Starting phenix.real_space_refine on Thu Jun 26 00:02:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jbx_6487/06_2025/3jbx_6487.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jbx_6487/06_2025/3jbx_6487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3jbx_6487/06_2025/3jbx_6487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jbx_6487/06_2025/3jbx_6487.map" model { file = "/net/cci-nas-00/data/ceres_data/3jbx_6487/06_2025/3jbx_6487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jbx_6487/06_2025/3jbx_6487.cif" } resolution = 3.4 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16666 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 112 5.49 5 Mg 4 5.21 5 S 106 5.16 5 C 10124 2.51 5 N 2948 2.21 5 O 3374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16670 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4435 Classifications: {'peptide': 550} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 524} Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 8, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 318} Chain: "C" Number of atoms: 4435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4435 Classifications: {'peptide': 550} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 524} Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "E" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "F" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "G" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "H" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "I" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 286 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "J" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "K" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 286 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "L" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2107 SG CYS A 749 93.964 80.081 63.615 1.00 33.47 S ATOM 2128 SG CYS A 752 96.115 82.432 64.621 1.00 57.22 S ATOM 9256 SG CYS C 749 55.638 25.828 62.765 1.00 53.94 S ATOM 9277 SG CYS C 752 53.932 23.158 64.357 1.00 64.33 S Time building chain proxies: 9.52, per 1000 atoms: 0.57 Number of scatterers: 16670 At special positions: 0 Unit cell: (151.29, 107.01, 111.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 112 15.00 Mg 4 11.99 O 3374 8.00 N 2948 7.00 C 10124 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: 3.94 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 749 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 752 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 752 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " Number of angles added : 4 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3352 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 34.9% alpha, 22.3% beta 35 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 6.05 Creating SS restraints... Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 518 through 526 removed outlier: 3.525A pdb=" N LEU A 522 " --> pdb=" O PRO A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 588 Processing helix chain 'A' and resid 589 through 600 Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 686 through 705 Proline residue: A 696 - end of helix Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 755 through 762 removed outlier: 3.552A pdb=" N ASN A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 790 through 798 Processing helix chain 'A' and resid 814 through 835 removed outlier: 4.605A pdb=" N GLY A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 864 Processing helix chain 'A' and resid 872 through 880 Processing helix chain 'A' and resid 881 through 889 removed outlier: 3.578A pdb=" N VAL A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 917 removed outlier: 4.182A pdb=" N GLU A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 900 " --> pdb=" O GLU A 896 " (cutoff:3.500A) Proline residue: A 913 - end of helix Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 924 through 930 Processing helix chain 'A' and resid 930 through 946 Processing helix chain 'A' and resid 946 through 951 removed outlier: 3.618A pdb=" N TYR A 950 " --> pdb=" O PHE A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 962 Processing helix chain 'A' and resid 964 through 973 removed outlier: 3.520A pdb=" N GLU A 970 " --> pdb=" O PRO A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 979 Processing helix chain 'A' and resid 980 through 985 Processing helix chain 'A' and resid 985 through 998 removed outlier: 3.875A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 998 " --> pdb=" O ARG A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1018 removed outlier: 3.764A pdb=" N ASP A1008 " --> pdb=" O PHE A1004 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A1018 " --> pdb=" O TRP A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1023 Processing helix chain 'A' and resid 1024 through 1026 No H-bonds generated for 'chain 'A' and resid 1024 through 1026' Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 496 through 510 Processing helix chain 'C' and resid 518 through 526 removed outlier: 3.512A pdb=" N LEU C 522 " --> pdb=" O PRO C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 587 Processing helix chain 'C' and resid 589 through 600 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 686 through 705 Proline residue: C 696 - end of helix Processing helix chain 'C' and resid 730 through 738 Processing helix chain 'C' and resid 755 through 762 removed outlier: 3.540A pdb=" N ASN C 762 " --> pdb=" O GLU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 784 Processing helix chain 'C' and resid 790 through 798 Processing helix chain 'C' and resid 814 through 835 removed outlier: 4.076A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 862 Processing helix chain 'C' and resid 872 through 880 Processing helix chain 'C' and resid 881 through 890 removed outlier: 3.835A pdb=" N ALA C 887 " --> pdb=" O GLU C 883 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL C 888 " --> pdb=" O ALA C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 912 removed outlier: 3.617A pdb=" N LEU C 902 " --> pdb=" O ARG C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 924 Processing helix chain 'C' and resid 924 through 930 Processing helix chain 'C' and resid 930 through 946 Processing helix chain 'C' and resid 946 through 951 removed outlier: 3.514A pdb=" N TYR C 950 " --> pdb=" O PHE C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 964 Processing helix chain 'C' and resid 964 through 973 Processing helix chain 'C' and resid 980 through 997 removed outlier: 3.779A pdb=" N LYS C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1018 removed outlier: 3.673A pdb=" N SER C1018 " --> pdb=" O TRP C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1027 removed outlier: 3.872A pdb=" N PHE C1024 " --> pdb=" O TYR C1020 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C1027 " --> pdb=" O LYS C1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 314 Processing