Starting phenix.real_space_refine on Wed Sep 17 07:22:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bap_44410/09_2025/9bap_44410.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bap_44410/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bap_44410/09_2025/9bap_44410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bap_44410/09_2025/9bap_44410.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bap_44410/09_2025/9bap_44410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bap_44410/09_2025/9bap_44410.map" } resolution = 2.88 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= 0.029 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6535 Number of models: 1 Model: "" Number of chains: 2 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: {'GLU:plan': 26, 'ARG:plan': 17, 'ASN:plan1': 10, 'ASP:plan': 15, 'TYR:plan': 8, 'GLN:plan1': 10, 'HIS:plan': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 387 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 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: 1.76, per 1000 atoms: 0.27 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: 0.57 Conformation dependent library (CDL) restraints added in 411.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.27 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: 1.33 Time building geometry restraints manager: 0.79 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: 1.060 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.080 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.920 ------------------------------------------------------------------------------- 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 : 0.005 0.216 6725 Z= 0.180 Angle : 0.725 31.081 9201 Z= 0.315 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (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 ARG 0.004 0.000 ARG A 431 TYR 0.015 0.001 TYR A1019 PHE 0.013 0.001 PHE A1090 TRP 0.015 0.001 TRP A1005 HIS 0.003 0.000 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6721) covalent geometry : angle 0.58164 ( 9198) hydrogen bonds : bond 0.17618 ( 207) hydrogen bonds : angle 6.53309 ( 627) metal coordination : bond 0.16724 ( 4) metal coordination : angle 24.01233 ( 3) *********************** 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 : 0.284 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: 0.4467 time to fit residues: 42.4840 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 : 0.261 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.0170 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.172408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.144082 restraints weight = 8866.962| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 3.01 r_work: 0.3778 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6725 Z= 0.150 Angle : 0.590 7.832 9201 Z= 0.296 Chirality : 0.042 0.139 1017 Planarity : 0.005 0.039 1205 Dihedral : 4.962 46.973 963 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.54 % Allowed : 26.17 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.28), residues: 874 helix: -0.04 (0.35), residues: 225 sheet: -0.60 (0.39), residues: 167 loop : -0.06 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 392 TYR 0.019 0.002 TYR A1019 PHE 0.034 0.002 PHE A 659 TRP 0.017 0.002 TRP A1005 HIS 0.007 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 6721) covalent geometry : angle 0.58331 ( 9198) hydrogen bonds : bond 0.04249 ( 207) hydrogen bonds : angle 5.12428 ( 627) metal coordination : bond 0.01180 ( 4) metal coordination : angle 5.03641 ( 3) *********************** 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 102 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 263 ARG cc_start: 0.5825 (mmt90) cc_final: 0.5552 (mmt90) REVERT: A 334 SER cc_start: 0.8567 (t) cc_final: 0.7444 (p) REVERT: A 338 GLN cc_start: 0.6703 (mm-40) cc_final: 0.6408 (mp-120) REVERT: A 730 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6104 (t80) REVERT: A 761 GLU cc_start: 0.7625 (tp30) cc_final: 0.7365 (tp30) REVERT: A 879 MET cc_start: 0.6717 (mmm) cc_final: 0.6217 (mmm) REVERT: A 888 THR cc_start: 0.7958 (m) cc_final: 0.7683 (t) REVERT: A 892 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6175 (tp) REVERT: A 981 ASP cc_start: 0.6188 (OUTLIER) cc_final: 0.5932 (m-30) REVERT: A 1192 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6453 (mm-30) REVERT: A 1203 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6798 (mt-10) outliers start: 33 outliers final: 12 residues processed: 98 average time/residue: 0.4255 time to fit residues: 44.7556 Evaluate side-chains 83 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 730 TYR Chi-restraints excluded: chain A residue 892 LEU 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 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 55 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 67 optimal weight: 0.1980 chunk 20 optimal weight: 0.0870 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 74 optimal weight: 0.0770 chunk 6 optimal weight: 5.