Starting phenix.real_space_refine on Wed Sep 17 19:41:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k7h_9932/09_2025/6k7h_9932.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7h_9932/09_2025/6k7h_9932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6k7h_9932/09_2025/6k7h_9932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7h_9932/09_2025/6k7h_9932.map" model { file = "/net/cci-nas-00/data/ceres_data/6k7h_9932/09_2025/6k7h_9932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7h_9932/09_2025/6k7h_9932.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 56 5.16 5 C 6857 2.51 5 N 1753 2.21 5 O 1911 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10577 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7860 Classifications: {'peptide': 987} Link IDs: {'PTRANS': 30, 'TRANS': 956} Chain breaks: 3 Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2615 Classifications: {'peptide': 325} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 299} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.67, per 1000 atoms: 0.25 Number of scatterers: 10577 At special positions: 0 Unit cell: (67.23, 109.56, 170.15, 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 56 16.00 O 1911 8.00 N 1753 7.00 C 6857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.02 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 492.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2470 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 13 sheets defined 49.1% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 101 through 127 Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.752A pdb=" N GLY A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 142 " --> pdb=" O ARG A 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 138 through 142' Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.693A pdb=" N ASP A 273 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 274 " --> pdb=" O GLY A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 274' Processing helix chain 'A' and resid 288 through 323 Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 352 through 355 removed outlier: 3.811A pdb=" N ILE A 355 " --> pdb=" O ASN A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 358 through 377 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.985A pdb=" N LEU A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 456 Processing helix chain 'A' and resid 458 through 472 removed outlier: 5.090A pdb=" N GLU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N PHE A 465 " --> pdb=" O ILE A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 503 Processing helix chain 'A' and resid 561 through 567 removed outlier: 3.974A pdb=" N ARG A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 588 removed outlier: 4.499A pdb=" N GLU A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 618 removed outlier: 4.196A pdb=" N VAL A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR A 616 " --> pdb=" O GLN A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 633 removed outlier: 3.731A pdb=" N LYS A 624 " --> pdb=" O ASN A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 662 Processing helix chain 'A' and resid 673 through 684 Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 762 through 778 removed outlier: 4.198A pdb=" N GLN A 776 " --> pdb=" O MET A 772 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A 778 " --> pdb=" O LYS A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 809 through 815 Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 824 through 831 Processing helix chain 'A' and resid 832 through 856 removed outlier: 4.011A pdb=" N ASN A 851 " --> pdb=" O CYS A 847 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 854 " --> pdb=" O LYS A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 862 Processing helix chain 'A' and resid 874 through 880 removed outlier: 3.515A pdb=" N ILE A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 896 removed outlier: 4.005A pdb=" N LEU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 908 Processing helix chain 'A' and resid 909 through 919 removed outlier: 4.293A pdb=" N LYS A 913 " --> pdb=" O PRO A 909 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN A 917 " --> pdb=" O LYS A 913 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 919 " --> pdb=" O SER A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 948 Proline residue: A 944 - end of helix Processing helix chain 'A' and resid 961 through 985 removed outlier: 4.059A pdb=" N LEU A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1011 Processing helix chain 'A' and resid 1025 through 1033 Processing helix chain 'A' and resid 1033 through 1062 removed outlier: 3.975A pdb=" N TRP A1037 " --> pdb=" O SER A1033 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET A1038 " --> pdb=" O GLY A1034 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU A1041 " --> pdb=" O TRP A1037 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 4.990A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 Proline residue: C 52 - end of helix