996 MET cc_start: 0.2727 (ttt) cc_final: 0.2165 (tpp) REVERT: C 1 MET cc_start: 0.2438 (tmm) cc_final: 0.1669 (ppp) REVERT: C 111 ARG cc_start: 0.5093 (mtp180) cc_final: 0.4814 (mtt180) REVERT: C 160 LEU cc_start: 0.1805 (OUTLIER) cc_final: 0.1178 (tt) REVERT: C 179 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7216 (mm-30) REVERT: C 410 PHE cc_start: 0.6460 (t80) cc_final: 0.6225 (OUTLIER) REVERT: B 48 LYS cc_start: 0.3992 (mttt) cc_final: 0.3789 (tttt) REVERT: B 138 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7175 (t0) REVERT: B 207 LYS cc_start: 0.5956 (OUTLIER) cc_final: 0.5440 (mtmm) REVERT: B 214 GLN cc_start: 0.5539 (OUTLIER) cc_final: 0.5232 (mp10) outliers start: 69 outliers final: 44 residues processed: 188 average time/residue: 1.1810 time to fit residues: 253.8741 Evaluate side-chains 182 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 127 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 71 THR 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 119 ILE Chi-restraints excluded: chain A residue 122 ASP 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 302 ARG 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 477 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 569 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 662 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 787 PHE Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain C residue 47 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 124 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 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 138 ASP 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 15 optimal weight: 0.6980 chunk 126 optimal weight: 30.0000 chunk 132 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5095 r_free = 0.5095 target = 0.287804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.4733 r_free = 0.4733 target = 0.235899 restraints weight = 16114.903| |-----------------------------------------------------------------------------| r_work (start): 0.4626 rms_B_bonded: 3.08 r_work: 0.4398 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4293 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 13746 Z= 0.280 Angle : 0.835 20.264 18576 Z= 0.433 Chirality : 0.052 0.218 2054 Planarity : 0.007 0.090 2366 Dihedral : 5.742 28.716 1822 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.89 % Favored : 89.05 % Rotamer: Outliers : 4.14 % Allowed : 23.70 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.20), residues: 1644 helix: -0.56 (0.21), residues: 565 sheet: -1.70 (0.33), residues: 226 loop : -2.59 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 212 HIS 0.012 0.002 HIS A 170 PHE 0.046 0.003 PHE A 526 TYR 0.027 0.003 TYR C 31 ARG 0.005 0.001 ARG A 519 Details of bonding type rmsd hydrogen bonds : bond 0.06221 ( 525) hydrogen bonds : angle 6.03155 ( 1491) covalent geometry : bond 0.00660 (13746) covalent geometry : angle 0.83467 (18576) ********************** 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 195 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 132 time to evaluate : 1.375 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 92 GLU cc_start: 0.5554 (OUTLIER) cc_final: 0.5205 (mt-10) REVERT: A 122 ASP cc_start: 0.6666 (OUTLIER) cc_final: 0.6248 (p0) REVERT: A 146 ARG cc_start: 0.7700 (tmt170) cc_final: 0.7153 (tmm-80) REVERT: A 215 GLU cc_start: 0.6231 (mp0) cc_final: 0.5937 (mp0) REVERT: A 285 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7288 (mm) REVERT: A 302 ARG cc_start: 0.6105 (OUTLIER) cc_final: 0.5881 (mmm-85) REVERT: A 357 MET cc_start: 0.5798 (mmt) cc_final: 0.5134 (mmt) REVERT: A 522 THR cc_start: 0.7256 (OUTLIER) cc_final: 0.6994 (t) REVERT: A 722 PHE cc_start: 0.6044 (OUTLIER) cc_final: 0.4702 (p90) REVERT: A 787 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.5529 (m-80) REVERT: A 859 MET cc_start: 0.0404 (pp-130) cc_final: -0.0727 (ppp) REVERT: C 1 MET cc_start: 0.2656 (tmm) cc_final: 0.1732 (ppp) REVERT: C 160 LEU cc_start: 0.1736 (OUTLIER) cc_final: 0.1210 (tt) REVERT: C 179 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7206 (mm-30) REVERT: C 259 ARG cc_start: 0.3636 (mmp-170) cc_final: 0.2424 (tpp-160) REVERT: C 399 SER cc_start: 0.7828 (t) cc_final: 0.7403 (p) REVERT: C 404 TYR cc_start: 0.5290 (t80) cc_final: 0.4972 (t80) REVERT: B 207 LYS cc_start: 0.5913 (OUTLIER) cc_final: 0.5424 (mtmm) outliers start: 63 outliers final: 44 residues processed: 181 average time/residue: 0.8670 time to fit residues: 178.2339 Evaluate side-chains 182 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 129 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 71 THR 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 119 ILE Chi-restraints excluded: chain A residue 122 ASP 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 203 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 302 ARG 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 522 THR 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 662 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 787 PHE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 47 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 124 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 142 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN C 397 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5128 r_free = 0.5128 target = 0.292446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.240910 restraints weight = 16160.482| |-----------------------------------------------------------------------------| r_work (start): 0.4680 rms_B_bonded: 2.73 r_work: 0.4480 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4378 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13746 Z= 0.137 Angle : 0.659 12.115 18576 Z= 0.339 Chirality : 0.045 0.185 2054 Planarity : 0.005 0.082 2366 Dihedral : 4.991 26.936 1822 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.82 % Favored : 91.12 % Rotamer: Outliers : 3.28 % Allowed : 24.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.20), residues: 1644 helix: 0.12 (0.22), residues: 558 sheet: -1.37 (0.33), residues: 220 loop : -2.32 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 212 HIS 0.008 0.001 HIS B 181 PHE 0.026 0.002 PHE C 410 TYR 0.027 0.001 TYR C 31 ARG 0.006 0.000 ARG A 577 Details of bonding type rmsd hydrogen bonds : bond 0.04332 ( 525) hydrogen bonds : angle 5.38995 ( 1491) covalent geometry : bond 0.00305 (13746) covalent geometry : angle 0.65914 (18576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15908.81 seconds wall clock time: 283 minutes 10.42 seconds (16990.42 seconds total)