Starting phenix.real_space_refine on Sat Aug 3 02:19:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bap_44410/08_2024/9bap_44410.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bap_44410/08_2024/9bap_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bap_44410/08_2024/9bap_44410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bap_44410/08_2024/9bap_44410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bap_44410/08_2024/9bap_44410.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bap_44410/08_2024/9bap_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 Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 6.83, per 1000 atoms: 1.05 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.07 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: 2.41 Time building geometry restraints manager: 2.63 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: 98.36 - 105.55: 193 105.55 - 112.73: 3483 112.73 - 119.92: 2218 119.92 - 127.11: 3189 127.11 - 134.29: 115 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: 2.200 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: 0.000 Check model and map are aligned: 0.010 Set scattering table: 0.060 Process input model: 26.640 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:13.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.890 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.695 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: 0.8527 time to fit residues: 81.5065 Evaluate side-chains 72 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 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 fitting. rotamer outliers: 38 poor density : 65 time to evaluate : 0.705 Fit side-chains REVERT: A 211 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6825 (pp) REVERT: A 263 ARG cc_start: 0.5973 (mmt90) cc_final: 0.5688 (mmt90) REVERT: A 338 GLN cc_start: 0.6752 (mm-40) cc_final: 0.6465 (mp-120) REVERT: A 761 GLU cc_start: 0.7632 (tp30) cc_final: 0.7379 (tp30) REVERT: A 879 MET cc_start: 0.6758 (mmm) cc_final: 0.6308 (mmm) REVERT: A 888 THR cc_start: 0.8119 (m) cc_final: 0.7839 (t) REVERT: A 981 ASP cc_start: 0.6223 (OUTLIER) cc_final: 0.5939 (m-30) REVERT: A 1192 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.6498 (mm-30) REVERT: A 1203 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6823 (mt-10) outliers start: 38 outliers final: 16 residues processed: 97 average time/residue: 0.7687 time to fit residues: 80.7309 Evaluate side-chains 85 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 65 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 44 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 54 optimal weight: 0.0670 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6721 Z= 0.256 Angle : 0.586 8.387 9198 Z= 0.296 Chirality : 0.043 0.142 1017 Planarity : 0.005 0.043 1205 Dihedral : 5.084 47.308 962 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 7.21 % Allowed : 25.84 % 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: -0.50 (0.28), residues: 874 helix: -0.02 (0.35), residues: 225 sheet: -0.63 (0.40), residues: 157 loop : -0.27 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 292 HIS 0.006 0.001 HIS A 299 PHE 0.024 0.002 PHE A 659 TYR 0.027 0.002 TYR A1019 ARG 0.003 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 120 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 77 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 263 ARG cc_start: 0.6008 (mmt90) cc_final: 0.5790 (mtt90) REVERT: A 334 SER cc_start: 0.8587 (t) cc_final: 0.7581 (p) REVERT: A 338 GLN cc_start: 0.6767 (mm-40) cc_final: 0.6497 (mp-120) REVERT: A 416 TYR cc_start: 0.6356 (t80) cc_final: 0.6122 (t80) REVERT: A 580 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7525 (ptt90) REVERT: A 879 MET cc_start: 0.6688 (mmm) cc_final: 0.6234 (mmm) REVERT: A 888 THR cc_start: 0.7960 (m) cc_final: 0.7689 (t) REVERT: A 1192 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6449 (mm-30) REVERT: A 1203 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6778 (mt-10) outliers start: 43 outliers final: 19 residues processed: 112 average time/residue: 0.7890 time to fit residues: 95.1944 Evaluate side-chains 90 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 68 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 264 SER 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 585 VAL Chi-restraints excluded: chain A residue 683 ILE 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 1092 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 41 optimal weight: 6.9990 chunk 8 optimal weight: 0.0070 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 76 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.3598 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6721 Z= 0.174 Angle : 0.562 8.950 9198 Z= 0.279 Chirality : 0.041 0.147 1017 Planarity : 