sheet with id=A, first strand: chain 'A' and resid 537 through 539 removed outlier: 7.143A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 620 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE A 644 " --> pdb=" O PRO A 676 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE A 572 " --> pdb=" O PHE A 681 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 537 through 539 removed outlier: 7.143A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 620 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N MET A 647 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLN A 664 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE A 649 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'B' and resid 3 through 6 removed outlier: 4.040A pdb=" N PHE B 345 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 318 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 20 through 23 removed outlier: 3.544A pdb=" N SER B 20 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'B' and resid 76 through 80 removed outlier: 6.687A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.530A pdb=" N GLU B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'B' and resid 141 through 147 Processing sheet with id=H, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=I, first strand: chain 'B' and resid 209 through 212 removed outlier: 3.629A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'B' and resid 263 through 264 removed outlier: 3.976A pdb=" N CYS B 287 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'C' and resid 537 through 539 Processing sheet with id=L, first strand: chain 'C' and resid 554 through 555 removed outlier: 6.110A pdb=" N PHE C 644 " --> pdb=" O PRO C 676 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL C 640 " --> pdb=" O MET C 680 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE C 651 " --> pdb=" O THR C 661 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N THR C 661 " --> pdb=" O ILE C 651 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'C' and resid 554 through 555 removed outlier: 6.110A pdb=" N PHE C 644 " --> pdb=" O PRO C 676 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL C 640 " --> pdb=" O MET C 680 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'D' and resid 2 through 6 removed outlier: 4.135A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 318 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'D' and resid 20 through 23 removed outlier: 4.247A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'D' and resid 76 through 80 removed outlier: 5.597A pdb=" N GLY D 94 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N SER D 105 " --> pdb=" O GLY D 94 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG D 96 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER D 103 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU D 106 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'D' and resid 141 through 147 Processing sheet with id=R, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=S, first strand: chain 'D' and resid 208 through 212 Processing sheet with id=T, first strand: chain 'D' and resid 263 through 265 removed outlier: 4.074A pdb=" N CYS D 287 " --> pdb=" O ARG D 302 " (cutoff:3.500A) 643 hydrogen bonds defined for protein. 1794 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 7.34 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2612 1.32 - 1.45: 5234 1.45 - 1.57: 9039 1.57 - 1.70: 225 1.70 - 1.83: 158 Bond restraints: 17268 Sorted by residual: bond pdb=" CA VAL D 9 " pdb=" CB VAL D 9 " ideal model delta sigma weight residual 1.540 1.595 -0.055 1.36e-02 5.41e+03 1.61e+01 bond pdb=" CA VAL B 9 " pdb=" CB VAL B 9 " ideal model delta sigma weight residual 1.540 1.594 -0.054 1.36e-02 5.41e+03 1.55e+01 bond pdb=" CA PRO B 339 " pdb=" C PRO B 339 " ideal model delta sigma weight residual 1.517 1.552 -0.035 9.30e-03 1.16e+04 1.42e+01 bond pdb=" C GLU C 731 " pdb=" O GLU C 731 " ideal model delta sigma weight residual 1.236 1.195 0.041 1.22e-02 6.72e+03 1.15e+01 bond pdb=" CA VAL A 562 " pdb=" CB VAL A 562 " ideal model delta sigma weight residual 1.540 1.581 -0.041 1.36e-02 5.41e+03 9.16e+00 ... (remaining 17263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 22789 2.71 - 5.43: 922 5.43 - 8.14: 89 8.14 - 10.85: 21 10.85 - 13.56: 7 Bond angle restraints: 23828 Sorted by residual: angle pdb=" C ASN A 842 " pdb=" N PRO A 843 " pdb=" CA PRO A 843 " ideal model delta sigma weight residual 120.31 130.61 -10.30 9.80e-01 1.04e+00 1.11e+02 angle pdb=" O MET C 733 " pdb=" C MET C 733 " pdb=" N VAL C 734 " ideal model delta sigma weight residual 122.09 112.14 9.95 1.08e+00 8.57e-01 8.49e+01 angle pdb=" N PRO D 339 " pdb=" CA PRO D 339 " pdb=" C PRO D 339 " ideal model delta sigma weight residual 110.70 119.58 -8.88 1.22e+00 6.72e-01 5.30e+01 angle pdb=" C LEU B 197 " pdb=" N PRO B 198 " pdb=" CA PRO B 198 " ideal model delta sigma weight residual 119.47 127.29 -7.82 1.16e+00 7.43e-01 4.54e+01 angle pdb=" N ARG A 999 " pdb=" CA ARG A 999 " pdb=" C ARG A 999 " ideal model delta sigma weight residual 111.24 119.81 -8.57 1.29e+00 6.01e-01 4.42e+01 ... (remaining 23823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.74: 8994 28.74 - 57.48: 998 57.48 - 86.22: 101 86.22 - 114.96: 5 114.96 - 143.70: 2 Dihedral angle restraints: 10100 sinusoidal: 4888 harmonic: 5212 Sorted by residual: dihedral pdb=" CD ARG A 992 " pdb=" NE ARG A 992 " pdb=" CZ ARG A 992 " pdb=" NH1 ARG A 992 " ideal model delta sinusoidal sigma weight residual 0.00 71.05 -71.05 1 1.00e+01 1.00e-02 6.48e+01 dihedral pdb=" CA LYS B 86 " pdb=" C LYS B 86 " pdb=" N PRO B 87 " pdb=" CA PRO B 87 " ideal model delta harmonic sigma weight residual -180.00 -143.29 -36.71 0 5.00e+00 4.00e-02 5.39e+01 dihedral pdb=" CA ALA C1027 " pdb=" C ALA C1027 " pdb=" N HIS C1028 " pdb=" CA HIS C1028 " ideal model delta harmonic sigma weight residual -180.00 -146.82 -33.18 0 5.00e+00 4.00e-02 4.40e+01 ... (remaining 10097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2366 0.083 - 0.165: 216 0.165 - 0.248: 14 0.248 - 0.331: 2 0.331 - 0.414: 2 Chirality restraints: 2600 Sorted by residual: chirality pdb=" CA ASN C 997 " pdb=" N ASN C 997 " pdb=" C ASN C 997 " pdb=" CB ASN C 997 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CA MET C 996 " pdb=" N MET C 996 " pdb=" C MET C 996 " pdb=" CB MET C 996 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA ASN A 997 " pdb=" N ASN A 997 " pdb=" C ASN A 997 " pdb=" CB ASN A 997 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 2597 not shown) Planarity restraints: 2682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 992 " 1.045 9.50e-02 1.11e+02 4.68e-01 1.32e+02 pdb=" NE ARG A 992 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG A 992 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 992 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 992 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 870 " 0.864 9.50e-02 1.11e+02 3.87e-01 9.10e+01 pdb=" NE ARG C 870 