Starting phenix.real_space_refine on Mon Sep 14 10:52:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/3jbx_6487/09_2026/3jbx_6487.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jbx_6487/09_2026/3jbx_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 { model { file = "/net/cci-nas-00/data/ceres_data/3jbx_6487/09_2026/3jbx_6487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jbx_6487/09_2026/3jbx_6487.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/3jbx_6487/09_2026/3jbx_6487.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/3jbx_6487/09_2026/3jbx_6487.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jbx_6487/09_2026/3jbx_6487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jbx_6487/09_2026/3jbx_6487.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 3.81, per 1000 atoms: 0.23 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: 1.60 Conformation dependent library (CDL) restraints added in 648.1 milliseconds 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: 2.17 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: 4.41 Time building geometry restraints manager: 2.10 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=" C3' DG H 5 " pdb=" C2' DG H 5 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.49e+01 bond pdb=" C3' DT L 5 " pdb=" C2' DT L 5 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.48e+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 ... (remaining 17263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 22774 2.71 - 5.43: 937 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: 2322 0.083 - 0.165: 259 0.165 - 0.248: 15 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: 0.02 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 22.030 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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= 0.479 Angle : 1.302 29.503 23832 Z= 0.892 Chirality : 0.052 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.004 0.001 ARG C 490 TYR 0.029 0.002 TYR C 729 PHE 0.032 0.002 PHE C1004 TRP 0.017 0.002 TRP C 978 HIS 0.006 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.45 (17268) covalent geometry : angle 1.26640 / 0.89 (23828) hydrogen bonds : bond 0.14751 / 9.82 ( 699) hydrogen bonds : angle 10.12595 / 7.05 ( 1944) metal coordination : bond 0.33337 / 24.95 ( 8) metal coordination : angle 23.37599 / 12.63 ( 4) *********************** 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 : 0.611 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: 0.8706 (m) REVERT: A 690 LEU cc_start: 0.8448 (tp) cc_final: 0.7968 (tp) REVERT: A 730 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7311 (p0) REVERT: A 732 LYS cc_start: 0.8896 (tttt) cc_final: 0.8456 (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: 0.8003 (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: 0.7503 (mp0) REVERT: A 863 MET cc_start: 0.8187 (mmp) cc_final: 0.7253 (tpp) REVERT: A 902 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8160 (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: 0.6775 (m) REVERT: B 33 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7968 (pt0) REVERT: B 80 PHE cc_start: 0.8531 (t80) cc_final: 0.8184 (t80) REVERT: B 192 CYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7691 (p) REVERT: B 200 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8039 (mp) REVERT: B 212 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6596 (ttp-170) REVERT: B 281 THR cc_start: 0.8405 (m) cc_final: 0.8168 (p) REVERT: B 285 MET cc_start: 0.8577 (mmm) cc_final: 0.8255 (mmm) REVERT: B 338 THR cc_start: 0.8425 (m) cc_final: 0.8151 (p) REVERT: C 487 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8203 (tp) REVERT: C 548 SER cc_start: 0.9121 (t) cc_final: 0.8739 (m) REVERT: C 578 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.6812 (t80) REVERT: C 622 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7417 (ptp) REVERT: C 677 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8576 (tp) REVERT: C 680 MET cc_start: 0.8082 (mtm) cc_final: 0.7731 (mtp) REVERT: C 860 ARG cc_start: 0.8570 (tpp80) cc_final: 0.8356 (ttm-80) REVERT: C 902 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8285 (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: 0.8006 (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: 0.7705 (p0) REVERT: D 186 ASP cc_start: 0.7895 (t0) cc_final: 0.7663 (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: 0.8754 (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: 0.1433 time to fit residues: 125.3855 Evaluate side-chains 320 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 264 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.4980 chunk 149 optimal weight: 8.