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.174748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.146931 restraints weight = 8779.450| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.02 r_work: 0.3806 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6725 Z= 0.103 Angle : 0.543 8.397 9201 Z= 0.269 Chirality : 0.041 0.137 1017 Planarity : 0.004 0.041 1205 Dihedral : 4.736 46.249 962 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.37 % Allowed : 27.01 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.29), residues: 874 helix: 0.33 (0.36), residues: 222 sheet: -0.65 (0.39), residues: 167 loop : 0.01 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 392 TYR 0.026 0.002 TYR A 287 PHE 0.024 0.001 PHE A 659 TRP 0.019 0.001 TRP A1005 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 6721) covalent geometry : angle 0.54016 ( 9198) hydrogen bonds : bond 0.03570 ( 207) hydrogen bonds : angle 4.82759 ( 627) metal coordination : bond 0.00947 ( 4) metal coordination : angle 3.20213 ( 3) *********************** 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 107 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.5350 (OUTLIER) cc_final: 0.4773 (ppp) REVERT: A 263 ARG cc_start: 0.5903 (mmt90) cc_final: 0.5632 (mmt90) REVERT: A 334 SER cc_start: 0.8532 (t) cc_final: 0.7330 (p) REVERT: A 338 GLN cc_start: 0.6772 (mm-40) cc_final: 0.6479 (mp10) REVERT: A 879 MET cc_start: 0.6682 (mmm) cc_final: 0.6246 (mmm) REVERT: A 981 ASP cc_start: 0.6276 (OUTLIER) cc_final: 0.6072 (m-30) REVERT: A 1192 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6399 (mm-30) REVERT: A 1203 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6840 (mt-10) outliers start: 32 outliers final: 13 residues processed: 102 average time/residue: 0.4911 time to fit residues: 53.2333 Evaluate side-chains 82 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 557 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 SER 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 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 72 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.3980 chunk 56 optimal weight: 0.3980 chunk 76 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.175001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.147159 restraints weight = 8917.695| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.02 r_work: 0.3827 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6725 Z= 0.104 Angle : 0.541 8.739 9201 Z= 0.266 Chirality : 0.041 0.132 1017 Planarity : 0.004 0.042 1205 Dihedral : 4.654 45.395 962 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.87 % Allowed : 27.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.29), residues: 874 helix: 0.37 (0.35), residues: 222 sheet: -0.65 (0.39), residues: 167 loop : 0.04 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 786 TYR 0.032 0.001 TYR A 287 PHE 0.020 0.001 PHE A 659 TRP 0.015 0.001 TRP A 658 HIS 0.003 0.000 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6721) covalent geometry : angle 0.53982 ( 9198) hydrogen bonds : bond 0.03264 ( 207) hydrogen bonds : angle 4.69547 ( 627) metal coordination : bond 0.00624 ( 4) metal coordination : angle 2.20650 ( 3) *********************** 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: 29 poor density : 75 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.5331 (OUTLIER) cc_final: 0.4738 (ppp) REVERT: A 263 ARG cc_start: 0.5853 (mmt90) cc_final: 0.5460 (ttt90) REVERT: A 334 SER cc_start: 0.8480 (t) cc_final: 0.7304 (p) REVERT: A 338 GLN cc_start: 0.6708 (mm-40) cc_final: 0.6465 (mp10) REVERT: A 871 TRP cc_start: 0.6064 (t60) cc_final: 0.5341 (t60) REVERT: A 879 MET cc_start: 0.6739 (mmm) cc_final: 0.6298 (mmm) REVERT: A 888 THR cc_start: 0.7857 (m) cc_final: 0.7619 (t) REVERT: A 1192 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6376 (mm-30) REVERT: A 1203 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6783 (mt-10) outliers start: 29 outliers final: 15 residues processed: 99 average time/residue: 0.4502 time to fit residues: 47.7314 Evaluate side-chains 87 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 588 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 22 optimal weight: 0.0370 chunk 84 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- 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 = 0.4207 r_free = 0.4207 target = 0.171907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.143622 restraints weight = 8959.134| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 3.02 r_work: 0.3778 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6725 Z= 0.145 Angle : 0.586 8.667 9201 Z= 0.291 Chirality : 0.042 0.140 1017 Planarity : 0.005 0.043 1205 Dihedral : 4.881 45.514 962 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.37 % Allowed : 27.