Starting phenix.real_space_refine on Tue Jan 14 12:30:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bap_44410/01_2025/9bap_44410.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bap_44410/01_2025/9bap_44410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bap_44410/01_2025/9bap_44410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bap_44410/01_2025/9bap_44410.map" model { file = "/net/cci-nas-00/data/ceres_data/9bap_44410/01_2025/9bap_44410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bap_44410/01_2025/9bap_44410.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 26 5.16 5 C 4198 2.51 5 N 1157 2.21 5 O 1153 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6535 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 886, 6508 Classifications: {'peptide': 886} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PTRANS': 58, 'TRANS': 827} Chain breaks: 5 Unresolved non-hydrogen bonds: 627 Unresolved non-hydrogen angles: 761 Unresolved non-hydrogen dihedrals: 527 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 3, 'TYR:plan': 8, 'ASN:plan1': 10, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 26, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 387 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2506 SG CYS A 635 30.352 43.644 28.469 1.00133.87 S ATOM 2519 SG CYS A 637 31.148 42.910 25.866 1.00128.15 S ATOM 2923 SG CYS A 692 33.962 42.961 27.064 1.00122.87 S Time building chain proxies: 4.16, per 1000 atoms: 0.64 Number of scatterers: 6535 At special positions: 0 Unit cell: (66.34, 93.09, 146.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 26 16.00 O 1153 8.00 N 1157 7.00 C 4198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 973.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 637 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 692 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 635 " pdb="ZN ZN A1502 " - pdb=" ND1 HIS A 694 " Number of angles added : 3 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1636 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 11 sheets defined 28.1% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 163 through 179 removed outlier: 4.162A pdb=" N ALA A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.775A pdb=" N VAL A 212 " --> pdb=" O PRO A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 311 Proline residue: A 289 - end of helix removed outlier: 3.902A pdb=" N TRP A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 322 removed outlier: 4.572A pdb=" N SER A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 329 Processing helix chain 'A' and resid 334 through 343 removed outlier: 3.987A pdb=" N GLN A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 356 removed outlier: 3.584A pdb=" N ASN A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 366 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.865A pdb=" N ARG A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.192A pdb=" N VAL A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 640 through 644 removed outlier: 3.754A pdb=" N ALA A 643 " --> pdb=" O GLY A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 690 removed outlier: 3.992A pdb=" N LEU A 690 " --> pdb=" O LYS A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 860 Processing helix chain 'A' and resid 871 through 882 Processing helix chain 'A' and resid 894 through 904 removed outlier: 3.501A pdb=" N LEU A 898 " --> pdb=" O SER A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 959 removed outlier: 3.551A pdb=" N VAL A 942 " --> pdb=" O VAL A 938 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A 948 " --> pdb=" O ASN A 944 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA A 949 " --> pdb=" O GLN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 993 Processing helix chain 'A' and resid 1005 through 1008 removed outlier: 3.707A pdb=" N GLY A1008 " --> pdb=" O TRP A1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1005 through 1008' Processing helix chain 'A' and resid 1068 through 1073 Processing helix chain 'A' and resid 1189 through 1197 Processing helix chain 'A' and resid 1208 through 1218 Processing helix chain 'A' and resid 1221 through 1237 Processing sheet with id=AA1, first strand: chain 'A' and resid 205 through 206 removed outlier: 3.611A pdb=" N GLU A 205 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 197 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 273 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A 188 " --> pdb=" O TYR A 273 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ASP A 192 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ASN A 194 " --> pdb=" O PRO A 279 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE A 272 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER A 264 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A 243 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY A 238 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE A 223 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL A 