Starting phenix.real_space_refine on Thu Jul 2 17:04:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vsg_32110/07_2026/7vsg_32110.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vsg_32110/07_2026/7vsg_32110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7vsg_32110/07_2026/7vsg_32110.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vsg_32110/07_2026/7vsg_32110.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vsg_32110/07_2026/7vsg_32110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vsg_32110/07_2026/7vsg_32110.map" model { file = "/net/cci-nas-00/data/ceres_data/7vsg_32110/07_2026/7vsg_32110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vsg_32110/07_2026/7vsg_32110.cif" } resolution = 3.9 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 1 5.49 5 S 45 5.16 5 Be 1 3.05 5 C 6072 2.51 5 N 1503 2.21 5 O 1699 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9324 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6600 Classifications: {'peptide': 815} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 792} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "B" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2604 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 298} Chain: "D" 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 chiralities: 3 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'17F': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.14, per 1000 atoms: 0.23 Number of scatterers: 9324 At special positions: 0 Unit cell: (102.09, 99.6, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 45 16.00 P 1 15.00 F 3 9.00 O 1699 8.00 N 1503 7.00 C 6072 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 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 D 2 " - " MAN D 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG B 401 " - " ASN B 107 " " NAG B 402 " - " ASN B 294 " " NAG D 1 " - " ASN B 180 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 320.1 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 51.1% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.814A pdb=" N ARG A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 87 through 122 removed outlier: 3.699A pdb=" N SER A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Proline residue: A 94 - end of helix Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 282 through 315 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 356 through 371 removed outlier: 3.969A pdb=" N TYR A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.992A pdb=" N SER A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 removed outlier: 3.770A pdb=" N LEU A 400 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 403 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 666 Processing helix chain 'A' and resid 677 through 688 removed outlier: 4.552A pdb=" N SER A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 686 " --> pdb=" O LYS A 682 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 726 removed outlier: 3.897A pdb=" N GLU A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 724 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU A 726 " --> pdb=" O TYR A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 745 No H-bonds generated for 'chain 'A' and resid 743 through 745' Processing helix chain 'A' and resid 752 through 762 Processing helix chain 'A' and resid 763 through 766 removed outlier: 3.532A pdb=" N SER A 766 " --> pdb=" O SER A 763 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 763 through 766' Processing helix chain 'A' and resid 770 through 780 Processing helix chain 'A' and resid 791 through 804 Processing helix chain 'A' and resid 820 through 827 Processing helix chain 'A' and resid 839 through 845 removed outlier: 3.890A pdb=" N ASN A 844 " --> pdb=" O GLN A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 895 removed outlier: 4.190A pdb=" N LYS A 857 " --> pdb=" O LYS A 853 " (cutoff:3.500A) Proline residue: A 887 - end of helix removed outlier: 3.669A pdb=" N GLN A 892 " --> pdb=" O GLN A 888 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE A 893 " --> pdb=" O PHE A 889 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE A 894 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 914 removed outlier: 4.697A pdb=" N ASN A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 926 removed outlier: 3.968A pdb=" N ILE A 920 " --> pdb=" O THR A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 938 removed outlier: 3.763A pdb=" N THR A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 944 removed outlier: 3.554A pdb=" N TYR A 942 " --> pdb=" O PRO A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 951 Processing helix chain 'A' and resid 952 through 978 Processing helix chain 'A' and resid 991 through 1015 Processing helix chain 'A' and resid 1019 through 1041 Processing helix chain 'A' and resid 