0.004 0.045 1205 Dihedral : 4.906 45.907 962 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.53 % Allowed : 28.02 % 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: -0.25 (0.28), residues: 874 helix: 0.20 (0.35), residues: 222 sheet: -0.62 (0.40), residues: 160 loop : -0.05 (0.29), residues: 492 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 0.021 0.001 PHE A 659 TYR 0.022 0.001 TYR A1019 ARG 0.003 0.000 ARG A 900 *********************** 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 100 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 73 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.6333 (OUTLIER) cc_final: 0.5341 (pmm) REVERT: A 334 SER cc_start: 0.8485 (t) cc_final: 0.7270 (p) REVERT: A 338 GLN cc_start: 0.6663 (mm-40) cc_final: 0.6429 (mp10) REVERT: A 580 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7493 (ptt90) REVERT: A 879 MET cc_start: 0.6707 (mmm) cc_final: 0.6268 (mmm) REVERT: A 888 THR cc_start: 0.7921 (m) cc_final: 0.7619 (t) REVERT: A 1192 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6409 (mm-30) REVERT: A 1203 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6833 (mt-10) outliers start: 27 outliers final: 17 residues processed: 94 average time/residue: 1.0111 time to fit residues: 101.2068 Evaluate side-chains 89 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 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 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 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 48 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 0 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 28 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.1445 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= 0.207 Angle : 0.576 8.662 9198 Z= 0.287 Chirality : 0.042 0.183 1017 Planarity : 0.005 0.046 1205 Dihedral : 4.941 45.556 962 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.03 % Allowed : 28.02 % 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: -0.26 (0.28), residues: 874 helix: 0.20 (0.35), residues: 220 sheet: -0.64 (0.40), residues: 161 loop : -0.05 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1005 HIS 0.005 0.001 HIS A 299 PHE 0.020 0.002 PHE A 659 TYR 0.024 0.002 TYR A1019 ARG 0.008 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 105 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 75 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.6312 (OUTLIER) cc_final: 0.5403 (pmm) REVERT: A 263 ARG cc_start: 0.6266 (mtt90) cc_final: 0.5723 (tpp80) REVERT: A 334 SER cc_start: 0.8498 (t) cc_final: 0.7277 (p) REVERT: A 338 GLN cc_start: 0.6737 (mm-40) cc_final: 0.6501 (mp10) REVERT: A 580 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7571 (ptt90) REVERT: A 879 MET cc_start: 0.6680 (mmm) cc_final: 0.6259 (mmm) REVERT: A 888 THR cc_start: 0.7894 (m) cc_final: 0.7604 (t) REVERT: A 1192 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6368 (mm-30) REVERT: A 1203 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6799 (mt-10) outliers start: 30 outliers final: 20 residues processed: 98 average time/residue: 0.8538 time to fit residues: 89.8061 Evaluate side-chains 94 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 70 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 227 LEU 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 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 784 CYS 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 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 76 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 0.0020 chunk 85 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6721 Z= 0.241 Angle : 0.590 8.722 9198 Z= 0.296 Chirality : 0.043 0.191 1017 Planarity : 0.005 0.046 1205 Dihedral : 5.034 45.415 962 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 6.21 % Allowed : 27.18 % 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: -0.24 (0.28), residues: 874 helix: 0.31 (0.36), residues: 214 sheet: -0.65 (0.40), residues: 160 loop : -0.09 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 292 HIS 0.006 0.001 HIS A 299 PHE 0.018 0.002 PHE A 659 TYR 0.026 0.002 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 106 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 69 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.6252 (OUTLIER) cc_final: 0.5465 (pmm) REVERT: A 263 ARG cc_start: 0.6350 (mtt90) cc_final: 0.6014 (ttt90) REVERT: A 334 SER cc_start: 0.8516 (t) cc_final: 0.7312 (p) REVERT: A 338 GLN cc_start: 0.6682 (mm-40) cc_final: 0.6453 (mp10) REVERT: A 580 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7599 (ptt90) REVERT: A 843 MET cc_start: 0.7380 (tmt) cc_final: 0.6190 (tmt) REVERT: A 879 MET cc_start: 0.6629 (mmm) cc_final: 0.6369 (mmm) REVERT: A 888 THR cc_start: 0.7925 (m) cc_final: 0.7614 (t) REVERT: A 1192 