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 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 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 ASN C 997 ASN C1000 GLN D 173 ASN D 269 HIS ** D 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.136379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.111471 restraints weight = 26387.152| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.26 r_work: 0.3320 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17276 Z= 0.189 Angle : 0.856 13.072 23832 Z= 0.464 Chirality : 0.049 0.310 2600 Planarity : 0.006 0.062 2682 Dihedral : 22.732 153.870 3332 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.73 % Favored : 97.16 % Rotamer: Outliers : 6.12 % Allowed : 17.74 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.17), residues: 1794 helix: -1.15 (0.20), residues: 534 sheet: -0.19 (0.26), residues: 316 loop : -1.77 (0.16), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 675 TYR 0.020 0.002 TYR B 271 PHE 0.023 0.002 PHE C1004 TRP 0.013 0.001 TRP C 851 HIS 0.008 0.002 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 (17268) covalent geometry : angle 0.85408 / 0.46 (23828) hydrogen bonds : bond 0.06158 / 4.19 ( 699) hydrogen bonds : angle 6.46627 / 4.58 ( 1944) metal coordination : bond 0.01574 / 1.09 ( 8) metal coordination : angle 4.91186 / 2.54 ( 4) *********************** 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 416 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 319 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 GLU cc_start: 0.7798 (pt0) cc_final: 0.7455 (pt0) REVERT: A 548 SER cc_start: 0.8985 (t) cc_final: 0.8696 (m) REVERT: A 680 MET cc_start: 0.8533 (mtp) cc_final: 0.8200 (mtm) REVERT: A 690 LEU cc_start: 0.8211 (tp) cc_final: 0.7915 (tt) REVERT: A 807 MET cc_start: 0.8167 (ptm) cc_final: 0.7936 (ptm) REVERT: A 894 SER cc_start: 0.8532 (t) cc_final: 0.8140 (p) REVERT: A 902 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7944 (mt) REVERT: A 981 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7670 (mm-30) REVERT: B 33 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7823 (pt0) REVERT: B 80 PHE cc_start: 0.8401 (t80) cc_final: 0.7963 (t80) REVERT: B 132 ASP cc_start: 0.7926 (t0) cc_final: 0.7530 (p0) REVERT: B 177 ASP cc_start: 0.8439 (m-30) cc_final: 0.8238 (m-30) REVERT: B 186 ASP cc_start: 0.8004 (t0) cc_final: 0.7700 (t0) REVERT: B 192 CYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7234 (p) REVERT: B 200 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7967 (mt) REVERT: B 212 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7075 (ttp80) REVERT: B 232 ARG cc_start: 0.8903 (tmm-80) cc_final: 0.8497 (ttp80) REVERT: B 252 LEU cc_start: 0.8294 (mm) cc_final: 0.7837 (mt) REVERT: B 285 MET cc_start: 0.8340 (mmm) cc_final: 0.8085 (mmm) REVERT: B 338 THR cc_start: 0.8231 (m) cc_final: 0.7870 (p) REVERT: C 548 SER cc_start: 0.8954 (t) cc_final: 0.8584 (m) REVERT: C 578 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.7266 (t80) REVERT: C 587 LYS cc_start: 0.8644 (tptm) cc_final: 0.8322 (tptp) REVERT: C 680 MET cc_start: 0.8309 (mtm) cc_final: 0.7670 (mtp) REVERT: C 782 TRP cc_start: 0.8855 (OUTLIER) cc_final: 0.8397 (t-100) REVERT: C 1007 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: D 80 PHE cc_start: 0.8161 (t80) cc_final: 0.7949 (t80) REVERT: D 117 ASN cc_start: 0.6225 (m-40) cc_final: 0.5992 (p0) REVERT: D 171 ASN cc_start: 0.8334 (m-40) cc_final: 0.7898 (p0) REVERT: D 186 ASP cc_start: 0.8004 (t0) cc_final: 0.7669 (t0) REVERT: D 212 ARG cc_start: 0.8037 (ptm160) cc_final: 0.7790 (ttp-170) REVERT: D 250 THR cc_start: 0.8822 (t) cc_final: 0.8595 (p) outliers start: 97 outliers final: 43 residues processed: 391 average time/residue: 0.1414 time to fit residues: 82.0355 Evaluate side-chains 295 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 244 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 622 MET 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 687 HIS Chi-restraints excluded: chain A residue 751 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 859 LEU 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 141 THR Chi-restraints excluded: chain B residue 147 SER 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 233 LEU 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 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 885 VAL 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 175 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 205 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 102 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 629 HIS B 65 ASN C 492 ASN ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS D 269 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.135778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109816 restraints weight = 27062.383| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.40 r_work: 0.3290 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17276 Z= 0.189 Angle : 0.774 13.051 23832 Z= 0.419 Chirality : 0.047 0.314 2600 Planarity : 0.006 0.068 2682 Dihedral : 22.715 151.279 3286 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.85 % Favored : 96.04 % Rotamer: Outliers : 5.18 % Allowed : 19.19 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.18), residues: 1794 helix: -0.40 (0.21), residues: 532 sheet: -0.30 (0.26), residues: 354 loop : -1.53 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 49 TYR 0.026 0.002 TYR D 217 PHE 0.023 0.002 PHE D 350 TRP 0.016 0.001 TRP D 317 HIS 0.009 0.001 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (17268) covalent geometry : angle 0.77116 / 0.42 (23828) hydrogen bonds : bond 0.05327 / 3.56 ( 699) hydrogen bonds : angle 5.94172 / 4.18 ( 1944) metal coordination : bond 0.01548 / 0.98 ( 8) metal coordination : angle 5.06586 / 2.60 ( 4) *********************** 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 364 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 282 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: A 526 GLU cc_start: 0.7945 (pt0) cc_final: 0.7559 (pt0) REVERT: A 548 SER cc_start: 0.9132 (t) cc_final: 0.8829 (m) REVERT: A 578 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7401 (t80) REVERT: A 680 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8251 (mtm) REVERT: A 894 SER cc_start: 0.8413 (t) cc_final: 0.7948 (p) REVERT: A 902 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7839 (mt) REVERT: B 33 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: B 80 PHE cc_start: 0.8373 (t80) cc_final: 0.7899 (t80) REVERT: B 119 LYS cc_start: 0.8616 (mttm) cc_final: 0.8397 (mttm) REVERT: B 171 ASN cc_start: 0.7703 (p0) cc_final: 0.7470 (p0) REVERT: B 177 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8197 (m-30) REVERT: B 186 ASP cc_start: 0.7921 (t0) cc_final: 0.7530 (t0) REVERT: B 234 ILE cc_start: 0.9125 (mm) cc_final: 0.8909 (mp) REVERT: B 235 ARG cc_start: 0.6690 (ttt90) cc_final: 0.6337 (ttt90) REVERT: B 252 LEU cc_start: 0.8351 (mm) cc_final: 0.7775 (mt) REVERT: B 285 MET cc_start: 0.8414 (mmm) cc_final: 0.8127 (mmm) REVERT: C 548 SER cc_start: 0.9099 (t) cc_final: 0.8732 (m) REVERT: C 578 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.7586 (t80) REVERT: C 587 LYS cc_start: 0.8719 (tptm) cc_final: 0.8341 (tptp) REVERT: C 594 MET cc_start: 0.8094 (mmm) cc_final: 0.7850 (mpp) REVERT: C 675 ARG cc_start: 0.8446 (mtp85) cc_final: 0.7744 (mmp80) REVERT: C 680 MET cc_start: 0.8462 (mtm) cc_final: 0.7898 (mtp) REVERT: C 748 ILE cc_start: 0.8289 (pt) cc_final: 0.8072 (pt) REVERT: C 762 ASN cc_start: 0.7418 (t0) cc_final: 0.7178 (p0) REVERT: C 782 TRP cc_start: 0.8818 (OUTLIER) cc_final: 0.8431 (t-100) REVERT: C 1007 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: D 117 ASN cc_start: 0.6105 (m-40) cc_final: 0.5780 (p0) REVERT: D 132 ASP cc_start: 0.6408 (OUTLIER) cc_final: 0.5719 (m-30) REVERT: D 171 ASN cc_start: 0.8340 (m-40) cc_final: 0.7781 (p0) REVERT: D 186 ASP cc_start: 0.8084 (t0) cc_final: 0.7686 (t0) REVERT: D 217 TYR cc_start: 0.7505 (m-10) cc_final: 0.7092 (m-80) REVERT: D 250 THR cc_start: 0.8811 (t) cc_final: 0.8573 (p) REVERT: D 251 ILE cc_start: 0.9047 (mm) cc_final: 0.8708 (tt) outliers start: 82 outliers final: 44 residues processed: 340 average time/residue: 0.1366 time to fit residues: 70.1105 Evaluate side-chains 287 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 234 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 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 622 MET 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 680 MET Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 751 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 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 927 GLN Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 1000 GLN 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 43 THR Chi-restraints excluded: chain B residue 62 PHE 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 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 622 MET Chi-restraints excluded: chain C residue 656 GLU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 687 HIS Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 782 TRP 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 1004 PHE Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain D residue 11 CYS 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 175 VAL Chi-restraints excluded: chain D residue 205 SER 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 130 optimal weight: 4.9990 chunk 175 optimal weight: 0.0030 chunk 87 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 105 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 482 HIS B 65 ASN B 170 GLN B 204 GLN ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.138123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.112662 restraints weight = 26470.642| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.37 r_work: 0.3333 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17276 Z= 0.151 Angle : 0.725 13.595 23832 Z= 0.390 Chirality : 0.046 0.335 2600 Planarity : 0.005 0.069 2682 Dihedral : 22.573 152.590 3274 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.60 % Rotamer: Outliers : 5.05 % Allowed : 20.20 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.18), residues: 1794 helix: -0.10 (0.22), residues: 534 sheet: -0.19 (0.27), residues: 352 loop : -1.43 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 882 TYR 0.020 0.002 TYR C 504 PHE 0.019 0.001 PHE B 350 TRP 0.014 0.001 TRP D 317 HIS 0.007 0.001 HIS A 959 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (17268) covalent geometry : angle 0.72244 / 0.39 (23828) hydrogen bonds : bond 0.04895 / 3.26 ( 699) hydrogen bonds : angle 5.62385 / 3.95 ( 1944) metal coordination : bond 0.02928 / 1.87 ( 8) metal coordination : angle 4.56490 / 2.56 ( 4) *********************** 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 353 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 273 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: A 548 SER cc_start: 0.9153 (t) cc_final: 0.8865 (m) REVERT: A 578 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.7531 (t80) REVERT: A 680 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8036 (mtm) REVERT: A 859 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8202 (mp) REVERT: A 894 SER cc_start: 0.8723 (t) cc_final: 0.8047 (p) REVERT: A 905 MET cc_start: 0.8374 (tpp) cc_final: 0.7848 (tpp) REVERT: B 34 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8171 (ttmt) REVERT: B 80 PHE cc_start: 0.8371 (t80) cc_final: 0.7670 (t80) REVERT: B 132 ASP cc_start: 0.7955 (t70) cc_final: 0.7101 (m-30) REVERT: B 177 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8238 (m-30) REVERT: B 232 ARG cc_start: 0.8790 (tmm-80) cc_final: 0.8432 (ttp80) REVERT: B 252 LEU cc_start: 0.8339 (mm) cc_final: 0.7855 (mt) REVERT: C 528 GLU cc_start: 0.8352 (tt0) cc_final: 0.8073 (tm-30) REVERT: C 548 SER cc_start: 0.9087 (t) cc_final: 0.8713 (m) REVERT: C 578 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7718 (t80) REVERT: C 587 LYS cc_start: 0.8629 (tptm) cc_final: 0.8270 (tptp) REVERT: C 680 MET cc_start: 0.8480 (mtm) cc_final: 0.8035 (mtp) REVERT: C 748 ILE cc_start: 0.8172 (pt) cc_final: 0.7939 (pt) REVERT: C 762 ASN cc_start: 0.7322 (t0) cc_final: 0.7070 (p0) REVERT: C 782 TRP cc_start: 0.8773 (OUTLIER) cc_final: 0.8504 (t-100) REVERT: C 981 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7913 (mm-30) REVERT: C 996 MET cc_start: 0.8057 (mpp) cc_final: 0.7777 (mmt) REVERT: D 117 ASN cc_start: 0.6124 (m-40) cc_final: 0.5715 (p0) REVERT: D 120 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7787 (p) REVERT: D 132 ASP cc_start: 0.6353 (OUTLIER) cc_final: 0.5539 (m-30) REVERT: D 171 ASN cc_start: 0.8330 (m-40) cc_final: 0.7935 (p0) REVERT: D 202 ASP cc_start: 0.6055 (OUTLIER) cc_final: 0.5707 (t0) REVERT: D 235 ARG cc_start: 0.6470 (ttt90) cc_final: 0.6242 (ttt90) REVERT: D 269 HIS cc_start: 0.7764 (OUTLIER) cc_final: 0.7460 (t-90) outliers start: 80 outliers final: 44 residues processed: 327 average time/residue: 0.1300 time to fit residues: 65.3728 Evaluate side-chains 290 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 235 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 751 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 859 LEU Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 927 GLN 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 67 SER Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 177 ASP 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 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 622 MET Chi-restraints excluded: chain C residue 656 GLU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 687 HIS Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 924 CYS Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain D residue 11 CYS 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 175 VAL Chi-restraints excluded: chain D residue 202 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 7 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 168 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 181 optimal weight: 30.0000 chunk 72 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 766 HIS A 822 ASN A1022 GLN B 65 ASN B 170 GLN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.134177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108260 restraints weight = 26786.524| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.37 r_work: 0.3261 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 17276 Z= 0.256 Angle : 0.773 12.819 23832 Z= 0.414 Chirality : 0.048 0.369 2600 Planarity : 0.006 0.071 2682 Dihedral : 22.651 153.550 3261 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.85 % Favored : 96.04 % Rotamer: Outliers : 5.18 % Allowed : 21.72 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.18), residues: 1794 helix: -0.07 (0.22), residues: 536 sheet: -0.22 (0.26), residues: 362 loop : -1.44 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 897 TYR 0.022 0.002 TYR A 875 PHE 0.033 0.002 PHE B 62 TRP 0.016 0.002 TRP B 317 HIS 0.011 0.002 