1055 through 1062 Processing helix chain 'A' and resid 1063 through 1090 Proline residue: A1080 - end of helix removed outlier: 3.552A pdb=" N ASN A1089 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL A1090 " --> pdb=" O VAL A1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 75 Proline residue: B 52 - end of helix removed outlier: 3.692A pdb=" N PHE B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Proline residue: B 63 - end of helix removed outlier: 3.519A pdb=" N THR B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 131 through 136 Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 146 through 152 removed outlier: 3.690A pdb=" N LEU B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 222 through 227 removed outlier: 3.570A pdb=" N ARG B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 227' Processing helix chain 'B' and resid 239 through 243 removed outlier: 4.185A pdb=" N LEU B 243 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 322 through 349 removed outlier: 4.227A pdb=" N GLY B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 132 through 136 removed outlier: 4.549A pdb=" N TYR A 126 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N VAL A 146 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR A 258 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 188 Processing sheet with id=AA4, first strand: chain 'A' and resid 381 through 382 removed outlier: 3.557A pdb=" N GLU A 387 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 391 removed outlier: 3.507A pdb=" N LEU A 390 " --> pdb=" O SER A 848 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 669 through 671 removed outlier: 6.656A pdb=" N THR A 811 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE A 831 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 696 through 700 removed outlier: 9.042A pdb=" N LEU A 786 " --> pdb=" O TYR A 747 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU A 749 " --> pdb=" O LEU A 786 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 81 removed outlier: 7.323A pdb=" N VAL B 118 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LEU B 275 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET B 120 " --> pdb=" O TYR B 273 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 104 through 109 removed outlier: 4.766A pdb=" N ARG B 290 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 188 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 184 " --> pdb=" O ASN B 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 162 through 163 431 hydrogen bonds defined for protein. 1233 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: 1.48 Time building geometry restraints manager: 1.27 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: 1547 1.32 - 1.45: 2610 1.45 - 1.57: 5323 1.57 - 1.69: 2 1.69 - 1.81: 71 Bond restraints: 9553 Sorted by residual: bond pdb=" F3 BFD A 409 " pdb="BE BFD A 409 " ideal model delta sigma weight residual 1.529 1.765 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" F2 BFD A 409 " pdb="BE BFD A 409 " ideal model delta sigma weight residual 1.535 1.752 -0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" F1 BFD A 409 " pdb="BE BFD A 409 " ideal model delta sigma weight residual 1.542 1.755 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" CG BFD A 409 " pdb=" OD1 BFD A 409 " ideal model delta sigma weight residual 1.269 1.454 -0.185 2.00e-02 2.50e+03 8.51e+01 bond pdb=" C1 MAN D 3 " pdb=" O5 MAN D 3 " ideal model delta sigma weight residual 1.399 1.445 -0.046 2.00e-02 2.50e+03 5.38e+00 ... (remaining 9548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 12909 3.41 - 6.81: 33 6.81 - 10.22: 6 10.22 - 13.63: 1 13.63 - 17.03: 4 Bond angle restraints: 12953 Sorted by residual: angle pdb=" O BFD A 409 " pdb=" C BFD A 409 " pdb=" N LYS A 410 " ideal model delta sigma weight residual 123.00 134.67 -11.67 1.60e+00 3.91e-01 5.32e+01 angle pdb=" F2 BFD A 409 " pdb="BE BFD A 409 " pdb=" F3 BFD A 409 " ideal model delta sigma weight residual 112.60 95.57 17.03 3.00e+00 1.11e-01 3.22e+01 angle pdb=" CA BFD A 409 " pdb=" C BFD A 409 " pdb=" O BFD A 409 " ideal model delta sigma weight residual 120.80 111.22 9.58 1.70e+00 3.46e-01 3.18e+01 angle pdb=" OD1 BFD A 409 " pdb="BE BFD A 409 " pdb=" F1 BFD A 409 " ideal model delta sigma weight residual 102.38 118.58 -16.20 3.00e+00 1.11e-01 2.92e+01 angle pdb=" F1 BFD A 409 " pdb="BE BFD A 409 " pdb=" F3 BFD A 409 " ideal model delta sigma weight residual 111.29 95.46 15.83 3.00e+00 1.11e-01 2.79e+01 ... (remaining 12948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.37: 5333 24.37 - 48.74: 267 48.74 - 73.12: 25 73.12 - 97.49: 5 97.49 - 121.86: 1 Dihedral angle restraints: 5631 sinusoidal: 2288 harmonic: 3343 Sorted by residual: dihedral pdb=" CB CYS B 91 " pdb=" SG CYS B 91 " pdb=" SG CYS B 104 " pdb=" CB CYS B 104 " ideal model