removed outlier: 3.985A pdb=" N LEU C 59 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 91 through 95 removed outlier: 3.721A pdb=" N LEU C 95 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 139 through 145 Processing helix chain 'C' and resid 146 through 151 Processing helix chain 'C' and resid 157 through 161 removed outlier: 4.171A pdb=" N ARG C 161 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 239 through 243 Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.839A pdb=" N PHE C 304 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP C 305 " --> pdb=" O HIS C 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 301 through 305' Processing helix chain 'C' and resid 323 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 137 Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 160 removed outlier: 6.811A pdb=" N TRP A 262 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N SER A 174 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N HIS A 264 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP A 168 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 164 Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 185 removed outlier: 4.843A pdb=" N THR A 185 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ASN A 193 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 219 through 221 Processing sheet with id=AA6, first strand: chain 'A' and resid 381 through 382 Processing sheet with id=AA7, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.723A pdb=" N GLY A 800 " --> pdb=" O TYR A 817 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE A 819 " --> pdb=" O GLY A 800 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLY A 802 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR A 781 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL A 801 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ALA A 783 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE A 803 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLY A 785 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL A 403 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU A 782 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR A 405 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE A 784 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE A 407 " --> pdb=" O ILE A 784 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS A 404 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TRP A 667 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE A 406 " --> pdb=" O TRP A 667 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU A 669 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER A 408 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 429 through 431 removed outlier: 3.681A pdb=" N VAL A 429 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE A 426 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA A 643 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 505 through 507 Processing sheet with id=AB1, first strand: chain 'A' and resid 540 through 545 Processing sheet with id=AB2, first strand: chain 'C' and resid 77 through 81 removed outlier: 7.247A pdb=" N VAL C 118 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU C 275 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET C 120 " --> pdb=" O TYR C 273 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 102 through 103 removed outlier: 4.030A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 106 through 109 removed outlier: 5.078A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1371 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1752 1.32 - 1.44: 2903 1.44 - 1.57: 6085 1.57 - 1.69: 1 1.69 - 1.81: 85 Bond restraints: 10826 Sorted by residual: bond pdb=" CB VAL A 969 " pdb=" CG2 VAL A 969 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.99e+00 bond pdb=" CB PRO C 170 " pdb=" CG PRO C 170 " ideal model delta sigma weight residual 1.506 1.417 0.089 3.90e-02 6.57e+02 5.23e+00 bond pdb=" CD LYS C 308 " pdb=" CE LYS C 308 " ideal model delta sigma weight residual 1.520 1.458 0.062 3.00e-02 1.11e+03 4.30e+00 bond pdb=" CB ARG C 262 " pdb=" CG ARG C 262 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.10e+00 bond pdb=" CG1 ILE A 996 " pdb=" CD1 ILE A 996 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.94e+00 ... (remaining 10821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 14227 2.76 - 5.52: 410 5.52 - 8.28: 45 8.28 - 11.04: 11 11.04 - 13.80: 3 Bond angle restraints: 14696 Sorted by residual: angle pdb=" C ARG A 75 " pdb=" N ALA A 76 " pdb=" CA ALA A 76 " ideal model delta sigma weight residual 121.54 130.50 -8.96 1.91e+00 2.74e-01 2.20e+01 angle pdb=" CA MET C 318 " pdb=" CB MET C 318 " pdb=" CG MET C 318 " ideal model delta sigma weight residual 114.10 123.09 -8.99 2.00e+00 2.50e-01 2.02e+01 angle pdb=" C MET A 830 " pdb=" N ILE A 831 " pdb=" CA ILE A 831 " ideal model delta sigma weight residual 122.76 116.22 6.54 1.57e+00 4.06e-01 1.74e+01 angle pdb=" C GLY C 251 " pdb=" N PHE C 252 " pdb=" CA PHE C 252 " ideal model delta sigma