226 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ASP A 192 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS A 228 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU A 190 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 400 through 402 Processing sheet with id=AA3, first strand: chain 'A' and resid 411 through 412 removed outlier: 5.385A pdb=" N THR A 411 " --> pdb=" O ARG A 431 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 556 through 559 removed outlier: 5.254A pdb=" N PHE A 582 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASP A 606 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL A 588 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER A 604 " --> pdb=" O VAL A 588 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL A 607 " --> pdb=" O HIS A 634 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N HIS A 634 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TRP A 609 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 556 through 559 removed outlier: 5.254A pdb=" N PHE A 582 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASP A 606 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL A 588 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER A 604 " --> pdb=" O VAL A 588 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 Processing sheet with id=AA7, first strand: chain 'A' and resid 673 through 676 Processing sheet with id=AA8, first strand: chain 'A' and resid 776 through 779 removed outlier: 3.636A pdb=" N GLY A 778 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 12.424A pdb=" N ASP A 723 " --> pdb=" O ARG A 748 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N ARG A 748 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR A 725 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 746 " --> pdb=" O TYR A 725 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL A 727 " --> pdb=" O ARG A 744 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG A 744 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A 729 " --> pdb=" O ARG A 742 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASP A 767 " --> pdb=" O LYS A 745 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU A 747 " --> pdb=" O THR A 765 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR A 765 " --> pdb=" O LEU A 747 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU A 762 " --> pdb=" O HIS A 808 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLN A 810 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N TYR A 764 " --> pdb=" O GLN A 810 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE A 781 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE A 806 " --> pdb=" O ILE A 781 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ARG A 783 " --> pdb=" O ILE A 806 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N HIS A 808 " --> pdb=" O ARG A 783 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 776 through 779 removed outlier: 3.636A pdb=" N GLY A 778 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 12.424A pdb=" N ASP A 723 " --> pdb=" O ARG A 748 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N ARG A 748 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR A 725 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 746 " --> pdb=" O TYR A 725 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL A 727 " --> pdb=" O ARG A 744 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG A 744 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A 729 " --> pdb=" O ARG A 742 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASP A 767 " --> pdb=" O LYS A 745 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU A 747 " --> pdb=" O THR A 765 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR A 765 " --> pdb=" O LEU A 747 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU A 762 " --> pdb=" O HIS A 808 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLN A 810 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N TYR A 764 " --> pdb=" O GLN A 810 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 891 through 892 removed outlier: 3.693A pdb=" N ASP A 869 " --> pdb=" O PHE A 891 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU A 840 " --> pdb=" O GLU A 863 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG A 865 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY A 842 " --> pdb=" O ARG A 865 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA A 867 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP A 844 " --> pdb=" O ALA A 867 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ASP A 869 " --> pdb=" O ASP A 844 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ARG A 841 " --> pdb=" O PHE A 919 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ALA A 921 " --> pdb=" O ARG A 841 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N MET A 843 " --> pdb=" O ALA A 921 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A 920 " --> pdb=" O VAL A 964 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLU A 966 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA A 922 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N VAL A 968 " --> pdb=" O ALA A 922 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1044 through 1045 230 hydrogen bonds defined for protein. 