delta sinusoidal sigma weight residual 93.00 156.03 -63.03 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" C6 17F A1101 " pdb=" C4 17F A1101 " pdb=" C5 17F A1101 " pdb=" O6 17F A1101 " ideal model delta sinusoidal sigma weight residual 67.29 -170.85 -121.86 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" CG ARG A 714 " pdb=" CD ARG A 714 " pdb=" NE ARG A 714 " pdb=" CZ ARG A 714 " ideal model delta sinusoidal sigma weight residual 90.00 132.66 -42.66 2 1.50e+01 4.44e-03 9.80e+00 ... (remaining 5628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1297 0.060 - 0.120: 158 0.120 - 0.180: 8 0.180 - 0.240: 1 0.240 - 0.300: 2 Chirality restraints: 1466 Sorted by residual: chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 107 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C1 NAG B 402 " pdb=" ND2 ASN B 294 " pdb=" C2 NAG B 402 " pdb=" O5 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 180 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1463 not shown) Planarity restraints: 1615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.292 2.00e-02 2.50e+03 2.43e-01 7.41e+02 pdb=" C7 NAG D 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.190 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.411 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.213 2.00e-02 2.50e+03 1.81e-01 4.08e+02 pdb=" C7 NAG D 1 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.038 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.294 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 402 " 0.175 2.00e-02 2.50e+03 1.45e-01 2.62e+02 pdb=" C7 NAG B 402 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG B 402 " 0.129 2.00e-02 2.50e+03 pdb=" N2 NAG B 402 " -0.234 2.00e-02 2.50e+03 pdb=" O7 NAG B 402 " -0.022 2.00e-02 2.50e+03 ... (remaining 1612 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1002 2.75 - 3.29: 9576 3.29 - 3.82: 15411 3.82 - 4.36: 18766 4.36 - 4.90: 31272 Nonbonded interactions: 76027 Sorted by model distance: nonbonded pdb=" OG SER A 763 " pdb=" NZ LYS A 772 " model vdw 2.210 3.120 nonbonded pdb=" O LEU A 983 " pdb=" OG SER A1063 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR A 907 " pdb=" OG SER A1037 " model vdw 2.260 3.040 nonbonded pdb=" O LEU A 758 " pdb=" OG SER A 762 " model vdw 2.266 3.040 nonbonded pdb=" O PHE A 915 " pdb=" OG SER A1029 " model vdw 2.268 3.040 ... (remaining 76022 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.230 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.005 0.236 9561 Z= 0.269 Angle : 0.678 17.035 12974 Z= 0.339 Chirality : 0.041 0.300 1466 Planarity : 0.010 0.243 1612 Dihedral : 13.366 121.862 3466 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.10 % Allowed : 0.39 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: -0.15 (0.24), residues: 1126 helix: 0.59 (0.22), residues: 498 sheet: 0.69 (0.45), residues: 137 loop : -1.01 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 135 TYR 0.016 0.001 TYR A 318 PHE 0.014 0.001 PHE A1047 TRP 0.012 0.001 TRP A 313 HIS 0.004 0.001 HIS A 864 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.27 ( 9553) covalent geometry : angle 0.67359 / 0.34 (12953) SS BOND : bond 0.00306 / 0.13 ( 3) SS BOND : angle 0.64412 / 0.39 ( 6) hydrogen bonds : bond 0.25408 / 16.85 ( 431) hydrogen bonds : angle 7.97322 / 6.15 ( 1233) link_ALPHA1-4 : bond 0.01254 / 0.66 ( 1) link_ALPHA1-4 : angle 2.49270 / 1.16 ( 3) link_BETA1-4 : bond 0.00266 / 0.14 ( 1) link_BETA1-4 : angle 0.94199 / 0.53 ( 3) link_NAG-ASN : bond 0.00549 / 0.28 ( 3) link_NAG-ASN : angle 2.56447 / 1.50 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.293 Fit side-chains REVERT: A 45 ILE cc_start: 0.6976 (pt) cc_final: 0.6121 (pt) REVERT: A 145 ASP cc_start: 0.8244 (t70) cc_final: 0.7882 (t70) REVERT: A 285 GLU cc_start: 0.7538 (tt0) cc_final: 0.7326 (tt0) REVERT: A 395 ASP cc_start: 0.7834 (m-30) cc_final: 0.7477 (t0) REVERT: A 816 ASP cc_start: 0.6971 (p0) cc_final: 0.6537 (p0) REVERT: A 846 ASP cc_start: 0.8086 (m-30) cc_final: 0.7827 (m-30) REVERT: B 31 THR cc_start: 0.8069 (m) cc_final: 0.7837 (p) REVERT: B 197 ILE cc_start: 0.8262 (mp) cc_final: 0.7750 (tp) REVERT: B 337 PHE cc_start: 0.7258 (t80) cc_final: 0.6943 (t80) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.1014 time to fit residues: 23.5022 Evaluate side-chains 111 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN B 131 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.162089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126423 restraints weight = 13211.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125880 restraints weight = 15094.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.127815 restraints weight = 12173.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127876 restraints weight = 9277.