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6409 (mm-30) REVERT: A 1203 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6832 (mt-10) outliers start: 37 outliers final: 19 residues processed: 100 average time/residue: 0.7925 time to fit residues: 85.7984 Evaluate side-chains 93 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 70 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 62 optimal weight: 0.0670 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 0.0980 chunk 84 optimal weight: 0.5980 chunk 53 optimal weight: 0.0980 chunk 51 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.3318 ------------------------------------------------------------------------------- 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 998 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6721 Z= 0.168 Angle : 0.572 8.910 9198 Z= 0.283 Chirality : 0.042 0.206 1017 Planarity : 0.004 0.047 1205 Dihedral : 4.847 44.483 962 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.87 % Allowed : 28.19 % Favored : 65.94 % 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: -0.10 (0.28), residues: 874 helix: 0.47 (0.36), residues: 216 sheet: -0.60 (0.40), residues: 160 loop : 0.01 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 292 HIS 0.003 0.000 HIS A 299 PHE 0.016 0.001 PHE A 659 TYR 0.026 0.001 TYR A1019 ARG 0.006 0.000 ARG A 263 *********************** 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 111 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 76 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.6249 (OUTLIER) cc_final: 0.5443 (pmm) REVERT: A 263 ARG cc_start: 0.6308 (mtt90) cc_final: 0.5964 (ttt90) REVERT: A 334 SER cc_start: 0.8495 (t) cc_final: 0.7277 (p) REVERT: A 338 GLN cc_start: 0.6789 (mm-40) cc_final: 0.6562 (mp10) REVERT: A 580 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7531 (ptt90) REVERT: A 871 TRP cc_start: 0.6042 (t60) cc_final: 0.5389 (t60) REVERT: A 879 MET cc_start: 0.6636 (mmm) cc_final: 0.6261 (mmm) REVERT: A 888 THR cc_start: 0.7868 (m) cc_final: 0.7565 (t) REVERT: A 1192 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6340 (mm-30) REVERT: A 1203 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6770 (mt-10) outliers start: 35 outliers final: 22 residues processed: 103 average time/residue: 0.7901 time to fit residues: 87.9428 Evaluate side-chains 98 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 72 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 356 ASN 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 628 GLU 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 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 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 50 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6721 Z= 0.239 Angle : 0.600 8.754 9198 Z= 0.299 Chirality : 0.043 0.161 1017 Planarity : 0.005 0.047 1205 Dihedral : 4.975 45.810 962 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.87 % Allowed : 28.36 % 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: -0.13 (0.28), residues: 874 helix: 0.61 (0.37), residues: 207 sheet: -0.70 (0.40), residues: 164 loop : -0.06 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 292 HIS 0.006 0.001 HIS A 299 PHE 0.015 0.002 PHE A 659 TYR 0.022 0.002 TYR A1019 ARG 0.006 0.000 ARG A 900 *********************** 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 107 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 72 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.6178 (OUTLIER) cc_final: 0.5618 (pmm) REVERT: A 263 ARG cc_start: 0.6381 (mtt90) cc_final: 0.6100 (ttt90) REVERT: A 334 SER cc_start: 0.8543 (OUTLIER) cc_final: 0.7324 (p) REVERT: A 338 GLN cc_start: 0.6745 (mm-40) cc_final: 0.6512 (mp10) REVERT: A 580 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7616 (ptt90) REVERT: A 871 TRP cc_start: 0.6064 (t60) cc_final: 0.5411 (t60) REVERT: A 879 MET cc_start: 0.6637 (mmm) cc_final: 0.6332 (mmm) REVERT: A 888 THR cc_start: 0.7899 (m) cc_final: 0.7592 (t) REVERT: A 1192 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6367 (mm-30) REVERT: A 1203 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6777 (mt-10) outliers start: 35 outliers final: 22 residues processed: 99 average time/residue: 0.8126 time to fit residues: 86.9884 Evaluate side-chains 99 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 72 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 334 SER 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 628 GLU 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 895 VAL Chi-restraints excluded: chain A residue 896 ASP 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 1092 ASP 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 79 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6721 Z= 0.219 Angle : 0.596 9.066 9198 Z= 0.296 Chirality : 0.042 