627 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2162 1.34 - 1.46: 1655 1.46 - 1.58: 2868 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 6721 Sorted by residual: bond pdb=" N PHE A 391 " pdb=" CA PHE A 391 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.23e-02 6.61e+03 8.03e+00 bond pdb=" N GLN A 393 " pdb=" CA GLN A 393 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.29e-02 6.01e+03 4.95e+00 bond pdb=" N ARG A 392 " pdb=" CA ARG A 392 " ideal model delta sigma weight residual 1.454 1.481 -0.027 1.32e-02 5.74e+03 4.04e+00 bond pdb=" N GLU A 394 " pdb=" CA GLU A 394 " ideal model delta sigma weight residual 1.462 1.483 -0.021 1.31e-02 5.83e+03 2.55e+00 bond pdb=" CB VAL A 982 " pdb=" CG1 VAL A 982 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.49e+00 ... (remaining 6716 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 9062 2.10 - 4.20: 118 4.20 - 6.29: 14 6.29 - 8.39: 1 8.39 - 10.49: 3 Bond angle restraints: 9198 Sorted by residual: angle pdb=" C CYS A 619 " pdb=" CA CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sigma weight residual 115.79 110.20 5.59 1.19e+00 7.06e-01 2.21e+01 angle pdb=" CB MET A1193 " pdb=" CG MET A1193 " pdb=" SD MET A1193 " ideal model delta sigma weight residual 112.70 123.19 -10.49 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CA ARG A 392 " pdb=" C ARG A 392 " pdb=" O ARG A 392 " ideal model delta sigma weight residual 121.87 118.38 3.49 1.10e+00 8.26e-01 1.01e+01 angle pdb=" N GLU A 394 " pdb=" CA GLU A 394 " pdb=" C GLU A 394 " ideal model delta sigma weight residual 112.72 108.48 4.24 1.36e+00 5.41e-01 9.70e+00 angle pdb=" CA TYR A 416 " pdb=" CB TYR A 416 " pdb=" CG TYR A 416 " ideal model delta sigma weight residual 113.90 119.33 -5.43 1.80e+00 3.09e-01 9.10e+00 ... (remaining 9193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 3371 16.08 - 32.15: 362 32.15 - 48.23: 119 48.23 - 64.30: 30 64.30 - 80.38: 6 Dihedral angle restraints: 3888 sinusoidal: 1341 harmonic: 2547 Sorted by residual: dihedral pdb=" CA LYS A1083 " pdb=" C LYS A1083 " pdb=" N PRO A1084 " pdb=" CA PRO A1084 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA TRP A1153 " pdb=" CB TRP A1153 " pdb=" CG TRP A1153 " pdb=" CD1 TRP A1153 " ideal model delta sinusoidal sigma weight residual 90.00 159.15 -69.15 2 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CA ASP A 884 " pdb=" CB ASP A 884 " pdb=" CG ASP A 884 " pdb=" OD1 ASP A 884 " ideal model delta sinusoidal sigma weight residual -30.00 -83.51 53.51 1 2.00e+01 2.50e-03 9.73e+00 ... (remaining 3885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 650 0.031 - 0.063: 242 0.063 - 0.094: 68 0.094 - 0.125: 50 0.125 - 0.156: 7 Chirality restraints: 1017 Sorted by residual: chirality pdb=" CA ARG A 392 " pdb=" N ARG A 392 " pdb=" C ARG A 392 " pdb=" CB ARG A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CG LEU A 986 " pdb=" CB LEU A 986 " pdb=" CD1 LEU A 986 " pdb=" CD2 LEU A 986 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA PHE A 659 " pdb=" N PHE A 659 " pdb=" C PHE A 659 " pdb=" CB PHE A 659 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 1014 not shown) Planarity restraints: 1205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 889 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO A 890 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 890 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 890 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 882 " -0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO A 883 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 883 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 883 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 716 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO A 717 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 717 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 717 " 0.020 5.00e-02 4.00e+02 ... (remaining 1202 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 187 2.71 - 3.26: 6270 3.26 - 3.80: 10300 3.80 - 4.35: 12699 4.35 - 4.90: 21552 Nonbonded interactions: 51008 Sorted by model distance: nonbonded pdb=" O TYR A 229 " pdb=" OG1 THR A 232 " model vdw 2.159 3.040 nonbonded pdb=" OH TYR A 303 " pdb=" OD2 ASP A 322 " model vdw 2.233 3.040 nonbonded pdb=" N GLU A 904 " pdb=" OE1 GLU A 904 " model vdw 2.272 3.120 nonbonded pdb=" NH2 ARG A 748 " pdb=" O ALA A1063 " model vdw 2.275 3.120 nonbonded pdb=" O PRO A 912 " pdb=" OH TYR A 958 " model vdw 2.288 3.040 ... (remaining 51003 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 20.320 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 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 : 0.003 0.040 6721 Z= 0.212 Angle : 0.582 10.491 9198 Z= 0.295 Chirality : 0.042 0.156 1017 