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.128428 restraints weight = 8586.076| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9561 Z= 0.161 Angle : 0.616 10.742 12974 Z= 0.317 Chirality : 0.044 0.284 1466 Planarity : 0.004 0.044 1612 Dihedral : 7.177 125.811 1285 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.38 % Allowed : 8.27 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: 0.22 (0.25), residues: 1126 helix: 1.15 (0.23), residues: 501 sheet: 0.32 (0.42), residues: 150 loop : -0.97 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 133 TYR 0.013 0.002 TYR A 318 PHE 0.018 0.002 PHE A 775 TRP 0.013 0.001 TRP A 313 HIS 0.006 0.001 HIS A 862 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 9553) covalent geometry : angle 0.61109 / 0.32 (12953) SS BOND : bond 0.00865 / 0.39 ( 3) SS BOND : angle 1.01708 / 0.59 ( 6) hydrogen bonds : bond 0.05558 / 3.58 ( 431) hydrogen bonds : angle 5.34061 / 4.09 ( 1233) link_ALPHA1-4 : bond 0.00163 / 0.09 ( 1) link_ALPHA1-4 : angle 3.34254 / 1.64 ( 3) link_BETA1-4 : bond 0.00459 / 0.24 ( 1) link_BETA1-4 : angle 2.13152 / 1.09 ( 3) link_NAG-ASN : bond 0.00408 / 0.19 ( 3) link_NAG-ASN : angle 1.87489 / 1.06 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.397 Fit side-chains REVERT: A 145 ASP cc_start: 0.8284 (t70) cc_final: 0.8009 (t70) REVERT: A 395 ASP cc_start: 0.7734 (m-30) cc_final: 0.7460 (t0) REVERT: A 790 MET cc_start: 0.8637 (mmm) cc_final: 0.8280 (mtp) REVERT: A 800 ARG cc_start: 0.6980 (ttm170) cc_final: 0.6530 (ttm110) REVERT: A 816 ASP cc_start: 0.7064 (p0) cc_final: 0.6696 (p0) REVERT: B 197 ILE cc_start: 0.8290 (mp) cc_final: 0.7787 (tp) REVERT: B 337 PHE cc_start: 0.7301 (t80) cc_final: 0.6821 (t80) outliers start: 14 outliers final: 11 residues processed: 124 average time/residue: 0.0767 time to fit residues: 13.7766 Evaluate side-chains 109 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 46 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 GLN A 314 GLN ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN B 126 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.156118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119518 restraints weight = 13423.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116817 restraints weight = 14905.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118233 restraints weight = 13479.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120688 restraints weight = 9627.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.120717 restraints weight = 8137.493| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9561 Z= 0.261 Angle : 0.695 10.727 12974 Z= 0.356 Chirality : 0.048 0.345 1466 Planarity : 0.005 0.043 1612 Dihedral : 7.421 119.273 1285 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.26 % Allowed : 12.30 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: -0.26 (0.24), residues: 1126 helix: 0.72 (0.23), residues: 505 sheet: 0.15 (0.46), residues: 132 loop : -1.18 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 133 TYR 0.018 0.002 TYR A 311 PHE 0.019 0.002 PHE A1036 TRP 0.015 0.002 TRP A1067 HIS 0.011 0.002 HIS A 862 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.26 ( 9553) covalent geometry : angle 0.69074 / 0.36 (12953) SS BOND : bond 0.00530 / 0.23 ( 3) SS BOND : angle 1.22518 / 0.65 ( 6) hydrogen bonds : bond 0.05709 / 3.60 ( 431) hydrogen bonds : angle 5.24212 / 3.99 ( 1233) link_ALPHA1-4 : bond 0.00831 / 0.44 ( 1) link_ALPHA1-4 : angle 1.86525 / 0.92 ( 3) link_BETA1-4 : bond 0.00281 / 0.15 ( 1) link_BETA1-4 : angle 2.46092 / 1.24 ( 3) link_NAG-ASN : bond 0.00328 / 0.14 ( 3) link_NAG-ASN : angle 2.23024 / 1.24 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8328 (t70) cc_final: 0.7931 (t70) REVERT: A 395 ASP cc_start: 0.7885 (m-30) cc_final: 0.7633 (t0) REVERT: A 790 MET cc_start: 0.8705 (mmm) cc_final: 0.8368 (mtp) REVERT: A 816 ASP cc_start: 0.7264 (p0) cc_final: 0.6787 (p0) REVERT: A 851 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7979 (mttm) REVERT: B 126 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8422 (t0) REVERT: B 197 ILE cc_start: 0.8392 (mp) cc_final: 0.7914 (tp) REVERT: B 337 PHE cc_start: 0.7249 (t80) cc_final: 0.6751 (t80) outliers start: 23 outliers final: 16 residues processed: 131 average time/residue: 0.0790 time to fit residues: 15.0787 Evaluate side-chains 118 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 1045 TRP Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 329 TYR Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 17 optimal weight: 0.0570 chunk 2 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.160664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.124247 restraints weight = 13373.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.123251 restraints weight = 14663.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.124914 restraints weight = 14163.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.125660 restraints weight = 9513.