weight residual 121.54 129.35 -7.81 1.91e+00 2.74e-01 1.67e+01 angle pdb=" C THR A 281 " pdb=" N SER A 282 " pdb=" CA SER A 282 " ideal model delta sigma weight residual 120.97 132.40 -11.43 2.84e+00 1.24e-01 1.62e+01 ... (remaining 14691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 5614 16.15 - 32.31: 724 32.31 - 48.46: 166 48.46 - 64.62: 41 64.62 - 80.77: 13 Dihedral angle restraints: 6558 sinusoidal: 2729 harmonic: 3829 Sorted by residual: dihedral pdb=" CA LYS A 483 " pdb=" C LYS A 483 " pdb=" N ILE A 484 " pdb=" CA ILE A 484 " ideal model delta harmonic sigma weight residual -180.00 -130.56 -49.44 0 5.00e+00 4.00e-02 9.78e+01 dihedral pdb=" CB CYS C 157 " pdb=" SG CYS C 157 " pdb=" SG CYS C 171 " pdb=" CB CYS C 171 " ideal model delta sinusoidal sigma weight residual 93.00 36.09 56.91 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CA SER C 316 " pdb=" C SER C 316 " pdb=" N TRP C 317 " pdb=" CA TRP C 317 " ideal model delta harmonic sigma weight residual 180.00 152.98 27.02 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 6555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1175 0.063 - 0.125: 414 0.125 - 0.188: 80 0.188 - 0.251: 11 0.251 - 0.314: 2 Chirality restraints: 1682 Sorted by residual: chirality pdb=" C4 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C5 NAG B 2 " pdb=" O4 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.53 -2.22 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CB ILE A 108 " pdb=" CA ILE A 108 " pdb=" CG1 ILE A 108 " pdb=" CG2 ILE A 108 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB VAL A 545 " pdb=" CA VAL A 545 " pdb=" CG1 VAL A 545 " pdb=" CG2 VAL A 545 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1679 not shown) Planarity restraints: 1839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " -0.317 2.00e-02 2.50e+03 2.77e-01 9.59e+02 pdb=" C7 NAG C 402 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " -0.114 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " 0.497 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " -0.134 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.238 2.00e-02 2.50e+03 1.97e-01 4.86e+02 pdb=" C7 NAG C 401 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " 0.166 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.325 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.132 2.00e-02 2.50e+03 1.15e-01 1.65e+02 pdb=" C7 NAG B 1 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.022 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.190 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.106 2.00e-02 2.50e+03 ... (remaining 1836 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2801 2.80 - 3.32: 9424 3.32 - 3.85: 17748 3.85 - 4.37: 21002 4.37 - 4.90: 36217 Nonbonded interactions: 87192 Sorted by model distance: nonbonded pdb=" O LEU A 400 " pdb=" OH TYR A 912 " model vdw 2.274 3.040 nonbonded pdb=" OG SER A 490 " pdb=" OD1 ASP A 492 " model vdw 2.308 3.040 nonbonded pdb=" OE2 GLU A 897 " pdb=" OG SER A 986 " model vdw 2.320 3.040 nonbonded pdb=" O SER A 814 " pdb=" OG SER A 814 " model vdw 2.325 3.040 nonbonded pdb=" ND2 ASN C 176 " pdb=" OD1 ASN C 235 " model vdw 2.333 3.120 ... (remaining 87187 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.030 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 : 0.011 0.089 10834 Z= 0.443 Angle : 1.116 13.796 14717 Z= 0.592 Chirality : 0.065 0.314 1682 Planarity : 0.012 0.277 1836 Dihedral : 15.571 80.770 4079 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.13 % Allowed : 10.94 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.82 (0.19), residues: 1302 helix: -2.60 (0.15), residues: 594 sheet: -1.24 (0.38), residues: 173 loop : -2.75 (0.23), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 37 TYR 0.029 0.003 TYR C 122 PHE 0.035 0.003 PHE C 179 TRP 0.037 0.003 TRP A1003 HIS 0.008 0.002 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.01089 (10826) covalent geometry : angle 1.10920 (14696) SS BOND : bond 0.00765 ( 3) SS BOND : angle 1.68030 ( 6) hydrogen bonds : bond 0.11682 ( 473) hydrogen bonds : angle 6.60536 ( 1371) link_ALPHA1-4 : bond 0.00426 ( 1) link_ALPHA1-4 : angle 5.60951 ( 3) link_BETA1-4 : bond 0.00083 ( 1) link_BETA1-4 : angle 3.28438 ( 3) link_NAG-ASN : bond 0.01152 ( 3) link_NAG-ASN : angle 3.25687 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.8754 (mttt) cc_final: 0.8185 (mtmt) REVERT: A 535 THR cc_start: 0.2267 (OUTLIER) cc_final: 0.1901 (t) REVERT: A 599 ILE cc_start: -0.1456 (OUTLIER) cc_final: -0.1900 (tp) REVERT: A 753 CYS cc_start: 0.7243 (m) cc_final: 0.6791 (m) REVERT: A 852 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8388 (mp) REVERT: C 146 ASP cc_start: 0.7661 (m-30) cc_final: 0.7333 (m-30) REVERT: C 201 LYS cc_start: 0.9085 (pttt) cc_final: 0.8829 (ptmt) REVERT: C 315 ILE cc_start: 0.8013 (pt) cc_final: 0.7719 (pt) outliers start: 13 outliers final: 2 residues processed: 144 average time/residue: 0.1224 time to fit residues: 23.9999 Evaluate side-chains 93 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain C residue 50 