Planarity : 0.005 0.057 1205 Dihedral : 15.770 80.379 2252 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.84 % Allowed : 32.21 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.28), residues: 874 helix: -0.06 (0.36), residues: 210 sheet: -0.55 (0.38), residues: 169 loop : -0.05 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1005 HIS 0.003 0.000 HIS A 299 PHE 0.013 0.001 PHE A1090 TYR 0.015 0.001 TYR A1019 ARG 0.004 0.000 ARG A 431 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 TYR cc_start: 0.7630 (t80) cc_final: 0.7386 (t80) REVERT: A 871 TRP cc_start: 0.6053 (t60) cc_final: 0.5375 (t60) REVERT: A 879 MET cc_start: 0.6759 (mmm) cc_final: 0.6270 (mmm) outliers start: 5 outliers final: 5 residues processed: 89 average time/residue: 0.9029 time to fit residues: 86.4370 Evaluate side-chains 72 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1161 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 393 GLN ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.170609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.142264 restraints weight = 8772.167| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.97 r_work: 0.3751 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6721 Z= 0.290 Angle : 0.611 7.952 9198 Z= 0.313 Chirality : 0.043 0.142 1017 Planarity : 0.005 0.039 1205 Dihedral : 5.109 47.392 963 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 6.38 % Allowed : 26.17 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.28), residues: 874 helix: -0.10 (0.35), residues: 219 sheet: -0.67 (0.39), residues: 167 loop : -0.12 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1005 HIS 0.007 0.001 HIS A 299 PHE 0.036 0.002 PHE A 659 TYR 0.022 0.002 TYR A1019 ARG 0.006 0.001 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 65 time to evaluate : 0.550 Fit side-chains REVERT: A 211 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6814 (pp) REVERT: A 263 ARG cc_start: 0.5902 (mmt90) cc_final: 0.5617 (mmt90) REVERT: A 338 GLN cc_start: 0.6723 (mm-40) cc_final: 0.6428 (mp-120) REVERT: A 761 GLU cc_start: 0.7648 (tp30) cc_final: 0.7393 (tp30) REVERT: A 879 MET cc_start: 0.6754 (mmm) cc_final: 0.6298 (mmm) REVERT: A 888 THR cc_start: 0.8080 (m) cc_final: 0.7792 (t) REVERT: A 981 ASP cc_start: 0.6247 (OUTLIER) cc_final: 0.5965 (m-30) REVERT: A 1192 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6495 (mm-30) REVERT: A 1203 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6800 (mt-10) outliers start: 38 outliers final: 16 residues processed: 97 average time/residue: 0.7817 time to fit residues: 81.8850 Evaluate side-chains 85 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1192 GLU Chi-restraints excluded: chain A residue 1203 GLU Chi-restraints excluded: chain A residue 1222 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 82 optimal weight: 0.2980 chunk 77 optimal weight: 0.0040 chunk 78 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.173614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.145583 restraints weight = 8853.749| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 3.02 r_work: 0.3798 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6721 Z= 0.178 Angle : 0.546 8.350 9198 Z= 0.273 Chirality : 0.041 0.139 1017 Planarity : 0.004 0.042 1205 Dihedral : 4.837 46.394 962 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.87 % Allowed : 26.85 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.28), residues: 874 helix: 0.26 (0.35), residues: 222 sheet: -0.69 (0.39), residues: 167 loop : -0.04 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 658 HIS 0.003 0.001 HIS A 299 PHE 0.024 0.001 PHE A 659 TYR 0.024 0.002 TYR A1019 ARG 0.004 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 78 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.5299 (OUTLIER) cc_final: 0.4675 (ppp) REVERT: A 263 ARG cc_start: 0.5874 (mmt90) cc_final: 0.5467 (ttt90) REVERT: A 334 SER cc_start: 0.8506 (t) cc_final: 0.7315 (p) REVERT: A 338 GLN cc_start: 0.6668 (mm-40) cc_final: 0.6363 (mp10) REVERT: A 580 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7435 (ptt90) REVERT: A 879 MET cc_start: 0.6671 (mmm) cc_final: 0.6167 (mmm) REVERT: A 888 THR cc_start: 0.7910 (m) cc_final: 0.7571 (t) REVERT: A 981 ASP cc_start: 0.6225 (OUTLIER) cc_final: 0.5985 (m-30) REVERT: A 1192 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6394 (mm-30) REVERT: A 1203 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6822 (mt-10) outliers start: 35 outliers final: 14 residues processed: 108 average time/residue: 0.9506 time to fit residues: 110.1740 Evaluate side-chains 86 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1192 GLU Chi-restraints excluded: chain A residue 1203 GLU Chi-restraints excluded: chain A residue 1222 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 77 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.0060 chunk 35 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 81 optimal weight: 9.