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG C 870 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG C 870 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 870 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 994 " -0.672 9.50e-02 1.11e+02 3.01e-01 5.53e+01 pdb=" NE ARG C 994 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG C 994 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 994 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 994 " -0.021 2.00e-02 2.50e+03 ... (remaining 2679 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 74 2.43 - 3.05: 10294 3.05 - 3.67: 26614 3.67 - 4.28: 40020 4.28 - 4.90: 63308 Nonbonded interactions: 140310 Sorted by model distance: nonbonded pdb=" OE2 GLU C 731 " pdb=" NZ LYS C 960 " model vdw 1.816 3.120 nonbonded pdb=" O LEU A 481 " pdb=" NE2 GLN A 517 " model vdw 2.168 3.120 nonbonded pdb=" O3' DG F 15 " pdb="MG MG C1102 " model vdw 2.170 2.170 nonbonded pdb=" NE2 GLN A 858 " pdb=" O ALA A 887 " model vdw 2.172 3.120 nonbonded pdb=" NZ LYS C1011 " pdb=" OP1 DC H 8 " model vdw 2.173 3.120 ... (remaining 140305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 45.470 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 : 0.009 0.739 17276 Z= 0.390 Angle : 1.275 29.503 23832 Z= 0.830 Chirality : 0.049 0.414 2600 Planarity : 0.014 0.468 2682 Dihedral : 21.203 143.696 6748 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.13 % Favored : 93.76 % Rotamer: Outliers : 11.74 % Allowed : 11.81 % Favored : 76.45 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % Twisted General : 0.06 % 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: -3.11 (0.15), residues: 1794 helix: -2.86 (0.16), residues: 550 sheet: -0.37 (0.25), residues: 296 loop : -2.12 (0.15), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 978 HIS 0.006 0.001 HIS B 269 PHE 0.032 0.002 PHE C1004 TYR 0.029 0.002 TYR C 729 ARG 0.004 0.001 ARG C 490 Details of bonding type rmsd hydrogen bonds : bond 0.14751 ( 699) hydrogen bonds : angle 10.12595 ( 1944) metal coordination : bond 0.33337 ( 8) metal coordination : angle 23.37599 ( 4) covalent geometry : bond 0.00554 (17268) covalent geometry : angle 1.23837 (23828) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 460 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 SER cc_start: 0.8975 (t) cc_final: 0.8705 (m) REVERT: A 690 LEU cc_start: 0.8448 (tp) cc_final: 0.7967 (tp) REVERT: A 730 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7309 (p0) REVERT: A 732 LYS cc_start: 0.8896 (tttt) cc_final: 0.8565 (ttmt) REVERT: A 749 CYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7663 (m) REVERT: A 792 ASP cc_start: 0.8242 (t0) cc_final: 0.8002 (t0) REVERT: A 814 ASP cc_start: 0.8250 (t0) cc_final: 0.7875 (t0) REVERT: A 833 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: A 863 MET cc_start: 0.8187 (mmp) cc_final: 0.7255 (tpp) REVERT: A 902 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8162 (mt) REVERT: A 981 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7408 (mm-30) REVERT: B 11 CYS cc_start: 0.8000 (m) cc_final: 0.6777 (m) REVERT: B 33 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7969 (pt0) REVERT: B 80 PHE cc_start: 0.8531 (t80) cc_final: 0.8185 (t80) REVERT: B 192 CYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7689 (p) REVERT: B 200 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8041 (mp) REVERT: B 212 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6598 (ttp-170) REVERT: B 281 THR cc_start: 0.8405 (m) cc_final: 0.8169 (p) REVERT: B 285 MET cc_start: 0.8577 (mmm) cc_final: 0.8254 (mmm) REVERT: B 338 THR cc_start: 0.8425 (m) cc_final: 0.8150 (p) REVERT: C 487 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8196 (tp) REVERT: C 548 SER cc_start: 0.9121 (t) cc_final: 0.8739 (m) REVERT: C 571 THR cc_start: 0.7806 (m) cc_final: 0.7604 (t) REVERT: C 578 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.6811 (t80) REVERT: C 622 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7419 (ptp) REVERT: C 677 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8577 (tp) REVERT: C 680 MET cc_start: 0.8082 (mtm) cc_final: 0.7734 (mtp) REVERT: C 860 ARG cc_start: 0.8570 (tpp80) cc_final: 0.8355 (ttm-80) REVERT: C 902 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8286 (mt) REVERT: C 1007 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: D 65 ASN cc_start: 0.8286 (p0) cc_final: 0.8005 (p0) REVERT: D 89 CYS cc_start: 0.8704 (t) cc_final: 0.8499 (t) REVERT: D 171 ASN cc_start: 0.8091 (m-40) cc_final: 0.7699 (p0) REVERT: D 186 ASP cc_start: 0.7895 (t0) cc_final: 0.7665 (t0) REVERT: D 224 LEU cc_start: 0.7953 (tp) cc_final: 0.7711 (tp) REVERT: D 250 THR cc_start: 0.8979 (t) cc_final: 0.8757 (p) REVERT: D 272 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7696 (tt) outliers start: 186 outliers final: 41 residues processed: 593 average time/residue: 0.3150 time to fit residues: 270.2016 Evaluate side-chains 322 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 266 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 656 GLU Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 711 ILE Chi-restraints excluded: chain C residue 720 PHE Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 981 GLU Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 338 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.3980 chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN A1000 GLN B 4 GLN B 33 GLN B 64 ASN B 65 ASN B 170 GLN C 492 ASN C 517 GLN C 858 GLN ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 997 ASN C1000 GLN D 173 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS D 269 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.135859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110392 restraints weight = 26592.513| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.35 r_work: 0.3302 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17276 Z= 0.205 Angle : 0.794 12.129 23832 Z= 0.431 Chirality : 0.046 0.224 2600 Planarity : 0.006 0.076 2682 Dihedral : 22.753 152.676 3332 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.56 % Favored : 97.32 % Rotamer: Outliers : 6.00 % Allowed : 18.06 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: -1.84 (0.17), residues: 1794 helix: -0.92 (0.20), residues: 528 sheet: -0.31 (0.26), residues: 314 loop : -1.72 (0.16), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 317 HIS 0.008 0.001 HIS B 269 PHE 0.019 0.002 PHE C1004 TYR 0.019 0.002 TYR C 504 ARG 0.009 0.001 ARG A 795 Details of bonding type rmsd hydrogen bonds : bond 0.05785 ( 699) hydrogen bonds : angle 6.12234 ( 1944) metal coordination : bond 0.01925 ( 8) metal coordination : angle 3.91111 ( 4) covalent geometry : bond 0.00448 (17268) covalent geometry : angle 0.79260 (23828) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 318 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 SER cc_start: 0.9131 (t) cc_final: 0.8825 (m) REVERT: A 578 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.7440 (t80) REVERT: A 680 MET cc_start: 