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.126464 restraints weight = 8290.937| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9561 Z= 0.122 Angle : 0.556 10.803 12974 Z= 0.280 Chirality : 0.042 0.282 1466 Planarity : 0.004 0.042 1612 Dihedral : 7.134 121.522 1285 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.67 % Allowed : 14.57 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: 0.00 (0.25), residues: 1126 helix: 1.08 (0.23), residues: 502 sheet: -0.03 (0.46), residues: 135 loop : -1.11 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 800 TYR 0.012 0.001 TYR A 324 PHE 0.016 0.001 PHE A 368 TRP 0.014 0.001 TRP A 313 HIS 0.004 0.001 HIS A 864 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9553) covalent geometry : angle 0.55323 / 0.28 (12953) SS BOND : bond 0.00382 / 0.15 ( 3) SS BOND : angle 0.84734 / 0.46 ( 6) hydrogen bonds : bond 0.04533 / 2.92 ( 431) hydrogen bonds : angle 4.85771 / 3.71 ( 1233) link_ALPHA1-4 : bond 0.00778 / 0.41 ( 1) link_ALPHA1-4 : angle 2.15751 / 1.03 ( 3) link_BETA1-4 : bond 0.00279 / 0.15 ( 1) link_BETA1-4 : angle 1.57215 / 0.80 ( 3) link_NAG-ASN : bond 0.00397 / 0.16 ( 3) link_NAG-ASN : angle 1.64595 / 0.92 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 72 PHE cc_start: 0.7453 (m-80) cc_final: 0.7073 (m-80) REVERT: A 145 ASP cc_start: 0.8361 (t70) cc_final: 0.7969 (t70) REVERT: A 349 VAL cc_start: 0.8867 (p) cc_final: 0.8317 (m) REVERT: A 395 ASP cc_start: 0.7886 (m-30) cc_final: 0.7590 (t0) REVERT: A 790 MET cc_start: 0.8633 (mmm) cc_final: 0.8377 (mtp) REVERT: A 800 ARG cc_start: 0.7412 (ttm170) cc_final: 0.7045 (ttm170) REVERT: A 816 ASP cc_start: 0.7090 (p0) cc_final: 0.6574 (p0) REVERT: B 197 ILE cc_start: 0.8307 (mp) cc_final: 0.7961 (tp) REVERT: B 337 PHE cc_start: 0.7241 (t80) cc_final: 0.6715 (t80) outliers start: 17 outliers final: 12 residues processed: 124 average time/residue: 0.0873 time to fit residues: 15.5615 Evaluate side-chains 110 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1045 TRP Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 329 TYR Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 52 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 881 ASN B 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.157730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.121970 restraints weight = 13415.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121639 restraints weight = 15461.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.123305 restraints weight = 14196.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.123431 restraints weight = 9866.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123887 restraints weight = 8904.038| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9561 Z= 0.165 Angle : 0.577 10.599 12974 Z= 0.293 Chirality : 0.043 0.302 1466 Planarity : 0.004 0.040 1612 Dihedral : 7.161 118.305 1285 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.35 % Allowed : 15.06 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: -0.01 (0.25), residues: 1126 helix: 1.12 (0.23), residues: 502 sheet: 0.05 (0.47), residues: 130 loop : -1.20 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 133 TYR 0.023 0.002 TYR A 879 PHE 0.016 0.002 PHE A 76 TRP 0.012 0.001 TRP A 313 HIS 0.007 0.001 HIS A 862 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 9553) covalent geometry : angle 0.57411 / 0.29 (12953) SS BOND : bond 0.00421 / 0.17 ( 3) SS BOND : angle 0.95735 / 0.51 ( 6) hydrogen bonds : bond 0.04723 / 2.99 ( 431) hydrogen bonds : angle 4.77538 / 3.64 ( 1233) link_ALPHA1-4 : bond 0.00561 / 0.30 ( 1) link_ALPHA1-4 : angle 1.68397 / 0.82 ( 3) link_BETA1-4 : bond 0.00139 / 0.07 ( 1) link_BETA1-4 : angle 2.15692 / 1.11 ( 3) link_NAG-ASN : bond 0.00327 / 0.14 ( 3) link_NAG-ASN : angle 1.79993 / 1.00 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 72 PHE cc_start: 0.7488 (m-80) cc_final: 0.7098 (m-80) REVERT: A 145 ASP cc_start: 0.8334 (t70) cc_final: 0.7982 (t70) REVERT: A 163 SER cc_start: 0.8148 (m) cc_final: 0.7786 (p) REVERT: A 395 ASP cc_start: 0.7921 (m-30) cc_final: 0.7624 (t0) REVERT: A 790 MET cc_start: 0.8635 (mmm) cc_final: 0.8365 (mtp) REVERT: A 800 ARG cc_start: 0.7413 (ttm170) cc_final: 0.7045 (ttm170) REVERT: A 816 ASP cc_start: 0.7075 (p0) cc_final: 0.6733 (p0) REVERT: B 197 ILE cc_start: 0.8394 (mp) cc_final: 0.7988 (tp) REVERT: B 337 PHE cc_start: 0.7272 (t80) cc_final: 0.6765 (t80) outliers start: 34 outliers final: 26 residues processed: 130 average time/residue: 0.0869 time to fit residues: 16.2472 Evaluate side-chains 122 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1045 TRP Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 329 TYR Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 55 optimal weight: 0.0040 chunk 98 optimal weight: 0.0070 chunk 99 optimal weight: 0.9980 overall best weight: 0.6012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.162155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125901 restraints weight = 13198.