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.26 (17268) covalent geometry : angle 0.77068 / 0.41 (23828) hydrogen bonds : bond 0.05223 / 3.52 ( 699) hydrogen bonds : angle 5.56341 / 3.90 ( 1944) metal coordination : bond 0.03591 / 2.25 ( 8) metal coordination : angle 4.51351 / 2.58 ( 4) *********************** 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 331 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 249 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 SER cc_start: 0.9246 (t) cc_final: 0.8897 (m) REVERT: A 578 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.7633 (t80) REVERT: A 680 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8238 (mtm) REVERT: A 905 MET cc_start: 0.8422 (tpp) cc_final: 0.7838 (tpp) REVERT: A 940 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8351 (p0) REVERT: B 80 PHE cc_start: 0.8448 (t80) cc_final: 0.7769 (t80) REVERT: B 108 MET cc_start: 0.7572 (ttm) cc_final: 0.7327 (ttp) REVERT: B 113 SER cc_start: 0.8737 (p) cc_final: 0.8407 (m) REVERT: B 232 ARG cc_start: 0.8749 (tmm-80) cc_final: 0.8402 (ttp80) REVERT: B 300 GLU cc_start: 0.7589 (tp30) cc_final: 0.7349 (tm-30) REVERT: C 504 TYR cc_start: 0.8911 (t80) cc_final: 0.8679 (t80) REVERT: C 528 GLU cc_start: 0.8310 (tt0) cc_final: 0.8073 (tm-30) REVERT: C 548 SER cc_start: 0.9201 (t) cc_final: 0.8785 (m) REVERT: C 587 LYS cc_start: 0.8767 (tptm) cc_final: 0.8416 (tptp) REVERT: C 595 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7897 (tm-30) REVERT: C 675 ARG cc_start: 0.8464 (mtp85) cc_final: 0.7619 (mmp80) REVERT: C 748 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.8000 (pt) REVERT: D 117 ASN cc_start: 0.6588 (m-40) cc_final: 0.6002 (p0) REVERT: D 132 ASP cc_start: 0.6633 (OUTLIER) cc_final: 0.5706 (m-30) REVERT: D 171 ASN cc_start: 0.8366 (m-40) cc_final: 0.8151 (p0) REVERT: D 202 ASP cc_start: 0.6332 (t70) cc_final: 0.6050 (t0) outliers start: 82 outliers final: 51 residues processed: 302 average time/residue: 0.1281 time to fit residues: 59.7888 Evaluate side-chains 294 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 622 MET Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 751 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 871 MET Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 940 ASP 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 233 LEU 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 B residue 308 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 656 GLU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 769 THR 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 879 LEU Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 924 CYS Chi-restraints excluded: chain C residue 1007 GLU 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 165 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 297 VAL 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 151 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 187 optimal weight: 40.0000 chunk 149 optimal weight: 0.8980 chunk 163 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 492 ASN D 100 ASN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.137301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.111554 restraints weight = 26428.989| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.37 r_work: 0.3312 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3998 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= 0.153 Angle : 0.706 13.251 23832 Z= 0.380 Chirality : 0.045 0.382 2600 Planarity : 0.005 0.091 2682 Dihedral : 22.547 155.690 3258 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.57 % Favored : 96.32 % Rotamer: Outliers : 4.86 % Allowed : 22.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.19), residues: 1794 helix: 0.10 (0.22), residues: 536 sheet: -0.18 (0.26), residues: 376 loop : -1.35 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 212 TYR 0.020 0.002 TYR A 908 PHE 0.033 0.001 PHE B 62 TRP 0.014 0.001 TRP D 317 HIS 0.008 0.001 HIS A 959 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (17268) covalent geometry : angle 0.70439 / 0.38 (23828) hydrogen bonds : bond 0.04752 / 3.17 ( 699) hydrogen bonds : angle 5.43129 / 3.81 ( 1944) metal coordination : bond 0.01584 / 1.01 ( 8) metal coordination : angle 3.40655 / 1.87 ( 4) *********************** 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 335 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 258 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 SER cc_start: 0.9360 (t) cc_final: 0.8986 (m) REVERT: A 578 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7496 (t80) REVERT: A 675 ARG cc_start: 0.8403 (mtp85) cc_final: 0.7713 (mtp85) REVERT: A 680 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8087 (mtm) REVERT: A 889 CYS cc_start: 0.7240 (m) cc_final: 0.6971 (p) REVERT: A 902 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7954 (mt) REVERT: A 905 MET cc_start: 0.8575 (tpp) cc_final: 0.7831 (tpp) REVERT: A 940 