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.173449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.145226 restraints weight = 8921.027| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 3.04 r_work: 0.3795 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6721 Z= 0.199 Angle : 0.561 8.943 9198 Z= 0.278 Chirality : 0.042 0.135 1017 Planarity : 0.004 0.044 1205 Dihedral : 4.849 45.764 962 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.37 % Allowed : 27.35 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.28), residues: 874 helix: 0.23 (0.35), residues: 222 sheet: -0.67 (0.40), residues: 162 loop : -0.03 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1005 HIS 0.005 0.001 HIS A 299 PHE 0.020 0.002 PHE A 659 TYR 0.022 0.001 TYR A1019 ARG 0.003 0.000 ARG A 786 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.5372 (OUTLIER) cc_final: 0.4802 (ppp) REVERT: A 334 SER cc_start: 0.8510 (t) cc_final: 0.7368 (p) REVERT: A 338 GLN cc_start: 0.6780 (mm-40) cc_final: 0.6510 (mp10) REVERT: A 580 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7497 (ptt90) REVERT: A 871 TRP cc_start: 0.6110 (t60) cc_final: 0.5389 (t60) REVERT: A 879 MET cc_start: 0.6731 (mmm) cc_final: 0.6292 (mmm) REVERT: A 888 THR cc_start: 0.7887 (m) cc_final: 0.7567 (t) REVERT: A 1192 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6434 (mm-30) REVERT: A 1203 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6829 (mt-10) outliers start: 32 outliers final: 16 residues processed: 99 average time/residue: 0.9422 time to fit residues: 99.6514 Evaluate side-chains 89 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1192 GLU Chi-restraints excluded: chain A residue 1203 GLU Chi-restraints excluded: chain A residue 1222 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 66 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 67 optimal weight: 0.0060 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.172363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.144195 restraints weight = 8942.191| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 3.01 r_work: 0.3773 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6721 Z= 0.217 Angle : 0.574 8.712 9198 Z= 0.286 Chirality : 0.042 0.136 1017 Planarity : 0.005 0.046 1205 Dihedral : 4.900 45.310 962 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.87 % Allowed : 27.35 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.28), residues: 874 helix: 0.38 (0.36), residues: 216 sheet: -0.68 (0.40), residues: 161 loop : -0.06 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 292 HIS 0.005 0.001 HIS A 299 PHE 0.019 0.002 PHE A 659 TYR 0.025 0.002 TYR A1019 ARG 0.009 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.5384 (OUTLIER) cc_final: 0.4795 (ppp) REVERT: A 263 ARG cc_start: 0.6380 (mtt90) cc_final: 0.5830 (tpp80) REVERT: A 334 SER cc_start: 0.8519 (t) cc_final: 0.7408 (p) REVERT: A 338 GLN cc_start: 0.6842 (mm-40) cc_final: 0.6613 (mp10) REVERT: A 580 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7576 (ptt90) REVERT: A 879 MET cc_start: 0.6657 (mmm) cc_final: 0.6360 (mmm) REVERT: A 888 THR cc_start: 0.7905 (m) cc_final: 0.7590 (t) REVERT: A 1094 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.7163 (mtm180) REVERT: A 1192 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6421 (mm-30) REVERT: A 1203 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6820 (mt-10) outliers start: 35 outliers final: 16 residues processed: 102 average time/residue: 0.9343 time to fit residues: 102.1862 Evaluate side-chains 92 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1094 ARG Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1192 GLU Chi-restraints excluded: chain A residue 1203 GLU Chi-restraints excluded: chain A residue 1222 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 61 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 chunk 43 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 0.0570 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 0.0030 overall best weight: 0.2266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 393 GLN ** A 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.174828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.146869 restraints weight = 8796.280| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 3.00 r_work: 0.3819 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6721 Z= 0.163 Angle : 0.553 9.023 9198 Z= 0.273 Chirality : 0.041 0.134 1017 Planarity : 0.004 0.045 1205 Dihedral : 4.718 44.359 962 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.20 % Allowed : 28.19 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.28), residues: 874 helix: 0.47 (0.36), residues: 217 sheet: -0.65 (0.40), residues: 160 loop : 0.07 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 292 HIS 0.003 0.000 HIS A 299 PHE 0.016 0.001 PHE A 659 TYR 0.024 0.001 TYR A1019 ARG 0.006 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.5286 (OUTLIER) cc_final: 0.4688 (ppp) REVERT: A 263 ARG cc_start: 0.6162 (mtt90) cc_final: 0.5664 (tpp80) REVERT: A 334 SER cc_start: 0.8487 (t) cc_final: 0.7309 (p) REVERT: A 338 GLN cc_start: 0.6744 (mm-40) cc_final: 0.6485 (mp10) REVERT: A 580 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7481 (ptt90) REVERT: A 879 MET cc_start: 0.6610 (mmm) cc_final: 0.6187 (mmm) REVERT: A 888 THR cc_start: 0.7853 (m) cc_final: 0.7485 (t) REVERT: A 1094 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.7054 (mtm180) REVERT: A 1192 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6338 (mm-30) REVERT: A 1203 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6667 (mt-10) outliers start: 31 outliers final: 17 residues processed: 102 average time/residue: 0.9555 time to fit residues: 104.8628 Evaluate side-chains 95 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1094 ARG Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1192 GLU Chi-restraints excluded: chain A residue 1203 GLU Chi-restraints excluded: chain A residue 1222 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 0.0170 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 76 optimal weight: 0.0270 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.174160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.146158 restraints weight = 8756.128| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.99 r_work: 0.3816 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6721 Z= 0.181 Angle : 0.564 8.969 9198 Z= 0.277 Chirality : 0.041 0.137 1017 Planarity : 0.004 0.046 1205 Dihedral : 4.691 44.241 962 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.20 % Allowed : 28.69 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.28), residues: 874 helix: 0.51 (0.36), residues: 217 sheet: -0.73 (0.39), residues: 162 loop : 0.09 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1005 HIS 0.004 0.000 HIS A 299 PHE 0.016 0.001 PHE A 659 TYR 0.020 0.001 TYR A1019 ARG 0.005 0.000 ARG A 786 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.5296 (OUTLIER) cc_final: 0.4732 (ppp) REVERT: A 263 ARG cc_start: 0.6253 (mtt90) cc_final: 0.5940 (ttt90) REVERT: A 334 SER cc_start: 0.8493 (t) cc_final: 0.7342 (p) REVERT: A 338 GLN cc_start: 0.6801 (mm-40) cc_final: 0.6548 (mp10) REVERT: A 580 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7487 (ptt90) REVERT: A 879 MET cc_start: 0.6623 (mmm) cc_final: 0.6218 (mmm) REVERT: A 888 THR cc_start: 0.7857 (m) cc_final: 0.7492 (t) REVERT: A 1089 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.5441 (mmp-170) REVERT: A 1094 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.7023 (mtm180) REVERT: A 1192 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6369 (mm-30) REVERT: A 1203 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6702 (mt-10) outliers start: 31 outliers final: 17 residues processed: 98 average time/residue: 0.8595 time to fit residues: 90.7600 Evaluate side-chains 96 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1089 ARG Chi-restraints excluded: chain A residue 1094 ARG Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1192 GLU Chi-restraints excluded: chain A residue 1203 GLU Chi-restraints excluded: chain A residue 1222 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 75 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 59 optimal weight: 0.0970 chunk 82 optimal weight: 3.9990 chunk 38 optimal weight: 0.0970 chunk 39 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.175356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.147678 restraints weight = 8835.745| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.99 r_work: 0.3826 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6721 Z= 0.166 Angle : 0.564 9.347 9198 Z= 0.274 Chirality : 0.042 0.148 1017 Planarity : 0.004 0.046 1205 Dihedral : 4.587 43.607 961 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.87 % Allowed : 29.36 % Favored : 65.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.28), residues: 874 helix: 0.71 (0.36), residues: 211 sheet: -0.76 (0.39), residues: 166 loop : 0.13 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1005 HIS 0.003 0.000 HIS A 299 PHE 0.014 0.001 PHE A 659 TYR 0.034 0.001 TYR A 287 ARG 0.005 0.000 ARG A 786 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.5329 (OUTLIER) cc_final: 0.4760 (ppp) REVERT: A 263 ARG cc_start: 0.6318 (mtt90) cc_final: 0.6055 (ttt90) REVERT: A 334 SER cc_start: 0.8476 (t) cc_final: 0.7293 (p) REVERT: A 338 GLN cc_start: 0.6804 (mm-40) cc_final: 0.6548 (mp10) REVERT: A 580 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7479 (ptt90) REVERT: A 879 MET cc_start: 0.6653 (mmm) cc_final: 0.6264 (mmm) REVERT: A 888 THR cc_start: 0.7821 (m) cc_final: 0.7436 (t) REVERT: A 1094 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.7071 (mtm180) REVERT: A 1192 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6281 (mm-30) REVERT: A 1203 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6622 (mt-10) outliers start: 29 outliers final: 16 residues processed: 101 average time/residue: 0.9438 time to fit residues: 102.1044 Evaluate side-chains 92 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1094 