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.125249 restraints weight = 13868.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.126561 restraints weight = 13321.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.127116 restraints weight = 9477.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.127594 restraints weight = 8390.716| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9561 Z= 0.104 Angle : 0.523 10.414 12974 Z= 0.263 Chirality : 0.041 0.245 1466 Planarity : 0.003 0.041 1612 Dihedral : 6.913 120.895 1285 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.97 % Allowed : 16.83 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: 0.25 (0.25), residues: 1126 helix: 1.34 (0.23), residues: 502 sheet: 0.24 (0.45), residues: 147 loop : -1.14 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 270 TYR 0.019 0.001 TYR A 879 PHE 0.020 0.001 PHE A 368 TRP 0.013 0.001 TRP A 313 HIS 0.003 0.001 HIS A 864 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 9553) covalent geometry : angle 0.52041 / 0.26 (12953) SS BOND : bond 0.00342 / 0.13 ( 3) SS BOND : angle 0.74684 / 0.40 ( 6) hydrogen bonds : bond 0.04037 / 2.61 ( 431) hydrogen bonds : angle 4.53229 / 3.45 ( 1233) link_ALPHA1-4 : bond 0.00896 / 0.47 ( 1) link_ALPHA1-4 : angle 1.92124 / 0.92 ( 3) link_BETA1-4 : bond 0.00486 / 0.26 ( 1) link_BETA1-4 : angle 1.28823 / 0.67 ( 3) link_NAG-ASN : bond 0.00395 / 0.16 ( 3) link_NAG-ASN : angle 1.36536 / 0.77 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 72 PHE cc_start: 0.7434 (m-80) cc_final: 0.7097 (m-80) REVERT: A 145 ASP cc_start: 0.8400 (t70) cc_final: 0.8029 (t70) REVERT: A 395 ASP cc_start: 0.7914 (m-30) cc_final: 0.7547 (t0) REVERT: A 714 ARG cc_start: 0.7069 (mmm160) cc_final: 0.6731 (mmp80) REVERT: A 800 ARG cc_start: 0.7388 (ttm170) cc_final: 0.7139 (ttm110) REVERT: A 820 ASP cc_start: 0.7211 (m-30) cc_final: 0.6937 (m-30) REVERT: A 826 GLU cc_start: 0.6978 (tp30) cc_final: 0.5753 (tp30) REVERT: B 70 VAL cc_start: 0.8746 (p) cc_final: 0.8533 (m) REVERT: B 197 ILE cc_start: 0.8355 (mp) cc_final: 0.8024 (tp) REVERT: B 337 PHE cc_start: 0.7223 (t80) cc_final: 0.6704 (t80) outliers start: 20 outliers final: 11 residues processed: 130 average time/residue: 0.0971 time to fit residues: 18.0320 Evaluate side-chains 115 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 1045 TRP Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 329 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.160344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124003 restraints weight = 13217.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.122881 restraints weight = 14496.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.124404 restraints weight = 14148.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.125227 restraints weight = 8794.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.125670 restraints weight = 7800.342| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9561 Z= 0.130 Angle : 0.540 9.955 12974 Z= 0.273 Chirality : 0.041 0.259 1466 Planarity : 0.004 0.039 1612 Dihedral : 6.925 119.809 1285 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.66 % Allowed : 17.32 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: 0.28 (0.25), residues: 1126 helix: 1.37 (0.23), residues: 503 sheet: 0.23 (0.46), residues: 140 loop : -1.10 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.026 0.001 TYR B 241 PHE 0.013 0.001 PHE A1036 TRP 0.011 0.001 TRP A 313 HIS 0.005 0.001 HIS A 862 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9553) covalent geometry : angle 0.53797 / 0.27 (12953) SS BOND : bond 0.00423 / 0.16 ( 3) SS BOND : angle 0.77348 / 0.42 ( 6) hydrogen bonds : bond 0.04182 / 2.68 ( 431) hydrogen bonds : angle 4.52960 / 3.45 ( 1233) link_ALPHA1-4 : bond 0.00682 / 0.36 ( 1) link_ALPHA1-4 : angle 1.59754 / 0.77 ( 3) link_BETA1-4 : bond 0.00214 / 0.11 ( 1) link_BETA1-4 : angle 1.63350 / 0.85 ( 3) link_NAG-ASN : bond 0.00298 / 0.13 ( 3) link_NAG-ASN : angle 1.49883 / 0.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 72 PHE cc_start: 0.7443 (m-80) cc_final: 0.7036 (m-80) REVERT: A 145 ASP cc_start: 0.8361 (t70) cc_final: 0.7999 (t70) REVERT: A 395 ASP cc_start: 0.7903 (m-30) cc_final: 0.7513 (t0) REVERT: A 714 ARG cc_start: 0.7183 (mmm160) cc_final: 0.6804 (mmp80) REVERT: A 786 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8301 (mt) REVERT: A 800 ARG cc_start: 0.7418 (ttm170) cc_final: 0.7038 (ttm170) REVERT: B 197 ILE cc_start: 0.8373 (mp) cc_final: 0.8017 (tp) REVERT: B 310 MET cc_start: 0.8508 (tmm) cc_final: 0.8265 (tmm) REVERT: B 337 PHE cc_start: 0.7195 (t80) cc_final: 0.6692 (t80) outliers start: 27 outliers final: 20 residues processed: 127 average time/residue: 0.0906 time to fit residues: 16.7458 Evaluate side-chains 124 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 1045 TRP Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 329 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 105 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN B 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.158217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.121563 restraints weight = 13230.