0.8495 (mtp) cc_final: 0.8059 (mtm) REVERT: A 705 MET cc_start: 0.8992 (mtm) cc_final: 0.8772 (mtm) REVERT: A 894 SER cc_start: 0.8366 (t) cc_final: 0.7957 (p) REVERT: A 902 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7886 (mt) REVERT: A 940 ASP cc_start: 0.8629 (p0) cc_final: 0.7795 (m-30) REVERT: A 968 ILE cc_start: 0.8872 (mt) cc_final: 0.8631 (mt) REVERT: B 11 CYS cc_start: 0.6612 (m) cc_final: 0.6394 (m) REVERT: B 33 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7967 (pt0) REVERT: B 58 ARG cc_start: 0.8240 (mmt180) cc_final: 0.7959 (mmt-90) REVERT: B 80 PHE cc_start: 0.8424 (t80) cc_final: 0.7993 (t80) REVERT: B 177 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8139 (m-30) REVERT: B 186 ASP cc_start: 0.7936 (t0) cc_final: 0.7542 (t0) REVERT: B 189 PHE cc_start: 0.6901 (m-80) cc_final: 0.6699 (m-80) REVERT: B 192 CYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7666 (p) REVERT: B 285 MET cc_start: 0.8368 (mmm) cc_final: 0.8131 (mmm) REVERT: C 548 SER cc_start: 0.9076 (t) cc_final: 0.8701 (m) REVERT: C 578 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7724 (t80) REVERT: C 587 LYS cc_start: 0.8733 (tptm) cc_final: 0.8331 (tptp) REVERT: C 680 MET cc_start: 0.8268 (mtm) cc_final: 0.7754 (mtp) REVERT: C 782 TRP cc_start: 0.8838 (OUTLIER) cc_final: 0.8513 (t-100) REVERT: C 1007 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: D 117 ASN cc_start: 0.6195 (m-40) cc_final: 0.5930 (p0) REVERT: D 171 ASN cc_start: 0.8254 (m-40) cc_final: 0.7979 (p0) REVERT: D 186 ASP cc_start: 0.8013 (t0) cc_final: 0.7614 (t0) outliers start: 95 outliers final: 51 residues processed: 385 average time/residue: 0.3124 time to fit residues: 175.5780 Evaluate side-chains 308 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 249 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 656 GLU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 711 ILE Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 269 HIS Chi-restraints excluded: chain D residue 338 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 3 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 HIS B 65 ASN B 204 GLN C 492 ASN C 822 ASN ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.132265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.106662 restraints weight = 26594.649| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.33 r_work: 0.3245 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 17276 Z= 0.288 Angle : 0.780 11.811 23832 Z= 0.421 Chirality : 0.047 0.219 2600 Planarity : 0.006 0.100 2682 Dihedral : 22.785 151.854 3289 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.12 % Favored : 95.76 % Rotamer: Outliers : 6.63 % Allowed : 19.32 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: -1.46 (0.18), residues: 1794 helix: -0.48 (0.21), residues: 544 sheet: -0.27 (0.26), residues: 348 loop : -1.54 (0.18), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 317 HIS 0.008 0.002 HIS D 269 PHE 0.021 0.002 PHE C1004 TYR 0.022 0.002 TYR A 875 ARG 0.010 0.001 ARG A 795 Details of bonding type rmsd hydrogen bonds : bond 0.05412 ( 699) hydrogen bonds : angle 5.82422 ( 1944) metal coordination : bond 0.02929 ( 8) metal coordination : angle 4.38754 ( 4) covalent geometry : bond 0.00650 (17268) covalent geometry : angle 0.77749 (23828) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 263 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 TYR cc_start: 0.9066 (t80) cc_final: 0.8787 (t80) REVERT: A 528 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7639 (tm-30) REVERT: A 548 SER cc_start: 0.9257 (t) cc_final: 0.8922 (m) REVERT: A 578 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.7752 (t80) REVERT: A 680 MET cc_start: 0.8560 (mtp) cc_final: 0.8234 (mtm) REVERT: A 863 MET cc_start: 0.7913 (mmm) cc_final: 0.7667 (mmm) REVERT: A 894 SER cc_start: 0.8404 (t) cc_final: 0.8156 (p) REVERT: B 80 PHE cc_start: 0.8467 (t80) cc_final: 0.7834 (t80) REVERT: B 108 MET cc_start: 0.7568 (ttm) cc_final: 0.7321 (ttp) REVERT: B 177 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8202 (m-30) REVERT: B 186 ASP cc_start: 0.7905 (t0) cc_final: 0.7600 (t0) REVERT: B 200 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7880 (mt) REVERT: B 232 ARG cc_start: 0.8839 (ttp80) cc_final: 0.8260 (ttp80) REVERT: B 235 ARG cc_start: 0.6849 (ttt90) cc_final: 0.6507 (ttt90) REVERT: B 293 ASP cc_start: 0.8254 (t0) cc_final: 0.7880 (m-30) REVERT: C 504 TYR cc_start: 0.8969 (t80) cc_final: 0.8635 (t80) REVERT: C 548 SER cc_start: 0.9236 (t) cc_final: 0.8819 (m) REVERT: C 578 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.7932 (t80) REVERT: C 587 LYS cc_start: 0.8839 (tptm) cc_final: 0.8409 (tptp) REVERT: C 677 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8637 (tp) REVERT: C 680 MET cc_start: 0.8464 (mtm) cc_final: 0.8109 (mtp) REVERT: C 782 TRP cc_start: 0.8809 (OUTLIER) cc_final: 0.8598 (t-100) REVERT: C 807 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7602 (ptm) REVERT: D 117 ASN cc_start: 0.6512 (m-40) cc_final: 0.6198 (p0) REVERT: D 132 ASP cc_start: 0.6495 (OUTLIER) cc_final: 0.5841 (m-30) REVERT: D 162 MET cc_start: 0.7985 (mtt) cc_final: 0.7668 (mtt) REVERT: D 171 ASN cc_start: 0.8445 (m-40) cc_final: 0.8021 (p0) REVERT: D 186 ASP cc_start: 0.8099 (t0) cc_final: 0.7779 (t0) REVERT: D 235 ARG cc_start: 0.6565 (ttt90) cc_final: 0.6346 (ttt90) REVERT: D 285 MET cc_start: 0.8446 (mmt) cc_final: 0.7668 (mmm) outliers start: 105 outliers final: 63 residues processed: 340 average time/residue: 0.2787 time to fit residues: 142.4958 Evaluate side-chains 297 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 226 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 656 GLU Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 711 ILE Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 807 MET Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain C residue 880 MET Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 338 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 105 optimal weight: 5.9990 chunk 138 optimal weight: 0.5980 chunk 153 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 143 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN C 492 ASN C 956 ASN D 298 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.138584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.112811 restraints weight = 26196.129| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.36 r_work: 0.3334 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17276 Z= 0.148 Angle : 0.682 12.326 23832 Z= 0.368 Chirality : 0.042 0.206 2600 Planarity : 0.005 0.069 2682 Dihedral : 22.540 157.490 3277 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.60 % Rotamer: Outliers : 5.05 % Allowed : 21.59 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: -1.06 (0.18), residues: 1794 helix: 0.03 (0.22), residues: 536 sheet: -0.24 (0.26), residues: 366 loop : -1.34 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 317 HIS 0.007 0.001 HIS A 964 PHE 0.020 0.001 PHE D 350 TYR 0.019 0.001 TYR A 908 ARG 