ARG Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1192 GLU Chi-restraints excluded: chain A residue 1203 GLU Chi-restraints excluded: chain A residue 1222 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 23 optimal weight: 0.0020 chunk 51 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.173032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.144785 restraints weight = 8946.036| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 3.03 r_work: 0.3788 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6721 Z= 0.216 Angle : 0.602 10.053 9198 Z= 0.293 Chirality : 0.042 0.142 1017 Planarity : 0.005 0.046 1205 Dihedral : 4.700 43.798 961 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.70 % Allowed : 29.87 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.28), residues: 874 helix: 0.66 (0.36), residues: 209 sheet: -0.78 (0.39), residues: 166 loop : 0.11 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A1005 HIS 0.005 0.001 HIS A 299 PHE 0.013 0.002 PHE A 659 TYR 0.022 0.002 TYR A1019 ARG 0.005 0.000 ARG A 786 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.5377 (OUTLIER) cc_final: 0.4782 (ppp) REVERT: A 263 ARG cc_start: 0.6346 (mtt90) cc_final: 0.6049 (ttt90) REVERT: A 334 SER cc_start: 0.8538 (t) cc_final: 0.7546 (p) REVERT: A 338 GLN cc_start: 0.6934 (mm-40) cc_final: 0.6706 (mp-120) REVERT: A 580 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7582 (ptt90) REVERT: A 879 MET cc_start: 0.6693 (mmm) cc_final: 0.6370 (mmm) REVERT: A 888 THR cc_start: 0.7874 (m) cc_final: 0.7497 (t) REVERT: A 1094 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.7094 (mtm180) REVERT: A 1192 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6320 (mm-30) REVERT: A 1203 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6689 (mt-10) outliers start: 28 outliers final: 19 residues processed: 96 average time/residue: 0.8341 time to fit residues: 86.4812 Evaluate side-chains 96 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain A residue 1094 ARG Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1192 GLU Chi-restraints excluded: chain A residue 1203 GLU Chi-restraints excluded: chain A residue 1222 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 76 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.172945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.144978 restraints weight = 8911.365| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 3.00 r_work: 0.3792 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6721 Z= 0.217 Angle : 0.604 9.818 9198 Z= 0.294 Chirality : 0.042 0.140 1017 Planarity : 0.005 0.046 1205 Dihedral : 4.724 44.759 961 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.87 % Allowed : 29.70 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.28), residues: 874 helix: 0.62 (0.36), residues: 211 sheet: -0.78 (0.39), residues: 166 loop : 0.09 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1005 HIS 0.005 0.001 HIS A 299 PHE 0.014 0.002 PHE A 659 TYR 0.023 0.001 TYR A1019 ARG 0.005 0.000 ARG A 786 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.5364 (OUTLIER) cc_final: 0.4783 (ppp) REVERT: A 263 ARG cc_start: 0.6373 (mtt90) cc_final: 0.6063 (ttt90) REVERT: A 334 SER cc_start: 0.8529 (t) cc_final: 0.7549 (p) REVERT: A 338 GLN cc_start: 0.6931 (mm-40) cc_final: 0.6705 (mp-120) REVERT: A 879 MET cc_start: 0.6681 (mmm) cc_final: 0.6360 (mmm) REVERT: A 888 THR cc_start: 0.7881 (m) cc_final: 0.7498 (t) REVERT: A 1094 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.7110 (mtm180) REVERT: A 1192 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6323 (mm-30) REVERT: A 1203 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6715 (mt-10) outliers start: 29 outliers final: 18 residues processed: 98 average time/residue: 0.8587 time to fit residues: 90.5964 Evaluate side-chains 91 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain A residue 1094 ARG Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1192 GLU Chi-restraints excluded: chain A residue 1203 GLU Chi-restraints excluded: chain A residue 1222 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.172725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.144712 restraints weight = 9029.325| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 3.01 r_work: 0.3796 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6721 Z= 0.216 Angle : 0.609 9.898 9198 Z= 0.297 Chirality : 0.042 0.139 1017 Planarity : 0.005 0.046 1205 Dihedral : 4.728 43.464 961 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.36 % Allowed : 29.87 % Favored : 65.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.28), residues: 874 helix: 0.61 (0.36), residues: 203 sheet: -0.80 (0.39), residues: 166 loop : 0.10 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1005 HIS 0.006 0.001 HIS A 299 PHE 0.014 0.002 PHE A 659 TYR 0.020 0.001 TYR A1019 ARG 0.008 0.001 ARG A1089 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4783.01 seconds wall clock time: 85 minutes 54.34 seconds (5154.34 seconds total)