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.120231 restraints weight = 13819.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123140 restraints weight = 12106.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.122979 restraints weight = 8229.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.123359 restraints weight = 8495.269| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9561 Z= 0.166 Angle : 0.576 10.042 12974 Z= 0.292 Chirality : 0.043 0.288 1466 Planarity : 0.004 0.040 1612 Dihedral : 7.132 112.243 1285 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.95 % Allowed : 17.62 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: 0.17 (0.25), residues: 1126 helix: 1.23 (0.23), residues: 510 sheet: 0.24 (0.48), residues: 130 loop : -1.14 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 290 TYR 0.016 0.002 TYR A 879 PHE 0.022 0.002 PHE A 368 TRP 0.011 0.001 TRP A 959 HIS 0.006 0.001 HIS A 862 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 9553) covalent geometry : angle 0.57319 / 0.29 (12953) SS BOND : bond 0.00429 / 0.17 ( 3) SS BOND : angle 0.92258 / 0.49 ( 6) hydrogen bonds : bond 0.04524 / 2.87 ( 431) hydrogen bonds : angle 4.60807 / 3.51 ( 1233) link_ALPHA1-4 : bond 0.00523 / 0.28 ( 1) link_ALPHA1-4 : angle 1.44460 / 0.70 ( 3) link_BETA1-4 : bond 0.00099 / 0.05 ( 1) link_BETA1-4 : angle 2.04661 / 1.04 ( 3) link_NAG-ASN : bond 0.00262 / 0.11 ( 3) link_NAG-ASN : angle 1.68630 / 0.93 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 72 PHE cc_start: 0.7437 (m-80) cc_final: 0.7022 (m-80) REVERT: A 145 ASP cc_start: 0.8361 (t70) cc_final: 0.7979 (t70) REVERT: A 395 ASP cc_start: 0.7884 (m-30) cc_final: 0.7514 (t0) REVERT: A 714 ARG cc_start: 0.7259 (mmm160) cc_final: 0.6904 (mmp80) REVERT: A 786 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8310 (mt) REVERT: A 826 GLU cc_start: 0.6836 (tp30) cc_final: 0.6273 (tp30) REVERT: B 197 ILE cc_start: 0.8393 (mp) cc_final: 0.8025 (tp) REVERT: B 337 PHE cc_start: 0.7163 (t80) cc_final: 0.6669 (t80) outliers start: 30 outliers final: 23 residues processed: 133 average time/residue: 0.0880 time to fit residues: 17.0334 Evaluate side-chains 124 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1045 TRP Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 329 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.0970 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 43 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.161671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.128471 restraints weight = 13144.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.127667 restraints weight = 13676.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128720 restraints weight = 13558.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.129561 restraints weight = 9402.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.129985 restraints weight = 8335.167| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9561 Z= 0.108 Angle : 0.538 9.691 12974 Z= 0.270 Chirality : 0.041 0.244 1466 Planarity : 0.004 0.043 1612 Dihedral : 6.930 114.783 1285 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.17 % Allowed : 18.41 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: 0.35 (0.26), residues: 1126 helix: 1.38 (0.23), residues: 509 sheet: 0.35 (0.46), residues: 139 loop : -1.06 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 290 TYR 0.013 0.001 TYR A 879 PHE 0.011 0.001 PHE A 995 TRP 0.012 0.001 TRP A 313 HIS 0.003 0.001 HIS A1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 9553) covalent geometry : angle 0.53617 / 0.27 (12953) SS BOND : bond 0.00341 / 0.13 ( 3) SS BOND : angle 0.94612 / 0.53 ( 6) hydrogen bonds : bond 0.03999 / 2.59 ( 431) hydrogen bonds : angle 4.48825 / 3.41 ( 1233) link_ALPHA1-4 : bond 0.00729 / 0.38 ( 1) link_ALPHA1-4 : angle 1.68967 / 0.81 ( 3) link_BETA1-4 : bond 0.00323 / 0.17 ( 1) link_BETA1-4 : angle 1.41787 / 0.74 ( 3) link_NAG-ASN : bond 0.00369 / 0.16 ( 3) link_NAG-ASN : angle 1.34676 / 0.75 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 72 PHE cc_start: 0.7421 (m-80) cc_final: 0.7047 (m-80) REVERT: A 145 ASP cc_start: 0.8263 (t70) cc_final: 0.7982 (t70) REVERT: A 395 ASP cc_start: 0.7897 (m-30) cc_final: 0.7464 (t0) REVERT: A 714 ARG cc_start: 0.7004 (mmm160) cc_final: 0.6714 (mmp80) REVERT: A 826 GLU cc_start: 0.6799 (tp30) cc_final: 0.6459 (tp30) REVERT: A 879 