0.010 0.001 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.04427 ( 699) hydrogen bonds : angle 5.40069 ( 1944) metal coordination : bond 0.01803 ( 8) metal coordination : angle 3.18269 ( 4) covalent geometry : bond 0.00320 (17268) covalent geometry : angle 0.68118 (23828) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 275 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 TYR cc_start: 0.8868 (t80) cc_final: 0.8632 (t80) REVERT: A 528 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7763 (tm-30) REVERT: A 548 SER cc_start: 0.9281 (t) cc_final: 0.8929 (m) REVERT: A 578 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7350 (t80) REVERT: A 664 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: A 680 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8032 (mtp) REVERT: A 792 ASP cc_start: 0.8211 (t0) cc_final: 0.8001 (t0) REVERT: A 894 SER cc_start: 0.8707 (t) cc_final: 0.8136 (p) REVERT: A 940 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8365 (p0) REVERT: B 34 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7933 (ttmt) REVERT: B 58 ARG cc_start: 0.8363 (mmt180) cc_final: 0.8025 (mtp180) REVERT: B 80 PHE cc_start: 0.8414 (t80) cc_final: 0.7768 (t80) REVERT: B 113 SER cc_start: 0.8316 (m) cc_final: 0.8066 (p) REVERT: B 186 ASP cc_start: 0.7867 (t0) cc_final: 0.7484 (t0) REVERT: B 189 PHE cc_start: 0.6331 (m-80) cc_final: 0.6063 (m-80) REVERT: B 232 ARG cc_start: 0.8799 (ttp80) cc_final: 0.8351 (ttp80) REVERT: B 293 ASP cc_start: 0.8308 (t0) cc_final: 0.8044 (m-30) REVERT: B 298 HIS cc_start: 0.7614 (p90) cc_final: 0.7038 (p90) REVERT: B 341 GLU cc_start: 0.7758 (mp0) cc_final: 0.7501 (pm20) REVERT: C 504 TYR cc_start: 0.8800 (t80) cc_final: 0.8551 (t80) REVERT: C 528 GLU cc_start: 0.8384 (tt0) cc_final: 0.8083 (tm-30) REVERT: C 548 SER cc_start: 0.9338 (t) cc_final: 0.8935 (m) REVERT: C 587 LYS cc_start: 0.8743 (tptm) cc_final: 0.8343 (tptp) REVERT: C 594 MET cc_start: 0.8140 (mmm) cc_final: 0.7711 (mmm) REVERT: C 595 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7942 (tm-30) REVERT: C 680 MET cc_start: 0.8431 (mtm) cc_final: 0.7907 (mtp) REVERT: C 905 MET cc_start: 0.8388 (tpp) cc_final: 0.7490 (tpp) REVERT: D 117 ASN cc_start: 0.6155 (m-40) cc_final: 0.5904 (p0) REVERT: D 132 ASP cc_start: 0.6546 (OUTLIER) cc_final: 0.5860 (m-30) REVERT: D 162 MET cc_start: 0.7914 (mtt) cc_final: 0.7551 (mtt) REVERT: D 171 ASN cc_start: 0.8397 (m-40) cc_final: 0.7909 (p0) REVERT: D 285 MET cc_start: 0.8424 (mmt) cc_final: 0.7650 (mmm) outliers start: 80 outliers final: 39 residues processed: 328 average time/residue: 0.2962 time to fit residues: 146.5773 Evaluate side-chains 293 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 248 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 940 ASP Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 656 GLU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 711 ILE Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 338 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 56 optimal weight: 0.0000 chunk 17 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN C 492 ASN C1028 HIS D 170 GLN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.137348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.111593 restraints weight = 26532.510| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.36 r_work: 0.3309 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 17276 Z= 0.181 Angle : 0.677 12.547 23832 Z= 0.367 Chirality : 0.043 0.208 2600 Planarity : 0.006 0.090 2682 Dihedral : 22.460 158.999 3258 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.57 % Favored : 96.32 % Rotamer: Outliers : 5.30 % Allowed : 21.40 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: -0.94 (0.19), residues: 1794 helix: 0.10 (0.22), residues: 536 sheet: -0.15 (0.26), residues: 384 loop : -1.27 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 317 HIS 0.005 0.001 HIS A 959 PHE 0.027 0.002 PHE D 62 TYR 0.026 0.002 TYR D 217 ARG 0.007 0.001 ARG C 882 Details of bonding type rmsd hydrogen bonds : bond 0.04486 ( 699) hydrogen bonds : angle 5.25944 ( 1944) metal coordination : bond 0.02252 ( 8) metal coordination : angle 3.81361 ( 4) covalent geometry : bond 0.00409 (17268) covalent geometry : angle 0.67575 (23828) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 257 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7765 (tm-30) REVERT: A 548 SER cc_start: 0.9380 (t) cc_final: 0.9006 (m) REVERT: A 578 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7440 (t80) REVERT: A 664 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8053 (tm-30) REVERT: A 677 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8641 (tp) REVERT: A 680 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8061 (mtp) REVERT: A 863 MET cc_start: 0.8230 (mmm) cc_final: 0.7995 (mmm) REVERT: A 894 SER cc_start: 0.8720 (t) cc_final: 0.8152 (p) REVERT: A 905 MET cc_start: 0.8282 (tpp) cc_final: 0.7645 (tpp) REVERT: A 940 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8423 (p0) REVERT: A 984 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7856 (tp30) REVERT: B 34 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8053 (ttmt) REVERT: B 58 ARG cc_start: 0.8399 (mmt180) cc_final: 0.8058 (ttp-170) REVERT: B 80 PHE cc_start: 0.8417 (t80) cc_final: 0.7691 (t80) REVERT: B 113 SER cc_start: 0.8177 (m) cc_final: 0.7957 (p) REVERT: B 186 ASP cc_start: 0.7971 (t0) cc_final: 0.7576 (t0) REVERT: B 232 ARG cc_start: 0.8755 (ttp80) cc_final: 0.8397 (ttp80) REVERT: C 504 TYR cc_start: 0.8864 (t80) cc_final: 0.8547 (t80) REVERT: C 548 SER cc_start: 0.9303 (t) cc_final: 0.8896 (m) REVERT: C 587 LYS cc_start: 0.8758 (tptm) cc_final: 0.8350 (tptp) REVERT: C 595 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7797 (tm-30) REVERT: C 598 ARG cc_start: 0.8351 (ttp-170) cc_final: 0.7932 (ptm-80) REVERT: C 680 MET cc_start: 0.8488 (mtm) cc_final: 0.7799 (mtp) REVERT: C 782 TRP cc_start: 0.8787 (OUTLIER) cc_final: 0.8549 (t-100) REVERT: C 905 MET cc_start: 0.8334 (tpp) cc_final: 0.7427 (tpp) REVERT: D 117 ASN cc_start: 0.6302 (m-40) cc_final: 0.6026 (p0) REVERT: D 132 ASP cc_start: 0.6574 (OUTLIER) cc_final: 0.5802 (m-30) REVERT: D 162 MET cc_start: 0.7826 (mtt) cc_final: 0.7551 (mtt) REVERT: D 171 ASN cc_start: 0.8366 (m-40) cc_final: 0.8138 (p0) REVERT: D 269 HIS cc_start: 0.7360 (OUTLIER) cc_final: 0.6842 (t-90) outliers start: 84 outliers final: 52 residues processed: 315 average time/residue: 0.3972 time to fit residues: 191.8709 Evaluate side-chains 305 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 243 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 940 ASP Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 656 GLU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 711 ILE Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 269 HIS Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 338 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 25 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN B 298 HIS C 492 