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 129 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: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN A 147 HIS A 234 ASN A 320 ASN A 323 HIS A 397 ASN A 453 GLN A 522 GLN A 583 GLN A 605 GLN A 679 ASN A 682 HIS A 744 GLN A 810 GLN A 949 GLN A 993 HIS C 92 ASN C 131 HIS C 142 GLN C 190 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.190595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.130928 restraints weight = 10976.285| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 5.23 r_work: 0.2854 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 10834 Z= 0.137 Angle : 0.638 7.923 14717 Z= 0.329 Chirality : 0.044 0.177 1682 Planarity : 0.005 0.050 1836 Dihedral : 7.048 58.235 1597 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.17 % Allowed : 13.45 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.21), residues: 1302 helix: -0.80 (0.20), residues: 592 sheet: -0.89 (0.39), residues: 180 loop : -2.18 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 226 TYR 0.015 0.001 TYR C 122 PHE 0.016 0.001 PHE C 108 TRP 0.034 0.001 TRP A1003 HIS 0.003 0.001 HIS A 993 Details of bonding type rmsd covalent geometry : bond 0.00310 (10826) covalent geometry : angle 0.63031 (14696) SS BOND : bond 0.00528 ( 3) SS BOND : angle 1.23507 ( 6) hydrogen bonds : bond 0.04684 ( 473) hydrogen bonds : angle 5.22652 ( 1371) link_ALPHA1-4 : bond 0.00027 ( 1) link_ALPHA1-4 : angle 4.31144 ( 3) link_BETA1-4 : bond 0.00003 ( 1) link_BETA1-4 : angle 2.97499 ( 3) link_NAG-ASN : bond 0.00361 ( 3) link_NAG-ASN : angle 2.51932 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.8880 (mttt) cc_final: 0.8319 (mtmt) REVERT: A 535 THR cc_start: 0.2085 (OUTLIER) cc_final: 0.1793 (t) REVERT: A 599 ILE cc_start: -0.0145 (OUTLIER) cc_final: -0.0984 (tp) REVERT: A 693 MET cc_start: 0.3391 (mpp) cc_final: 0.2571 (ttt) REVERT: A 753 CYS cc_start: 0.7591 (m) cc_final: 0.7231 (m) REVERT: A 852 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8761 (mp) REVERT: A 905 MET cc_start: 0.8396 (mtp) cc_final: 0.8182 (mtp) REVERT: A 1059 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6773 (tpt-90) REVERT: C 92 ASN cc_start: 0.8764 (t0) cc_final: 0.8488 (t0) REVERT: C 146 ASP cc_start: 0.7857 (m-30) cc_final: 0.7549 (m-30) REVERT: C 201 LYS cc_start: 0.9023 (pttt) cc_final: 0.8799 (ptpt) REVERT: C 223 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7997 (tt) REVERT: C 315 ILE cc_start: 0.8017 (pt) cc_final: 0.7748 (pt) outliers start: 25 outliers final: 9 residues processed: 128 average time/residue: 0.0980 time to fit residues: 17.9461 Evaluate side-chains 113 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 682 HIS Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 302 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 61 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 117 optimal weight: 0.0070 chunk 75 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.189122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132938 restraints weight = 11042.995| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.59 r_work: 0.2869 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10834 Z= 0.151 Angle : 0.626 12.003 14717 Z= 0.317 Chirality : 0.045 0.185 1682 Planarity : 0.004 0.045 1836 Dihedral : 6.580 57.876 1597 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.43 % Allowed : 13.98 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.22), residues: 1302 helix: -0.16 (0.21), residues: 593 sheet: -0.73 (0.39), residues: 181 loop : -2.01 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 290 TYR 0.017 0.001 TYR C 122 PHE 0.014 0.001 PHE A 968 TRP 0.017 0.001 TRP A1003 HIS 0.008 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00354 (10826) covalent geometry : angle 0.61853 (14696) SS BOND : bond 0.00262 ( 3) SS BOND : angle 1.07268 ( 6) hydrogen bonds : bond 0.04549 ( 473) hydrogen bonds : angle 4.99794 ( 1371) link_ALPHA1-4 : bond 0.00080 ( 1) link_ALPHA1-4 : angle 4.34345 ( 3) link_BETA1-4 : bond 0.00224 ( 1) link_BETA1-4 : angle 3.16506 ( 3) link_NAG-ASN : bond 0.00396 ( 3) link_NAG-ASN : angle 2.28635 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 MET cc_start: 0.5657 (ptm) cc_final: 0.5386 (ptp) REVERT: A 326 LYS cc_start: 0.8904 (mttt) cc_final: 0.8394 (mtmt) REVERT: A 535 THR cc_start: 0.2391 (OUTLIER) cc_final: 0.2034 (t) REVERT: A 599 ILE cc_start: -0.0329 (OUTLIER) cc_final: -0.1240 (tp) REVERT: A 693 MET cc_start: 0.3650 (mpp) cc_final: 0.2743 (ttt) REVERT: A 727 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7706 (mp) REVERT: A 753 CYS cc_start: 0.7851 (m) cc_final: 0.7178 (m) REVERT: A 874 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: A 900 CYS cc_start: 0.7669 (OUTLIER) cc_final: 0.6907 (t) REVERT: A 905 MET cc_start: 0.8500 (mtp) cc_final: 0.8213 (mtp) REVERT: A 1059 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6872 (tpt-90) REVERT: C 92 ASN cc_start: 0.8788 (t0) cc_final: 0.8318 (t0) REVERT: C 146 ASP cc_start: 0.7912 (m-30) cc_final: 0.7621 (m-30) REVERT: C 223 