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.28), residues: 874 helix: 0.28 (0.35), residues: 222 sheet: -0.67 (0.40), residues: 161 loop : -0.02 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 900 TYR 0.036 0.002 TYR A 287 PHE 0.019 0.002 PHE A 659 TRP 0.026 0.002 TRP A1005 HIS 0.006 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6721) covalent geometry : angle 0.58455 ( 9198) hydrogen bonds : bond 0.03466 ( 207) hydrogen bonds : angle 4.76450 ( 627) metal coordination : bond 0.00615 ( 4) metal coordination : angle 2.32774 ( 3) *********************** 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 103 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 71 time to evaluate : 0.230 Fit side-chains REVERT: A 239 MET cc_start: 0.5338 (OUTLIER) cc_final: 0.4799 (ppp) REVERT: A 334 SER cc_start: 0.8573 (t) cc_final: 0.7408 (p) REVERT: A 338 GLN cc_start: 0.6857 (mm-40) cc_final: 0.6613 (mp10) REVERT: A 879 MET cc_start: 0.6702 (mmm) cc_final: 0.6439 (mmm) REVERT: A 1192 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6416 (mm-30) REVERT: A 1203 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6906 (mt-10) outliers start: 32 outliers final: 16 residues processed: 99 average time/residue: 0.4283 time to fit residues: 45.4028 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 : 0.252 ------------------------------------------------------------------------------- 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 557 ILE Chi-restraints excluded: chain A residue 588 VAL 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 899 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 948 VAL 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 21 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.0870 chunk 39 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 0.6560 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.172340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.144151 restraints weight = 9011.944| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 3.03 r_work: 0.3777 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6725 Z= 0.128 Angle : 0.571 8.800 9201 Z= 0.283 Chirality : 0.042 0.138 1017 Planarity : 0.005 0.045 1205 Dihedral : 4.840 44.879 962 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.70 % Allowed : 28.86 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.28), residues: 874 helix: 0.61 (0.36), residues: 211 sheet: -0.73 (0.39), residues: 164 loop : 0.01 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 263 TYR 0.039 0.002 TYR A 287 PHE 0.016 0.002 PHE A 659 TRP 0.018 0.002 TRP A 292 HIS 0.005 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6721) covalent geometry : angle 0.57000 ( 9198) hydrogen bonds : bond 0.03281 ( 207) hydrogen bonds : angle 4.70247 ( 627) metal coordination : bond 0.00542 ( 4) metal coordination : angle 1.91059 ( 3) *********************** 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 98 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.251 Fit side-chains REVERT: A 239 MET cc_start: 0.5296 (OUTLIER) cc_final: 0.4702 (ppp) REVERT: A 334 SER cc_start: 0.8506 (t) cc_final: 0.7361 (p) REVERT: A 338 GLN cc_start: 0.6811 (mm-40) cc_final: 0.6553 (mp10) REVERT: A 1094 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7118 (mtm180) REVERT: A 1192 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6319 (mm-30) REVERT: A 1203 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6840 (mt-10) outliers start: 28 outliers final: 16 residues processed: 93 average time/residue: 0.4142 time to fit residues: 41.1862 Evaluate side-chains 88 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 557 ILE 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 888 THR 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 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 15 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 78 optimal weight: 0.0270 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.171650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.143371 restraints weight = 8832.944| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 3.00 r_work: 0.3781 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6725 Z= 0.133 Angle : 0.575 8.880 9201 Z= 0.288 Chirality : 0.042 0.137 1017 Planarity : 0.005 0.044 1205 Dihedral : 4.874 44.276 962 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.70 % Allowed : 28.