ASN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.138391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112594 restraints weight = 26476.067| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.37 r_work: 0.3328 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17276 Z= 0.167 Angle : 0.671 12.802 23832 Z= 0.361 Chirality : 0.042 0.201 2600 Planarity : 0.005 0.070 2682 Dihedral : 22.410 157.967 3254 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.51 % Favored : 96.38 % Rotamer: Outliers : 5.05 % Allowed : 22.03 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: -0.83 (0.19), residues: 1794 helix: 0.20 (0.22), residues: 536 sheet: -0.02 (0.27), residues: 372 loop : -1.23 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 317 HIS 0.005 0.001 HIS D 313 PHE 0.028 0.002 PHE B 62 TYR 0.026 0.002 TYR C 931 ARG 0.006 0.000 ARG C 882 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 699) hydrogen bonds : angle 5.16987 ( 1944) metal coordination : bond 0.01813 ( 8) metal coordination : angle 3.35049 ( 4) covalent geometry : bond 0.00373 (17268) covalent geometry : angle 0.66989 (23828) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 266 time to evaluate : 3.649 Fit side-chains revert: symmetry clash REVERT: A 528 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7839 (tm-30) REVERT: A 548 SER cc_start: 0.9392 (t) cc_final: 0.9007 (m) REVERT: A 578 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.7332 (t80) REVERT: A 664 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: A 677 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8583 (tp) REVERT: A 680 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8045 (mtp) REVERT: A 765 LEU cc_start: 0.8876 (tp) cc_final: 0.8632 (tp) REVERT: A 795 ARG cc_start: 0.8312 (ttp80) cc_final: 0.7642 (ttp80) REVERT: A 863 MET cc_start: 0.8218 (mmm) cc_final: 0.7801 (tpp) REVERT: A 894 SER cc_start: 0.8704 (t) cc_final: 0.8113 (p) REVERT: A 905 MET cc_start: 0.8356 (tpp) cc_final: 0.7698 (tpp) REVERT: A 940 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8408 (p0) REVERT: A 984 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7816 (tp30) REVERT: B 34 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8013 (ttmt) REVERT: B 58 ARG cc_start: 0.8383 (mmt180) cc_final: 0.8098 (mtp180) REVERT: B 62 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.6961 (t80) REVERT: B 80 PHE cc_start: 0.8369 (t80) cc_final: 0.7683 (t80) REVERT: B 113 SER cc_start: 0.8174 (m) cc_final: 0.7962 (p) REVERT: B 186 ASP cc_start: 0.7924 (t0) cc_final: 0.7519 (t0) REVERT: B 232 ARG cc_start: 0.8805 (ttp80) cc_final: 0.8457 (ttp80) REVERT: B 293 ASP cc_start: 0.8456 (t0) cc_final: 0.8018 (m-30) REVERT: C 504 TYR cc_start: 0.8878 (t80) cc_final: 0.8623 (t80) REVERT: C 548 SER cc_start: 0.9340 (t) cc_final: 0.8940 (m) REVERT: C 587 LYS cc_start: 0.8710 (tptm) cc_final: 0.8332 (tptp) REVERT: C 594 MET cc_start: 0.8138 (mmm) cc_final: 0.7618 (mmm) REVERT: C 595 GLU cc_start: 0.8470 (tm-30) cc_final: 0.7716 (tm-30) REVERT: C 598 ARG cc_start: 0.8299 (ttp-170) cc_final: 0.7890 (ptm-80) REVERT: C 675 ARG cc_start: 0.8262 (mtp85) cc_final: 0.7474 (mmp80) REVERT: C 680 MET cc_start: 0.8489 (mtm) cc_final: 0.7535 (mtm) REVERT: C 765 LEU cc_start: 0.8863 (tp) cc_final: 0.8594 (mp) REVERT: C 905 MET cc_start: 0.8353 (tpp) cc_final: 0.7370 (tpp) REVERT: C 996 MET cc_start: 0.8139 (mpp) cc_final: 0.7922 (mmt) REVERT: D 117 ASN cc_start: 0.6533 (m-40) cc_final: 0.6068 (p0) REVERT: D 132 ASP cc_start: 0.6621 (OUTLIER) cc_final: 0.5847 (m-30) REVERT: D 162 MET cc_start: 0.7824 (mtt) cc_final: 0.7494 (mtm) REVERT: D 171 ASN cc_start: 0.8328 (m-40) cc_final: 0.8124 (p0) REVERT: D 186 ASP cc_start: 0.7931 (t0) cc_final: 0.7585 (t0) REVERT: D 189 PHE cc_start: 0.6431 (m-10) cc_final: 0.6143 (m-10) REVERT: D 269 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.7167 (t-90) outliers start: 80 outliers final: 51 residues processed: 322 average time/residue: 0.3258 time to fit residues: 162.0650 Evaluate side-chains 305 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 244 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 940 ASP Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 656 GLU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 711 ILE Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 269 HIS Chi-restraints excluded: chain D residue 299 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 125 optimal weight: 0.8980 chunk 156 optimal weight: 10.0000 chunk 146 optimal weight: 0.0270 chunk 148 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 0.0060 chunk 153 optimal weight: 6.9990 chunk 150 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 overall best weight: 0.7256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN C 822 ASN D 269 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.141933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.116388 restraints weight = 26067.807| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.36 r_work: 0.3384 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17276 Z= 0.138 Angle : 0.642 12.798 23832 Z= 0.346 Chirality : 0.041 0.198 2600 Planarity : 0.005 0.071 2682 Dihedral : 22.120 155.021 3253 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.62 % Favored : 96.27 % Rotamer: Outliers : 4.42 % Allowed : 23.17 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: -0.63 (0.19), residues: 1794 helix: 0.35 (0.22), residues: 538 sheet: 0.23 (0.27), residues: 360 loop : -1.16 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 317 HIS 0.004 0.001 HIS D 298 PHE 0.018 0.001 PHE D 62 TYR 0.019 0.002 TYR C 931 ARG 0.014 0.001 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 699) hydrogen bonds : angle 4.99575 ( 1944) metal coordination : bond 0.01122 ( 8) metal coordination : angle 3.04953 ( 4) covalent geometry : bond 0.00301 (17268) covalent geometry : angle 0.64050 (23828) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 297 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 528 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7791 (tm-30) REVERT: A 548 SER cc_start: 0.9314 (t) cc_final: 0.8999 (m) REVERT: A 578 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7256 (t80) REVERT: A 664 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: A 677 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8492 (tp) REVERT: A 680 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7913 (mtm) REVERT: A 795 ARG cc_start: 0.8254 (ttp80) cc_final: 0.7588 (ttp80) REVERT: A 863 MET cc_start: 0.8172 (mmm) cc_final: 0.7935 (mmm) REVERT: A 894 SER cc_start: 0.8616 (t) cc_final: 0.8036 (p) REVERT: A 902 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7960 (mt) REVERT: A 905 MET cc_start: 0.8531 (tpp) cc_final: 0.7602 (tpp) REVERT: A 940 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8361 (p0) REVERT: B 34 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7959 (ttmt) REVERT: B 61 SER cc_start: 0.8690 (m) cc_final: 0.8443 (p) REVERT: B 62 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.6965 (t80) REVERT: B 80 PHE cc_start: 0.8315 (t80) cc_final: 0.7675 (t80) REVERT: B 186 ASP cc_start: 0.8020 (t0) cc_final: 0.7591 (t0) REVERT: B 232 ARG cc_start: 0.8738 (ttp80) cc_final: 0.8450 (ttp80) REVERT: B 285 MET cc_start: 0.8561 (mmt) cc_final: 0.8126 (mmm) REVERT: B 293 ASP cc_start: 0.8356 (t0) cc_final: 0.7999 (m-30) REVERT: B 301 SER cc_start: 0.8540 (t) cc_final: 0.8249 (p) REVERT: C 548 SER cc_start: 0.9284 (t) cc_final: 0.8913 (m) REVERT: C 587 LYS cc_start: 0.8682 (tptm) cc_final: 0.8340 (tptp) REVERT: C 594 MET cc_start: 0.8137 (mmm) cc_final: 0.7539 (mmm) REVERT: C 598 ARG cc_start: 0.8310 (ttp-170) cc_final: 0.7860 (ptm-80) REVERT: C 680 MET cc_start: 0.8415 (mtm) cc_final: 0.7882 (mtp) REVERT: C 688 GLU cc_start: 0.8156 (mp0) cc_final: 0.7930 (mp0) REVERT: C 765 LEU cc_start: 0.8792 (tp) cc_final: 0.8591 (mp) REVERT: C 905 MET cc_start: 0.8332 (tpp) cc_final: 0.7593 (tpp) REVERT: D 113 SER cc_start: 0.8769 (p) cc_final: 0.8334 (m) REVERT: D 117 ASN cc_start: 0.6386 (m-40) cc_final: 0.6049 (p0) REVERT: D 162 MET cc_start: 0.7884 (mtt) cc_final: 0.7650 (mtt) REVERT: D 195 HIS cc_start: 0.7500 (m-70) cc_final: 0.7257 (m-70) outliers start: 70 outliers final: 42 residues processed: 344 average time/residue: 0.2679 time to fit residues: 140.6327 Evaluate side-chains 323 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 273 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 940 ASP Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 711 ILE Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 927 GLN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 348 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 55 optimal weight: 0.9980 chunk 153 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN C 492 ASN D 298 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.137737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111918 restraints weight = 26490.720| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.37 r_work: 0.3318 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17276 Z= 0.211 Angle : 0.693 12.609 23832 Z= 0.372 Chirality : 0.043 0.278 2600 Planarity : 0.005 0.072 2682 Dihedral : 22.137 154.769 3243 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.96 % Favored : 95.93 % Rotamer: Outliers : 4.42 % Allowed : 23.99 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: -0.69 (0.19), residues: 1794 helix: 0.32 (0.22), residues: 532 sheet: 0.27 (0.28), residues: 338 loop : -1.19 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 317 HIS 0.009 0.001 HIS C 959 PHE 0.025 0.002 PHE D 62 TYR 0.022 0.002 TYR C 500 ARG 0.011 0.001 ARG C 882 Details of bonding type rmsd hydrogen bonds : bond 0.04333 ( 699) hydrogen bonds : angle 5.06881 ( 1944) metal coordination : bond 0.02572 ( 8) metal coordination : angle 3.51234 ( 4) covalent geometry : bond 0.00478 (17268) covalent geometry : angle 0.69132 (23828) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 266 time to evaluate : 1.553 Fit side-chains revert: symmetry clash REVERT: A 528 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7818 (tm-30) REVERT: A 548 SER cc_start: 0.9317 (t) cc_final: 0.9001 (m) REVERT: A 578 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7365 (t80) REVERT: A 664 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7956 (tm-30) REVERT: A 677 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8580 (tp) REVERT: A 680 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8149 (mtp) REVERT: A 863 MET cc_start: 0.8215 (mmm) cc_final: 0.7813 (tpp) REVERT: A 894 SER cc_start: 0.8832 (t) cc_final: 0.8299 (p) REVERT: A 940 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8394 (p0) REVERT: B 34 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8027 (ttmt) REVERT: B 58 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7951 (ttp-170) REVERT: B 62 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.7103 (t80) REVERT: B 80 PHE cc_start: 0.8361 (t80) cc_final: 0.7703 (t80) REVERT: B 171 ASN cc_start: 0.8138 (p0) cc_final: 0.7702 (p0) REVERT: B 186 ASP cc_start: 0.7910 (t0) cc_final: 0.7525 (t0) REVERT: B 232 ARG cc_start: 0.8802 (ttp80) cc_final: 0.8478 (ttp80) REVERT: B 293 ASP cc_start: 0.8374 (t0) cc_final: 0.8025 (m-30) REVERT: C 504 TYR cc_start: 0.8909 (t80) cc_final: 0.8497 (t80) REVERT: C 548 SER cc_start: 0.9303 (t) cc_final: 0.8927 (m) REVERT: C 598 ARG cc_start: 0.8270 (ttp-170) cc_final: 0.7856 (ptm-80) REVERT: C 647 MET cc_start: 0.8406 (mmt) cc_final: 0.8105 (mmm) REVERT: C 660 ILE cc_start: 0.8814 (mp) cc_final: 0.8434 (tt) REVERT: C 675 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7432 (tpp80) REVERT: C 680 MET cc_start: 0.8531 (mtm) cc_final: 0.8188 (mtp) REVERT: D 117 ASN cc_start: 0.6767 (m-40) cc_final: 0.6199 (p0) REVERT: D 195 HIS cc_start: 0.7548 (m-70) cc_final: 0.7281 (m-70) REVERT: D 202 ASP cc_start: 0.6281 (t70) cc_final: 0.6032 (t0) REVERT: D 269 HIS cc_start: 0.6920 (t70) cc_final: 0.6614 (t-170) outliers start: 70 outliers final: 46 residues processed: 317 average time/residue: 0.2868 time to fit residues: 138.3072 Evaluate side-chains 304 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 250 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 940 ASP Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain C residue 927 GLN Chi-restraints excluded: chain C residue 945 MET Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 338 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 84 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 56 optimal weight: 0.0030 chunk 37 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN C 822 ASN D 100 ASN D 171 ASN D 298 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.136924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111152 restraints weight = 26532.128| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.36 r_work: 0.3301 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17276 Z= 0.222 Angle : 0.710 13.323 23832 Z= 0.381 Chirality : 0.044 0.244 2600 Planarity : 0.007 0.165 2682 Dihedral : 22.168 154.244 3241 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.18 % Favored : 95.71 % Rotamer: Outliers : 3.91 % Allowed : 24.87 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: -0.82 (0.19), residues: 1794 helix: 0.23 (0.22), residues: 544 sheet: 0.24 (0.28), residues: 338 loop : -1.33 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 317 HIS 0.008 0.001 HIS D 269 PHE 0.024 0.002 PHE D 62 TYR 0.024 0.002 TYR D 217 ARG 0.013 0.001 ARG D 235 Details of bonding type rmsd hydrogen bonds : bond 0.04522 ( 699) hydrogen bonds : angle 5.11551 ( 1944) metal coordination : bond 0.02867 ( 8) metal coordination : angle 4.80268 ( 4) covalent geometry : bond 0.00505 (17268) covalent geometry : angle 0.70719 (23828) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 250 time to evaluate : 1.796 Fit side-chains revert: symmetry clash REVERT: A 528 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7841 (tm-30) REVERT: A 548 SER cc_start: 0.9323 (t) cc_final: 0.9008 (m) REVERT: A 578 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.7456 (t80) REVERT: A 664 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7993 (tm-30) REVERT: A 680 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8203 (mtp) REVERT: A 863 MET cc_start: 0.8175 (mmm) cc_final: 0.7789 (tpp) REVERT: A 880 MET cc_start: 0.8806 (tpp) cc_final: 0.8525 (mmm) REVERT: A 894 SER cc_start: 0.8835 (t) cc_final: 0.8294 (p) REVERT: A 905 MET cc_start: 0.8361 (tpp) cc_final: 0.7843 (tpp) REVERT: A 940 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8368 (p0) REVERT: B 34 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8020 (ttmt) REVERT: B 80 PHE cc_start: 0.8373 (t80) cc_final: 0.7709 (t80) REVERT: B 171 ASN cc_start: 0.8254 (p0) cc_final: 0.7815 (p0) REVERT: B 232 ARG cc_start: 0.8792 (ttp80) cc_final: 0.8457 (ttp80) REVERT: B 235 ARG cc_start: 0.6883 (ttt90) cc_final: 0.6524 (ttt90) REVERT: C 504 TYR cc_start: 0.8932 (t80) cc_final: 0.8616 (t80) REVERT: C 548 SER cc_start: 0.9315 (t) cc_final: 0.8937 (m) REVERT: C 647 MET cc_start: 0.8463 (mmt) cc_final: 0.8130 (mmm) REVERT: C 675 ARG cc_start: 0.7861 (mtp85) cc_final: 0.7517 (tpp80) REVERT: C 680 MET cc_start: 0.8503 (mtm) cc_final: 0.7555 (mtm) REVERT: C 880 MET cc_start: 0.8084 (mmm) cc_final: 0.7852 (mmm) REVERT: D 58 ARG cc_start: 0.8522 (ptm-80) cc_final: 0.8173 (mtm110) REVERT: D 195 HIS cc_start: 0.7458 (m-70) cc_final: 0.7161 (m-70) REVERT: D 202 ASP cc_start: 0.6235 (t70) cc_final: 0.5998 (t0) outliers start: 62 outliers final: 47 residues processed: 289 average time/residue: 0.3275 time to fit residues: 144.8022 Evaluate side-chains 296 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 244 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 940 ASP Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 927 GLN Chi-restraints excluded: chain C residue 945 MET Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 338 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 67 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 31 optimal weight: 0.0970 chunk 128 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN D 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.140802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.116057 restraints weight = 26369.111| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.30 r_work: 0.3362 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 17276 Z= 0.156 Angle : 0.691 13.816 23832 Z= 0.370 Chirality : 0.042 0.232 2600 Planarity : 0.006 0.120 2682 Dihedral : 22.019 153.448 3241 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.96 % Favored : 95.93 % Rotamer: Outliers : 3.16 % Allowed : 26.26 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: -0.71 (0.19), residues: 1794 helix: 0.36 (0.22), residues: 544 sheet: 0.29 (0.28), residues: 338 loop : -1.29 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 317 HIS 0.006 0.001 HIS D 269 PHE 0.029 0.002 PHE D 350 TYR 0.024 0.002 TYR C 500 ARG 0.010 0.001 ARG C 882 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 699) hydrogen bonds : angle 5.04579 ( 1944) metal coordination : bond 0.01726 ( 8) metal coordination : angle 4.49032 ( 4) covalent geometry : bond 0.00348 (17268) covalent geometry : angle 0.68841 (23828) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 272 time to evaluate : 1.723 Fit side-chains REVERT: A 528 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7819 (tm-30) REVERT: A 548 SER cc_start: 0.9245 (t) cc_final: 0.8980 (m) REVERT: A 578 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7310 (t80) REVERT: A 664 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: A 677 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8524 (tp) REVERT: A 680 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8002 (mtm) REVERT: A 795 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7583 (ttp80) REVERT: A 863 MET cc_start: 0.8114 (mmm) cc_final: 0.7706 (tpp) REVERT: A 880 MET cc_start: 0.8609 (tpp) cc_final: 0.8409 (mmm) REVERT: A 894 SER cc_start: 0.8860 (t) cc_final: 0.8323 (p) REVERT: A 902 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7914 (mt) REVERT: A 905 MET cc_start: 0.8343 (tpp) cc_final: 0.7688 (tpp) REVERT: A 940 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8364 (p0) REVERT: B 34 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8002 (ttmt) REVERT: B 62 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7171 (t80) REVERT: B 80 PHE cc_start: 0.8356 (t80) cc_final: 0.7709 (t80) REVERT: B 171 ASN cc_start: 0.8264 (p0) cc_final: 0.7999 (p0) REVERT: B 186 ASP cc_start: 0.7960 (t0) cc_final: 0.7607 (t0) REVERT: B 232 ARG cc_start: 0.8717 (ttp80) cc_final: 0.8428 (ttp80) REVERT: B 235 ARG cc_start: 0.6793 (ttt90) cc_final: 0.6065 (ttt90) REVERT: C 504 TYR cc_start: 0.8862 (t80) cc_final: 0.8497 (t80) REVERT: C 548 SER cc_start: 0.9287 (t) cc_final: 0.8922 (m) REVERT: C 647 MET cc_start: 0.8433 (mmt) cc_final: 0.8053 (mmm) REVERT: C 680 MET cc_start: 0.8424 (mtm) cc_final: 0.7509 (mtm) REVERT: D 58 ARG cc_start: 0.8494 (ptm-80) cc_final: 0.8122 (mtm110) REVERT: D 113 SER cc_start: 0.8718 (p) cc_final: 0.8442 (p) REVERT: D 195 HIS cc_start: 0.7297 (m-70) cc_final: 0.7059 (m-70) REVERT: D 202 ASP cc_start: 0.6160 (t70) cc_final: 0.5905 (t0) outliers start: 50 outliers final: 32 residues processed: 303 average time/residue: 0.2761 time to fit residues: 127.4218 Evaluate side-chains 289 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 249 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 940 ASP Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 927 GLN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 338 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 1 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 HIS C 492 ASN D 171 ASN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.138810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.113788 restraints weight = 26797.882| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.33 r_work: 0.3342 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17276 Z= 0.165 Angle : 0.701 13.637 23832 Z= 0.372 Chirality : 0.042 0.224 2600 Planarity : 0.006 0.109 2682 Dihedral : 21.986 153.901 3241 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.07 % Favored : 95.82 % Rotamer: Outliers : 3.09 % Allowed : 26.58 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: -0.66 (0.19), residues: 1794 helix: 0.41 (0.22), residues: 544 sheet: 0.34 (0.28), residues: 338 loop : -1.27 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 317 HIS 0.015 0.001 HIS D 269 PHE 0.031 0.002 PHE D 350 TYR 0.022 0.002 TYR C 500 ARG 0.010 0.001 ARG A 992 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 699) hydrogen bonds : angle 5.01959 ( 1944) metal coordination : bond 0.01963 ( 8) metal coordination : angle 4.24773 ( 4) covalent geometry : bond 0.00370 (17268) covalent geometry : angle 0.69898 (23828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7513.52 seconds wall clock time: 134 minutes 48.83 seconds (8088.83 seconds total)