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.8374 (t80) REVERT: B 197 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8035 (tp) REVERT: B 310 MET cc_start: 0.8468 (tmm) cc_final: 0.8212 (tmm) REVERT: B 337 PHE cc_start: 0.7152 (t80) cc_final: 0.6674 (t80) outliers start: 22 outliers final: 16 residues processed: 125 average time/residue: 0.0867 time to fit residues: 15.6463 Evaluate side-chains 120 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 879 TYR Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1045 TRP Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 329 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 0.0170 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.159335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123395 restraints weight = 13270.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.122125 restraints weight = 14590.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.123158 restraints weight = 13424.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.125303 restraints weight = 9484.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125229 restraints weight = 7864.716| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9561 Z= 0.150 Angle : 0.570 10.507 12974 Z= 0.287 Chirality : 0.042 0.270 1466 Planarity : 0.004 0.041 1612 Dihedral : 7.022 110.900 1285 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.66 % Allowed : 18.21 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: 0.26 (0.25), residues: 1126 helix: 1.30 (0.23), residues: 510 sheet: 0.26 (0.49), residues: 123 loop : -1.05 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 133 TYR 0.015 0.001 TYR A 879 PHE 0.021 0.001 PHE A 368 TRP 0.009 0.001 TRP A 959 HIS 0.005 0.001 HIS A 862 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9553) covalent geometry : angle 0.56779 / 0.29 (12953) SS BOND : bond 0.00361 / 0.14 ( 3) SS BOND : angle 1.00258 / 0.54 ( 6) hydrogen bonds : bond 0.04295 / 2.73 ( 431) hydrogen bonds : angle 4.53769 / 3.44 ( 1233) link_ALPHA1-4 : bond 0.00517 / 0.27 ( 1) link_ALPHA1-4 : angle 1.42489 / 0.69 ( 3) link_BETA1-4 : bond 0.00344 / 0.18 ( 1) link_BETA1-4 : angle 2.00400 / 1.03 ( 3) link_NAG-ASN : bond 0.00251 / 0.11 ( 3) link_NAG-ASN : angle 1.56462 / 0.87 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 72 PHE cc_start: 0.7389 (m-80) cc_final: 0.6956 (m-80) REVERT: A 145 ASP cc_start: 0.8274 (t70) cc_final: 0.7882 (t70) REVERT: A 395 ASP cc_start: 0.7889 (m-30) cc_final: 0.7461 (t0) REVERT: A 714 ARG cc_start: 0.7254 (mmm160) cc_final: 0.6897 (mmp80) REVERT: B 197 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8028 (tp) REVERT: B 310 MET cc_start: 0.8517 (tmm) cc_final: 0.8159 (tmm) REVERT: B 337 PHE cc_start: 0.7061 (t80) cc_final: 0.6598 (t80) outliers start: 27 outliers final: 23 residues processed: 123 average time/residue: 0.0823 time to fit residues: 14.7011 Evaluate side-chains 121 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1045 TRP Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 329 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 82 optimal weight: 0.3980 chunk 13 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.161779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126414 restraints weight = 13046.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.126578 restraints weight = 14489.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.128086 restraints weight = 12323.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.128561 restraints weight = 7733.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.128914 restraints weight = 7179.158| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9561 Z= 0.107 Angle : 0.547 10.464 12974 Z= 0.273 Chirality : 0.041 0.240 1466 Planarity : 0.004 0.043 1612 Dihedral : 6.941 112.261 1285 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.26 % Allowed : 18.90 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 are not related in a simple way. whole: 0.39 (0.26), residues: 1126 helix: 1.41 (0.23), residues: 511 sheet: 0.31 (0.45), residues: 140 loop : -1.04 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 723 TYR 0.013 0.001 TYR A 879 PHE 0.011 0.001 PHE A 995 TRP 0.011 0.001 TRP A 313 HIS 0.003 0.001 HIS A 864 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 9553) covalent geometry : angle 0.54519 / 0.27 (12953) SS BOND : bond 0.00344 / 0.13 ( 3) SS BOND : angle 0.84854 / 0.47 ( 6) hydrogen bonds : bond 0.03943 / 2.55 ( 431) hydrogen bonds : angle 4.45807 / 3.38 ( 1233) link_ALPHA1-4 : bond 0.00502 / 0.26 ( 1) link_ALPHA1-4 : angle 1.45031 / 0.70 ( 3) link_BETA1-4 : bond 0.00474 / 0.25 ( 1) link_BETA1-4 : angle 1.48893 / 0.77 ( 3) link_NAG-ASN : bond 0.00321 / 0.14 ( 3) link_NAG-ASN : angle 1.40871 / 0.79 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1349.78 seconds wall clock time: 24 minutes 17.50 seconds (1457.50 seconds total)