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.28), residues: 874 helix: 0.58 (0.36), residues: 211 sheet: -0.79 (0.39), residues: 164 loop : 0.03 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 263 TYR 0.027 0.002 TYR A1019 PHE 0.015 0.002 PHE A 659 TRP 0.021 0.002 TRP A 292 HIS 0.005 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6721) covalent geometry : angle 0.57459 ( 9198) hydrogen bonds : bond 0.03309 ( 207) hydrogen bonds : angle 4.70431 ( 627) metal coordination : bond 0.00502 ( 4) metal coordination : angle 1.86994 ( 3) *********************** 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 108 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 74 time to evaluate : 0.254 Fit side-chains REVERT: A 239 MET cc_start: 0.5375 (OUTLIER) cc_final: 0.4789 (ppp) REVERT: A 263 ARG cc_start: 0.6435 (ttt90) cc_final: 0.6103 (tpp-160) REVERT: A 334 SER cc_start: 0.8524 (t) cc_final: 0.7433 (p) REVERT: A 338 GLN cc_start: 0.6876 (mm-40) cc_final: 0.6640 (mp10) REVERT: A 879 MET cc_start: 0.7242 (mmm) cc_final: 0.6698 (mmm) REVERT: A 1094 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7178 (mtm180) REVERT: A 1192 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6401 (mm-30) REVERT: A 1203 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6892 (mt-10) outliers start: 34 outliers final: 18 residues processed: 101 average time/residue: 0.3847 time to fit residues: 41.9712 Evaluate side-chains 92 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 661 THR Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 888 THR 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 Chi-restraints excluded: chain A residue 1239 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 33 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 35 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.171651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.143338 restraints weight = 8855.266| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 3.01 r_work: 0.3772 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6725 Z= 0.137 Angle : 0.586 8.850 9201 Z= 0.291 Chirality : 0.042 0.137 1017 Planarity : 0.005 0.046 1205 Dihedral : 4.893 44.937 962 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.20 % Allowed : 29.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.28), residues: 874 helix: 0.56 (0.36), residues: 211 sheet: -0.82 (0.39), residues: 164 loop : 0.03 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 263 TYR 0.039 0.002 TYR A 287 PHE 0.015 0.002 PHE A 659 TRP 0.024 0.002 TRP A 292 HIS 0.005 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6721) covalent geometry : angle 0.58493 ( 9198) hydrogen bonds : bond 0.03313 ( 207) hydrogen bonds : angle 4.71219 ( 627) metal coordination : bond 0.00510 ( 4) metal coordination : angle 1.76786 ( 3) *********************** 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 103 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.253 Fit side-chains REVERT: A 239 MET cc_start: 0.5366 (OUTLIER) cc_final: 0.4786 (ppp) REVERT: A 263 ARG cc_start: 0.6402 (ttt90) cc_final: 0.6083 (tpp-160) REVERT: A 334 SER cc_start: 0.8512 (t) cc_final: 0.7432 (p) REVERT: A 338 GLN cc_start: 0.6871 (mm-40) cc_final: 0.6625 (mp10) REVERT: A 879 MET cc_start: 0.7224 (mmm) cc_final: 0.6739 (mmm) REVERT: A 1094 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7169 (mtm180) REVERT: A 1192 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6431 (mm-30) REVERT: A 1203 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6880 (mt-10) outliers start: 31 outliers final: 20 residues processed: 96 average time/residue: 0.4145 time to fit residues: 42.7793 Evaluate side-chains 95 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 557 ILE 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 784 CYS Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 888 THR 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 Chi-restraints excluded: chain A residue 1239 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 0.0270 chunk 84 optimal weight: 0.7980 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.171893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.143483 restraints weight = 9077.273| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 3.05 r_work: 0.3777 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6725 Z= 0.130 Angle : 0.599 9.890 9201 Z= 0.294 Chirality : 0.042 0.137 1017 Planarity : 0.005 0.045 1205 Dihedral : 4.848 43.534 962 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.20 % Allowed : 29.