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8205 (tt) REVERT: C 262 ARG cc_start: 0.8724 (mmt-90) cc_final: 0.8448 (ttm-80) REVERT: C 315 ILE cc_start: 0.8045 (pt) cc_final: 0.7779 (pt) outliers start: 28 outliers final: 12 residues processed: 122 average time/residue: 0.1088 time to fit residues: 18.9707 Evaluate side-chains 113 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 900 CYS Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 302 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 43 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 52 optimal weight: 30.0000 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 HIS C 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.193101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.135407 restraints weight = 11028.444| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.45 r_work: 0.2842 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10834 Z= 0.177 Angle : 0.631 9.905 14717 Z= 0.320 Chirality : 0.046 0.246 1682 Planarity : 0.004 0.045 1836 Dihedral : 6.335 57.851 1595 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.04 % Allowed : 15.02 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.23), residues: 1302 helix: 0.17 (0.22), residues: 590 sheet: -0.78 (0.38), residues: 187 loop : -1.79 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 226 TYR 0.019 0.001 TYR C 122 PHE 0.015 0.001 PHE A 968 TRP 0.015 0.001 TRP A 927 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00426 (10826) covalent geometry : angle 0.62408 (14696) SS BOND : bond 0.00337 ( 3) SS BOND : angle 1.12645 ( 6) hydrogen bonds : bond 0.04587 ( 473) hydrogen bonds : angle 4.96058 ( 1371) link_ALPHA1-4 : bond 0.00198 ( 1) link_ALPHA1-4 : angle 4.29413 ( 3) link_BETA1-4 : bond 0.00170 ( 1) link_BETA1-4 : angle 3.23262 ( 3) link_NAG-ASN : bond 0.00468 ( 3) link_NAG-ASN : angle 2.35510 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 MET cc_start: 0.5536 (ptm) cc_final: 0.5260 (ptp) REVERT: A 326 LYS cc_start: 0.8909 (mttt) cc_final: 0.8369 (mtmt) REVERT: A 535 THR cc_start: 0.2285 (OUTLIER) cc_final: 0.1916 (t) REVERT: A 693 MET cc_start: 0.3821 (mpp) cc_final: 0.2886 (ttt) REVERT: A 727 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7622 (mp) REVERT: A 742 VAL cc_start: 0.5798 (OUTLIER) cc_final: 0.5519 (t) REVERT: A 753 CYS cc_start: 0.7791 (m) cc_final: 0.7124 (m) REVERT: A 874 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: A 900 CYS cc_start: 0.7570 (OUTLIER) cc_final: 0.6795 (t) REVERT: A 1059 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6849 (tpt-90) REVERT: C 92 ASN cc_start: 0.8751 (t0) cc_final: 0.8476 (t0) REVERT: C 146 ASP cc_start: 0.7845 (m-30) cc_final: 0.7589 (m-30) REVERT: C 262 ARG cc_start: 0.8779 (mmt-90) cc_final: 0.8541 (ttm-80) REVERT: C 315 ILE cc_start: 0.8039 (pt) cc_final: 0.7809 (pt) outliers start: 35 outliers final: 19 residues processed: 129 average time/residue: 0.0942 time to fit residues: 17.7051 Evaluate side-chains 120 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 900 CYS Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 302 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 125 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 99 optimal weight: 0.0050 chunk 102 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.193920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135774 restraints weight = 10971.300| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.42 r_work: 0.2858 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10834 Z= 0.151 Angle : 0.599 8.802 14717 Z= 0.304 Chirality : 0.044 0.175 1682 Planarity : 0.004 0.045 1836 Dihedral : 6.099 57.718 1595 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.47 % Allowed : 15.10 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.23), residues: 1302 helix: 0.38 (0.22), residues: 591 sheet: -0.58 (0.39), residues: 182 loop : -1.68 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 226 TYR 0.016 0.001 TYR C 122 PHE 0.014 0.001 PHE A 968 TRP 0.015 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00357 (10826) covalent geometry : angle 0.59206 (14696) SS BOND : bond 0.00290 ( 3) SS BOND : angle 0.97638 ( 6) hydrogen bonds : bond 0.04336 ( 473) hydrogen bonds : angle 4.83733 ( 1371) link_ALPHA1-4 : bond 0.00100 ( 1) link_ALPHA1-4 : angle 4.17518 ( 3) link_BETA1-4 : bond 0.00074 ( 1) link_BETA1-4 : angle 3.15597 ( 3) link_NAG-ASN : bond 0.00427 ( 3) link_NAG-ASN : angle 2.17153 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 136 GLN cc_start: 0.7444 (mp10) cc_final: 0.7216 (mp10) REVERT: A 165 ILE cc_start: 0.8309 (mt) cc_final: 0.7987 (tp) REVERT: A 213 MET cc_start: 0.5504 (ptm) cc_final: 0.5231 (ptp) REVERT: A 326 LYS cc_start: 0.8875 (mttt) cc_final: 0.8330 (mtmt) REVERT: A 535 THR cc_start: 0.2448 (OUTLIER) cc_final: 0.2058 (t) REVERT: A 693 MET cc_start: 0.3849 (mpp) cc_final: 0.2996 (ttt) REVERT: A 727 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7581 (mp) REVERT: A 742 VAL cc_start: 0.5817 (OUTLIER) cc_final: 0.5544 (t) REVERT: A 753 CYS cc_start: 