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8382 (p0) REVERT: A 945 MET cc_start: 0.7868 (mmm) cc_final: 0.7596 (mmm) REVERT: A 984 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7556 (tp30) REVERT: B 34 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7953 (ttmt) REVERT: B 58 ARG cc_start: 0.8366 (mmt-90) cc_final: 0.7739 (mtp180) REVERT: B 62 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.7307 (t80) REVERT: B 80 PHE cc_start: 0.8407 (t80) cc_final: 0.7706 (t80) REVERT: B 108 MET cc_start: 0.7426 (ttm) cc_final: 0.7186 (ttp) REVERT: B 113 SER cc_start: 0.8658 (p) cc_final: 0.8367 (p) REVERT: B 177 ASP cc_start: 0.8509 (m-30) cc_final: 0.8226 (m-30) REVERT: B 186 ASP cc_start: 0.7995 (t0) cc_final: 0.7552 (t0) REVERT: B 189 PHE cc_start: 0.6180 (m-10) cc_final: 0.5877 (m-10) REVERT: B 232 ARG cc_start: 0.8785 (tmm-80) cc_final: 0.8257 (ttp80) REVERT: B 300 GLU cc_start: 0.7557 (tp30) cc_final: 0.7305 (tm-30) REVERT: C 528 GLU cc_start: 0.8337 (tt0) cc_final: 0.8050 (tm-30) REVERT: C 548 SER cc_start: 0.9249 (t) cc_final: 0.8819 (m) REVERT: C 587 LYS cc_start: 0.8727 (tptm) cc_final: 0.8357 (tptp) REVERT: C 594 MET cc_start: 0.8075 (mmm) cc_final: 0.7656 (mmm) REVERT: C 595 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7926 (tm-30) REVERT: C 675 ARG cc_start: 0.8326 (mtp85) cc_final: 0.7619 (mmp80) REVERT: C 680 MET cc_start: 0.8562 (mtm) cc_final: 0.8089 (mtp) REVERT: C 748 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7905 (pt) REVERT: D 117 ASN cc_start: 0.6389 (m-40) cc_final: 0.5864 (p0) REVERT: D 171 ASN cc_start: 0.8335 (m-40) cc_final: 0.8089 (p0) REVERT: D 202 ASP cc_start: 0.6271 (t70) cc_final: 0.5969 (t0) REVERT: D 217 TYR cc_start: 0.7402 (m-80) cc_final: 0.7169 (m-10) REVERT: D 269 HIS cc_start: 0.7600 (OUTLIER) cc_final: 0.6849 (t-90) REVERT: D 346 TYR cc_start: 0.8338 (m-10) cc_final: 0.8110 (m-10) outliers start: 77 outliers final: 54 residues processed: 308 average time/residue: 0.1294 time to fit residues: 61.3089 Evaluate side-chains 311 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 248 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 598 ARG Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 687 HIS Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 751 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 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 940 ASP Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 62 PHE 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 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 492 ASN Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 580 VAL 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 687 HIS Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 748 ILE 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 879 LEU Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 924 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 141 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 182 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 168 optimal weight: 0.3980 chunk 68 optimal weight: 0.0670 chunk 62 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 139 optimal weight: 0.0040 chunk 128 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.4932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.139533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.113858 restraints weight = 26224.763| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.38 r_work: 0.3346 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17276 Z= 0.141 Angle : 0.686 13.586 23832 Z= 0.372 Chirality : 0.045 0.376 2600 Planarity : 0.005 0.081 2682 Dihedral : 22.399 157.151 3258 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.79 % Favored : 96.10 % Rotamer: Outliers : 4.17 % Allowed : 22.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.19), residues: 1794 helix: 0.23 (0.22), residues: 534 sheet: -0.01 (0.27), residues: 374 loop : -1.29 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 148 TYR 0.022 0.002 TYR A 908 PHE 0.017 0.001 PHE B 62 TRP 0.011 0.001 TRP D 317 HIS 0.006 0.001 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (17268) covalent geometry : angle 0.68482 / 0.37 (23828) hydrogen bonds : bond 0.04487 / 2.95 ( 699) hydrogen bonds : angle 5.30150 / 3.72 ( 1944) metal coordination : bond 0.01285 / 0.82 ( 8) metal coordination : angle 2.85852 / 1.61 ( 4) *********************** 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 323 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 257 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 SER cc_start: 0.9360 (t) cc_final: 0.8996 (m) REVERT: A 578 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7433 (t80) REVERT: A 675 ARG cc_start: 0.8397 (mtp85) cc_final: 0.7620 (mtp85) REVERT: A 677 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8570 (tp) REVERT: A 680 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7948 (mtm) REVERT: A 694 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8173 (mp) REVERT: A 774 GLU cc_start: 0.8135 (pp20) cc_final: 0.7867 (pp20) REVERT: A 795 ARG cc_start: 0.8247 (ttp80) cc_final: 0.7503 (ttp80) REVERT: A 863 MET cc_start: 0.8064 (mmm) cc_final: 0.7717 (mmm) REVERT: A 902 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7850 (mt) REVERT: A 905 MET cc_start: 0.8590 (tpp) cc_final: 0.7879 (tpp) REVERT: A 940 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8411 (p0) REVERT: A 945 MET cc_start: 0.7828 (mmm) cc_final: 0.7582 (mmm) REVERT: A 984 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7495 (tp30) REVERT: B 34 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7964 (ttmt) REVERT: B 61 SER cc_start: 0.8746 (m) cc_final: 0.8512 (p) REVERT: B 62 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7208 (t80) REVERT: B 80 PHE cc_start: 0.8390 (t80) cc_final: 0.7682 (t80) REVERT: B 108 MET cc_start: 0.7318 (ttm) cc_final: 0.7112 (ttp) REVERT: B 113 SER cc_start: 0.8634 (p) cc_final: 0.8354 (p) REVERT: B 119 LYS cc_start: 0.8245 (mttm) cc_final: 0.8013 (mttm) REVERT: B 232 ARG cc_start: 0.8805 (tmm-80) cc_final: 0.8315 (ttp80) REVERT: B 285 MET cc_start: 0.8557 (mmt) cc_final: 0.8104 (mmm) REVERT: B 300 GLU cc_start: 0.7754 (tp30) cc_final: 0.7490 (tm-30) REVERT: C 528 GLU cc_start: 0.8369 (tt0) cc_final: 0.8072 (tm-30) REVERT: C 548 SER cc_start: 0.9315 (t) cc_final: 0.8913 (m) REVERT: C 587 LYS cc_start: 0.8646 (tptm) cc_final: 0.8297 (tptp) REVERT: C 594 MET cc_start: 0.7905 (mmm) cc_final: 0.7543 (mmm) REVERT: C 595 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7732 (tm-30) REVERT: C 598 ARG cc_start: 0.8323 (ttp-170) cc_final: 0.7933 (ptm-80) REVERT: C 680 MET cc_start: 0.8525 (mtm) cc_final: 0.8022 (mtt) REVERT: C 765 LEU cc_start: 0.8877 (tp) cc_final: 0.8593 (mp) REVERT: C 880 MET cc_start: 0.8057 (tpp) cc_final: 0.7693 (mmt) REVERT: C 996 MET cc_start: 0.8141 (mpp) cc_final: 0.7844 (mmt) REVERT: D 117 ASN cc_start: 0.6319 (m-40) cc_final: 0.5786 (p0) REVERT: D 171 ASN cc_start: 0.8306 (m-40) cc_final: 0.8076 (p0) REVERT: D 186 ASP cc_start: 0.7899 (t0) cc_final: 0.7507 (t0) REVERT: D 202 ASP cc_start: 0.6198 (t70) cc_final: 0.5945 (t0) REVERT: D 269 HIS cc_start: 0.7396 (OUTLIER) cc_final: 0.7087 (t70) REVERT: D 346 TYR cc_start: 0.8296 (m-10) cc_final: 0.8079 (m-10) outliers start: 66 outliers final: 39 residues processed: 299 average time/residue: 0.1252 time to fit residues: 57.0132 Evaluate side-chains 297 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 248 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 586 LEU Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 694 LEU 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 902 LEU Chi-restraints excluded: chain A residue 940 ASP Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 62 PHE 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 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 542 LEU Chi-restraints excluded: chain C residue 543 LYS Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 656 GLU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 716 LEU 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 879 LEU Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 924 CYS Chi-restraints excluded: chain C residue 1004 PHE 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 241 LEU Chi-restraints excluded: chain D residue 269 HIS Chi-restraints excluded: chain D residue 338 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 62 optimal weight: 0.5980 chunk 83 optimal weight: 0.0670 chunk 181 optimal weight: 30.0000 chunk 101 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 146 optimal weight: 0.0170 chunk 169 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 298 HIS ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.140493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.115103 restraints weight = 26451.194| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.37 r_work: 0.3361 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17276 Z= 0.141 Angle : 0.677 13.928 23832 Z= 0.367 Chirality : 0.044 0.365 2600 Planarity : 0.005 0.070 2682 Dihedral : 22.235 157.244 3249 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.96 % Favored : 95.93 % Rotamer: Outliers : 4.10 % Allowed : 22.85 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.19), residues: 1794 helix: 0.32 (0.22), residues: 532 sheet: 0.04 (0.27), residues: 374 loop : -1.22 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 148 TYR 0.032 0.002 TYR A 908 PHE 0.028 0.001 PHE D 350 TRP 0.011 0.001 TRP B 317 HIS 0.005 0.001 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (17268) covalent geometry : angle 0.67595 / 0.37 (23828) hydrogen bonds : bond 0.04419 / 2.90 ( 699) hydrogen bonds : angle 5.20924 / 3.65 ( 1944) metal coordination : bond 0.01387 / 0.90 ( 8) metal coordination : angle 2.38396 / 1.41 ( 4) *********************** 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 330 