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.28), residues: 874 helix: 0.60 (0.36), residues: 211 sheet: -0.85 (0.39), residues: 164 loop : 0.05 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 900 TYR 0.023 0.002 TYR A1019 PHE 0.014 0.002 PHE A 659 TRP 0.026 0.002 TRP A 292 HIS 0.005 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6721) covalent geometry : angle 0.59806 ( 9198) hydrogen bonds : bond 0.03268 ( 207) hydrogen bonds : angle 4.68521 ( 627) metal coordination : bond 0.00437 ( 4) metal coordination : angle 1.66528 ( 3) *********************** 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 105 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.233 Fit side-chains REVERT: A 239 MET cc_start: 0.5442 (OUTLIER) cc_final: 0.4869 (ppp) REVERT: A 263 ARG cc_start: 0.6484 (ttt90) cc_final: 0.6216 (ttt90) REVERT: A 334 SER cc_start: 0.8537 (t) cc_final: 0.7445 (p) REVERT: A 338 GLN cc_start: 0.6842 (mm-40) cc_final: 0.6593 (mp10) REVERT: A 879 MET cc_start: 0.7143 (mmm) cc_final: 0.6641 (mmm) REVERT: A 1094 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.7168 (mtm180) REVERT: A 1192 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6400 (mm-30) REVERT: A 1203 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6877 (mt-10) outliers start: 31 outliers final: 20 residues processed: 99 average time/residue: 0.4296 time to fit residues: 45.4565 Evaluate side-chains 93 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 557 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 888 THR 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 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 Chi-restraints excluded: chain A residue 1239 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 47 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.172246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.144168 restraints weight = 8865.654| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.99 r_work: 0.3782 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6725 Z= 0.123 Angle : 0.606 9.161 9201 Z= 0.297 Chirality : 0.042 0.139 1017 Planarity : 0.004 0.046 1205 Dihedral : 4.812 42.906 962 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.19 % Allowed : 30.54 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.28), residues: 874 helix: 0.59 (0.36), residues: 209 sheet: -0.81 (0.39), residues: 164 loop : 0.10 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 900 TYR 0.024 0.002 TYR A1019 PHE 0.014 0.002 PHE A 659 TRP 0.030 0.002 TRP A 292 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6721) covalent geometry : angle 0.60567 ( 9198) hydrogen bonds : bond 0.03246 ( 207) hydrogen bonds : angle 4.66020 ( 627) metal coordination : bond 0.00405 ( 4) metal coordination : angle 1.58724 ( 3) ********************** 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 92 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.303 Fit side-chains REVERT: A 239 MET cc_start: 0.5417 (OUTLIER) cc_final: 0.4839 (ppp) REVERT: A 263 ARG cc_start: 0.6460 (ttt90) cc_final: 0.6176 (ttt90) REVERT: A 334 SER cc_start: 0.8517 (t) cc_final: 0.7450 (p) REVERT: A 338 GLN cc_start: 0.6819 (mm-40) cc_final: 0.6566 (mp10) REVERT: A 879 MET cc_start: 0.7114 (mmm) cc_final: 0.6614 (mmm) REVERT: A 1094 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.7119 (mtm180) REVERT: A 1192 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6359 (mm-30) REVERT: A 1203 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6802 (mt-10) outliers start: 25 outliers final: 18 residues processed: 88 average time/residue: 0.3811 time to fit residues: 36.4684 Evaluate side-chains 88 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 661 THR Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 888 THR 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 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 Chi-restraints excluded: chain A residue 1239 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 53 optimal weight: 0.0040 chunk 60 optimal weight: 1.9990 chunk 86 optimal weight: 0.2980 chunk 36 optimal weight: 0.6980 chunk 72 optimal weight: 0.0060 chunk 61 optimal weight: 0.8980 overall best weight: 0.3608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.172398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.144450 restraints weight = 8924.313| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 3.00 r_work: 0.3783 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.378 6725 Z= 0.319 Angle : 1.017 65.887 9201 Z= 0.606 Chirality : 0.042 0.138 1017 Planarity : 0.009 0.277 1205 Dihedral : 4.815 42.899 962 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.69 % Allowed : 31.04 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.28), residues: 874 helix: 0.59 (0.36), residues: 209 sheet: -0.81 (0.39), residues: 164 loop : 0.10 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1089 TYR 0.012 0.001 TYR A 273 PHE 0.015 0.002 PHE A 659 TRP 0.028 0.002 TRP A 292 HIS 0.005 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00703 ( 6721) covalent geometry : angle 1.01710 ( 9198) hydrogen bonds : bond 0.03239 ( 207) hydrogen bonds : angle 4.66036 ( 627) metal coordination : bond 0.00387 ( 4) metal coordination : angle 1.59260 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2530.05 seconds wall clock time: 43 minutes 50.00 seconds (2630.00 seconds total)