0.7826 (m) cc_final: 0.7118 (m) REVERT: A 852 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8801 (mp) REVERT: A 874 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: A 1059 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6845 (tpt-90) REVERT: C 92 ASN cc_start: 0.8725 (t0) cc_final: 0.8451 (t0) REVERT: C 146 ASP cc_start: 0.7791 (m-30) cc_final: 0.7530 (m-30) REVERT: C 315 ILE cc_start: 0.8076 (pt) cc_final: 0.7858 (pt) outliers start: 40 outliers final: 24 residues processed: 130 average time/residue: 0.1021 time to fit residues: 19.3651 Evaluate side-chains 126 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 302 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 63 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 95 optimal weight: 0.0060 chunk 109 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** A 264 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 = 0.4095 r_free = 0.4095 target = 0.192365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.135554 restraints weight = 11026.421| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.74 r_work: 0.2822 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10834 Z= 0.160 Angle : 0.603 8.642 14717 Z= 0.306 Chirality : 0.045 0.177 1682 Planarity : 0.004 0.045 1836 Dihedral : 6.000 57.488 1595 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.73 % Allowed : 15.10 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.24), residues: 1302 helix: 0.46 (0.22), residues: 591 sheet: -0.52 (0.39), residues: 182 loop : -1.61 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 226 TYR 0.017 0.001 TYR C 122 PHE 0.025 0.001 PHE A 368 TRP 0.015 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00380 (10826) covalent geometry : angle 0.59618 (14696) SS BOND : bond 0.00319 ( 3) SS BOND : angle 1.04134 ( 6) hydrogen bonds : bond 0.04365 ( 473) hydrogen bonds : angle 4.80222 ( 1371) link_ALPHA1-4 : bond 0.00061 ( 1) link_ALPHA1-4 : angle 4.10265 ( 3) link_BETA1-4 : bond 0.00190 ( 1) link_BETA1-4 : angle 3.19208 ( 3) link_NAG-ASN : bond 0.00475 ( 3) link_NAG-ASN : angle 2.15696 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 103 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 136 GLN cc_start: 0.7457 (mp10) cc_final: 0.7202 (mp10) REVERT: A 326 LYS cc_start: 0.8861 (mttt) cc_final: 0.8303 (mtmt) REVERT: A 535 THR cc_start: 0.2491 (OUTLIER) cc_final: 0.2067 (t) REVERT: A 693 MET cc_start: 0.3867 (mpp) cc_final: 0.3017 (ttt) REVERT: A 727 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7607 (mp) REVERT: A 753 CYS cc_start: 0.7899 (m) cc_final: 0.7219 (m) REVERT: A 852 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8796 (mp) REVERT: A 874 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: A 1059 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6870 (tpt-90) REVERT: C 92 ASN cc_start: 0.8715 (t0) cc_final: 0.8415 (t0) REVERT: C 310 MET cc_start: 0.8806 (tmm) cc_final: 0.8583 (ttp) REVERT: C 315 ILE cc_start: 0.8118 (pt) cc_final: 0.7897 (pt) outliers start: 43 outliers final: 28 residues processed: 141 average time/residue: 0.0925 time to fit residues: 19.4076 Evaluate side-chains 130 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 939 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 302 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 85 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 chunk 75 optimal weight: 0.0980 chunk 106 optimal weight: 2.9990 chunk 49 optimal weight: 40.0000 chunk 55 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 126 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.195047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.135264 restraints weight = 10866.999| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 5.25 r_work: 0.2818 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10834 Z= 0.138 Angle : 0.601 10.540 14717 Z= 0.303 Chirality : 0.044 0.170 1682 Planarity : 0.004 0.045 1836 Dihedral : 5.859 57.289 1595 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.39 % Allowed : 16.49 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.24), residues: 1302 helix: 0.61 (0.22), residues: 592 sheet: -0.49 (0.39), residues: 182 loop : -1.55 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 226 TYR 0.015 0.001 TYR C 122 PHE 0.021 0.001 PHE A 368 TRP 0.015 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00321 (10826) covalent geometry : angle 0.59425 (14696) SS BOND : bond 0.00292 ( 3) SS BOND : angle 0.90466 ( 6) hydrogen bonds : bond 0.04166 ( 473) hydrogen bonds : angle 4.77000 ( 1371) link_ALPHA1-4 : bond 0.00023 ( 1) link_ALPHA1-4 : angle 4.03157 ( 3) link_BETA1-4 : bond 0.00240 ( 1) link_BETA1-4 : angle 3.12094 ( 3) link_NAG-ASN : bond 0.00399 ( 3) link_NAG-ASN : angle 2.01260 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.441 Fit side-chains REVERT: A 136 GLN cc_start: 0.7491 (mp10) cc_final: 0.6826 (tp40) REVERT: A 326 LYS cc_start: 0.8841 (mttt) cc_final: 0.8242 (mtmt) REVERT: A 693 MET cc_start: 0.3723 (mpp) cc_final: 0.2837 (ttt) REVERT: A 727 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7476 (mp) REVERT: A 753 CYS cc_start: 0.7789 (m) cc_final: 0.7066 (m) REVERT: A 852 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8701 (mp) REVERT: A 874 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: A 1059 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6763 (tpt-90) REVERT: C 92 ASN cc_start: 0.8656 (t0) cc_final: 0.8336 (t0) REVERT: C 315 ILE cc_start: 0.8103 (pt) cc_final: 0.7902 (pt) REVERT: C 348 HIS cc_start: 0.7671 (t70) cc_final: 0.7424 (t-90) outliers start: 39 outliers final: 25 residues processed: 132 average time/residue: 0.0945 time to fit residues: 18.6001 Evaluate side-chains 124 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 939 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 302 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 94 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 62 optimal weight: 0.1980 chunk 63 optimal weight: 0.0370 chunk 87 optimal weight: 2.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 264 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.192437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.137701 restraints weight = 10913.839| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.82 r_work: 0.2867 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 10834 Z= 0.111 Angle : 0.595 8.995 14717 Z= 0.300 Chirality : 0.043 0.164 1682 Planarity : 0.004 0.045 1836 Dihedral : 5.606 56.845 1594 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.69 % Allowed : 17.36 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.24), residues: 1302 helix: 0.77 (0.22), residues: 593 sheet: -0.39 (0.39), residues: 181 loop : -1.51 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A 743 TYR 0.019 0.001 TYR A 849 PHE 0.021 0.001 PHE A 368 TRP 0.018 0.001 TRP A 143 HIS 0.003 0.001 HIS A 473 Details of bonding type rmsd covalent geometry : bond 0.00248 (10826) covalent geometry : angle 0.58978 (14696) SS BOND : bond 0.00190 ( 3) SS BOND : angle 0.70852 ( 6) hydrogen bonds : bond 0.03835 ( 473) hydrogen bonds : angle 4.66868 ( 1371) link_ALPHA1-4 : bond 0.00111 ( 1) link_ALPHA1-4 : angle 3.85312 ( 3) link_BETA1-4 : bond 0.00155 ( 1) link_BETA1-4 : angle 2.94289 ( 3) link_NAG-ASN : bond 0.00300 ( 3) link_NAG-ASN : angle 1.82389 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.374 Fit side-chains REVERT: A 136 GLN cc_start: 0.7439 (mp10) cc_final: 0.6806 (tm-30) REVERT: A 165 ILE cc_start: 0.8407 (mt) cc_final: 0.8076 (tp) REVERT: A 180 MET cc_start: 0.5533 (mmt) cc_final: 0.4858 (mmt) REVERT: A 326 LYS cc_start: 0.8822 (mttt) cc_final: 0.8274 (mtmt) REVERT: A 693 MET cc_start: 0.3787 (mpp) cc_final: 0.2820 (ttt) REVERT: A 727 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7571 (mp) REVERT: A 753 CYS cc_start: 0.7879 (m) cc_final: 0.7182 (m) REVERT: A 849 TYR cc_start: 0.9013 (OUTLIER) cc_final: 0.8752 (t80) REVERT: A 852 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8676 (mp) REVERT: A 1059 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6808 (tpt170) REVERT: C 92 ASN cc_start: 0.8673 (t0) cc_final: 0.8384 (t0) REVERT: C 310 MET cc_start: 0.8798 (tmm) cc_final: 0.8551 (ttp) REVERT: C 315 ILE cc_start: 0.8048 (pt) cc_final: 0.7845 (pt) outliers start: 31 outliers final: 20 residues processed: 123 average time/residue: 0.0913 time to fit residues: 16.7893 Evaluate side-chains 118 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 849 TYR Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 939 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 302 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 71 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.190834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.129421 restraints weight = 10948.382| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 5.73 r_work: 0.2767 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10834 Z= 0.139 Angle : 0.606 8.902 14717 Z= 0.306 Chirality : 0.044 0.176 1682 Planarity : 0.004 0.044 1836 Dihedral : 5.603 56.626 1594 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.86 % Allowed : 17.45 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.24), residues: 1302 helix: 0.79 (0.22), residues: 592 sheet: -0.32 (0.39), residues: 181 loop : -1.46 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 743 TYR 0.016 0.001 TYR A 849 PHE 0.020 0.001 PHE A 368 TRP 0.014 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00329 (10826) covalent geometry : angle 0.60051 (14696) SS BOND : bond 0.00290 ( 3) SS BOND : angle 0.93363 ( 6) hydrogen bonds : bond 0.04102 ( 473) hydrogen bonds : angle 4.71824 ( 1371) link_ALPHA1-4 : bond 0.00038 ( 1) link_ALPHA1-4 : angle 3.78770 ( 3) link_BETA1-4 : bond 0.00245 ( 1) link_BETA1-4 : angle 3.16889 ( 3) link_NAG-ASN : bond 0.00443 ( 3) link_NAG-ASN : angle 1.98086 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.427 Fit side-chains REVERT: A 136 GLN cc_start: 0.7412 (mp10) cc_final: 0.6743 (tm-30) REVERT: A 165 ILE cc_start: 0.8321 (mt) cc_final: 0.8016 (tp) REVERT: A 326 LYS cc_start: 0.8832 (mttt) cc_final: 0.8243 (mtmt) REVERT: A 