0.141 1017 Planarity : 0.005 0.047 1205 Dihedral : 4.965 44.300 962 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.70 % Allowed : 28.36 % Favored : 65.94 % 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: -0.14 (0.28), residues: 874 helix: 0.61 (0.37), residues: 209 sheet: -0.75 (0.40), residues: 164 loop : -0.04 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 292 HIS 0.005 0.001 HIS A 299 PHE 0.015 0.002 PHE A 659 TYR 0.022 0.002 TYR A1019 ARG 0.007 0.001 ARG A 900 *********************** 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 106 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 72 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.6181 (OUTLIER) cc_final: 0.5741 (pmm) REVERT: A 263 ARG cc_start: 0.6417 (mtt90) cc_final: 0.6114 (ttt90) REVERT: A 334 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.7301 (p) REVERT: A 338 GLN cc_start: 0.6750 (mm-40) cc_final: 0.6515 (mp10) REVERT: A 580 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7644 (ptt90) REVERT: A 871 TRP cc_start: 0.6122 (t60) cc_final: 0.5454 (t60) REVERT: A 879 MET cc_start: 0.6602 (mmm) cc_final: 0.6318 (mmm) REVERT: A 888 THR cc_start: 0.7900 (m) cc_final: 0.7584 (t) REVERT: A 1192 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6373 (mm-30) REVERT: A 1203 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6772 (mt-10) outliers start: 34 outliers final: 21 residues processed: 99 average time/residue: 0.8575 time to fit residues: 91.5661 Evaluate side-chains 95 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 69 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 334 SER 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 628 GLU 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 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 1092 ASP 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 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 42 optimal weight: 0.0030 chunk 55 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6721 Z= 0.194 Angle : 0.594 9.146 9198 Z= 0.295 Chirality : 0.042 0.141 1017 Planarity : 0.005 0.047 1205 Dihedral : 4.909 43.552 962 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.87 % Allowed : 29.19 % Favored : 65.94 % 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: -0.09 (0.28), residues: 874 helix: 0.72 (0.37), residues: 201 sheet: -0.76 (0.40), residues: 164 loop : -0.03 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 292 HIS 0.004 0.001 HIS A 299 PHE 0.015 0.001 PHE A 659 TYR 0.026 0.002 TYR A1019 ARG 0.004 0.000 ARG A 900 ********************** 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 fitting. rotamer outliers: 29 poor density : 72 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.6233 (OUTLIER) cc_final: 0.5696 (pmm) REVERT: A 263 ARG cc_start: 0.6421 (mtt90) cc_final: 0.6098 (ttt90) REVERT: A 334 SER cc_start: 0.8456 (t) cc_final: 0.7269 (p) REVERT: A 338 GLN cc_start: 0.6735 (mm-40) cc_final: 0.6498 (mp10) REVERT: A 580 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7573 (ptt90) REVERT: A 871 TRP cc_start: 0.6119 (t60) cc_final: 0.5445 (t60) REVERT: A 879 MET cc_start: 0.6612 (mmm) cc_final: 0.6325 (mmm) REVERT: A 888 THR cc_start: 0.7902 (m) cc_final: 0.7574 (t) REVERT: A 1192 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6344 (mm-30) REVERT: A 1203 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6741 (mt-10) outliers start: 29 outliers final: 19 residues processed: 96 average time/residue: 0.7750 time to fit residues: 80.7380 Evaluate side-chains 94 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 71 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 393 GLN Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 628 GLU 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 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 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 21 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.171230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.142898 restraints weight = 8813.566| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.99 r_work: 0.3773 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6721 Z= 0.244 Angle : 0.610 9.117 9198 Z= 0.303 Chirality : 0.043 0.145 1017 Planarity : 0.005 0.058 1205 Dihedral : 4.933 42.140 962 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.19 % Allowed : 29.70 % 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: -0.14 (0.28), residues: 874 helix: 0.67 (0.37), residues: 201 sheet: -0.77 (0.40), residues: 164 loop : -0.06 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 292 HIS 0.006 0.001 HIS A 299 PHE 0.015 0.002 PHE A 659 TYR 0.017 0.002 TYR A1019 ARG 0.004 0.000 ARG A 900 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2589.81 seconds wall clock time: 48 minutes 40.56 seconds (2920.56 seconds total)