693 MET cc_start: 0.3642 (mpp) cc_final: 0.2833 (ttt) REVERT: A 727 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7418 (mp) REVERT: A 753 CYS cc_start: 0.7857 (m) cc_final: 0.7198 (m) REVERT: A 849 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.8799 (t80) REVERT: A 852 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8713 (mp) REVERT: A 1059 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6713 (tpt170) REVERT: C 92 ASN cc_start: 0.8651 (t0) cc_final: 0.8319 (t0) REVERT: C 310 MET cc_start: 0.8869 (tmm) cc_final: 0.8614 (ttp) REVERT: C 315 ILE cc_start: 0.8012 (pt) cc_final: 0.7795 (pt) outliers start: 33 outliers final: 24 residues processed: 127 average time/residue: 0.0884 time to fit residues: 16.9802 Evaluate side-chains 122 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 849 TYR Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 939 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 302 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 90 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.0020 chunk 87 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.191370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.129735 restraints weight = 10853.497| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 5.03 r_work: 0.2847 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10834 Z= 0.166 Angle : 0.636 11.942 14717 Z= 0.319 Chirality : 0.045 0.169 1682 Planarity : 0.004 0.044 1836 Dihedral : 5.699 56.802 1594 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.52 % Allowed : 17.62 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.24), residues: 1302 helix: 0.78 (0.22), residues: 585 sheet: -0.38 (0.40), residues: 180 loop : -1.34 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 743 TYR 0.018 0.001 TYR A 849 PHE 0.022 0.001 PHE A 368 TRP 0.014 0.001 TRP A 927 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00397 (10826) covalent geometry : angle 0.62994 (14696) SS BOND : bond 0.00372 ( 3) SS BOND : angle 1.04070 ( 6) hydrogen bonds : bond 0.04333 ( 473) hydrogen bonds : angle 4.80086 ( 1371) link_ALPHA1-4 : bond 0.00093 ( 1) link_ALPHA1-4 : angle 3.91298 ( 3) link_BETA1-4 : bond 0.00205 ( 1) link_BETA1-4 : angle 3.18048 ( 3) link_NAG-ASN : bond 0.00491 ( 3) link_NAG-ASN : angle 1.98441 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.331 Fit side-chains REVERT: A 136 GLN cc_start: 0.7350 (mp10) cc_final: 0.6764 (tm-30) REVERT: A 165 ILE cc_start: 0.8264 (mt) cc_final: 0.7926 (tp) REVERT: A 326 LYS cc_start: 0.8858 (mttt) cc_final: 0.8281 (mtmt) REVERT: A 693 MET cc_start: 0.3809 (mpp) cc_final: 0.2924 (ttt) REVERT: A 727 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7475 (mp) REVERT: A 753 CYS cc_start: 0.7836 (m) cc_final: 0.7130 (m) REVERT: A 849 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.8774 (t80) REVERT: A 852 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8737 (mp) REVERT: A 1059 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6652 (tpt170) REVERT: C 92 ASN cc_start: 0.8702 (t0) cc_final: 0.8373 (t0) REVERT: C 310 MET cc_start: 0.8725 (tmm) cc_final: 0.8476 (ttp) outliers start: 29 outliers final: 24 residues processed: 122 average time/residue: 0.0832 time to fit residues: 15.3122 Evaluate side-chains 121 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 849 TYR Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 939 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 302 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 62 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 30.0000 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 0.0050 chunk 117 optimal weight: 0.1980 chunk 76 optimal weight: 2.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.195127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.135565 restraints weight = 10863.616| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 4.67 r_work: 0.2900 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10834 Z= 0.113 Angle : 0.599 11.982 14717 Z= 0.300 Chirality : 0.043 0.164 1682 Planarity : 0.004 0.044 1836 Dihedral : 5.442 56.218 1594 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.17 % Allowed : 18.14 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.24), residues: 1302 helix: 0.97 (0.22), residues: 589 sheet: -0.28 (0.39), residues: 181 loop : -1.28 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 226 TYR 0.018 0.001 TYR A 849 PHE 0.023 0.001 PHE A 368 TRP 0.016 0.001 TRP A 927 HIS 0.003 0.001 HIS A 473 Details of bonding type rmsd covalent geometry : bond 0.00253 (10826) covalent geometry : angle 0.59355 (14696) SS BOND : bond 0.00198 ( 3) SS BOND : angle 0.70747 ( 6) hydrogen bonds : bond 0.03827 ( 473) hydrogen bonds : angle 4.63891 ( 1371) link_ALPHA1-4 : bond 0.00151 ( 1) link_ALPHA1-4 : angle 3.76721 ( 3) link_BETA1-4 : bond 0.00383 ( 1) link_BETA1-4 : angle 2.93876 ( 3) link_NAG-ASN : bond 0.00305 ( 3) link_NAG-ASN : angle 1.70488 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2731.54 seconds wall clock time: 47 minutes 31.43 seconds (2851.43 seconds total)