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 265 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 SER cc_start: 0.9346 (t) cc_final: 0.8966 (m) REVERT: A 578 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7304 (t80) REVERT: A 675 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7521 (mtp85) REVERT: A 677 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8579 (tp) REVERT: A 680 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7969 (mtm) REVERT: A 774 GLU cc_start: 0.8137 (pp20) cc_final: 0.7863 (pp20) REVERT: A 795 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7495 (ttp80) REVERT: A 863 MET cc_start: 0.8073 (mmm) cc_final: 0.7531 (tpp) REVERT: A 902 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7834 (mt) REVERT: A 905 MET cc_start: 0.8546 (tpp) cc_final: 0.7783 (tpp) REVERT: A 940 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8524 (p0) REVERT: A 945 MET cc_start: 0.7833 (mmm) cc_final: 0.7590 (mmm) REVERT: A 984 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7540 (tp30) REVERT: B 34 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7964 (ttmt) REVERT: B 61 SER cc_start: 0.8681 (m) cc_final: 0.8457 (p) REVERT: B 62 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7143 (t80) REVERT: B 80 PHE cc_start: 0.8385 (t80) cc_final: 0.7701 (t80) REVERT: B 108 MET cc_start: 0.7264 (ttm) cc_final: 0.7062 (ttp) REVERT: B 113 SER cc_start: 0.8564 (p) cc_final: 0.8277 (p) REVERT: B 177 ASP cc_start: 0.8515 (m-30) cc_final: 0.8257 (m-30) REVERT: B 186 ASP cc_start: 0.7920 (t0) cc_final: 0.7425 (t0) REVERT: B 189 PHE cc_start: 0.6399 (m-10) cc_final: 0.6094 (m-10) REVERT: B 232 ARG cc_start: 0.8649 (tmm-80) cc_final: 0.8178 (tmm-80) REVERT: B 233 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8115 (mp) REVERT: B 285 MET cc_start: 0.8586 (mmt) cc_final: 0.8054 (mmm) REVERT: C 528 GLU cc_start: 0.8333 (tt0) cc_final: 0.8065 (tm-30) REVERT: C 548 SER cc_start: 0.9297 (t) cc_final: 0.8897 (m) REVERT: C 587 LYS cc_start: 0.8645 (tptm) cc_final: 0.8302 (tptp) REVERT: C 594 MET cc_start: 0.7913 (mmm) cc_final: 0.7446 (mmm) REVERT: C 595 GLU cc_start: 0.8486 (tm-30) cc_final: 0.7645 (tm-30) REVERT: C 598 ARG cc_start: 0.8291 (ttp-170) cc_final: 0.7868 (ptm-80) REVERT: C 680 MET cc_start: 0.8532 (mtm) cc_final: 0.8059 (mtt) REVERT: C 765 LEU cc_start: 0.8863 (tp) cc_final: 0.8591 (mp) REVERT: C 880 MET cc_start: 0.7826 (tpp) cc_final: 0.7487 (mmt) REVERT: C 996 MET cc_start: 0.8097 (mpp) cc_final: 0.7784 (mmt) REVERT: D 117 ASN cc_start: 0.6364 (m-40) cc_final: 0.5867 (p0) REVERT: D 186 ASP cc_start: 0.7874 (t0) cc_final: 0.7495 (t0) REVERT: D 202 ASP cc_start: 0.6217 (t70) cc_final: 0.5958 (t0) REVERT: D 269 HIS cc_start: 0.7373 (OUTLIER) cc_final: 0.7167 (t70) REVERT: D 346 TYR cc_start: 0.8263 (m-10) cc_final: 0.8055 (m-10) outliers start: 65 outliers final: 44 residues processed: 305 average time/residue: 0.1206 time to fit residues: 57.1964 Evaluate side-chains 301 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 247 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 590 GLU Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 656 GLU 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 751 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 902 LEU 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 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 233 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 HIS 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 542 LEU Chi-restraints excluded: chain C residue 543 LYS Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 656 GLU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 924 CYS 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 120 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 269 HIS Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 294 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 5 optimal weight: 0.0770 chunk 171 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 33 optimal weight: 0.0670 chunk 13 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.140616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.115678 restraints weight = 26073.094| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.31 r_work: 0.3370 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17276 Z= 0.143 Angle : 0.688 13.630 23832 Z= 0.371 Chirality : 0.045 0.361 2600 Planarity : 0.005 0.073 2682 Dihedral : 22.189 156.501 3248 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.01 % Favored : 95.88 % Rotamer: Outliers : 3.79 % Allowed : 23.93 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.19), residues: 1794 helix: 0.27 (0.22), residues: 536 sheet: 0.07 (0.27), residues: 372 loop : -1.20 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 148 TYR 0.027 0.002 TYR C 500 PHE 0.015 0.001 PHE C 644 TRP 0.011 0.001 TRP D 317 HIS 0.020 0.001 HIS B 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (17268) covalent geometry : angle 0.68686 / 0.37 (23828) hydrogen bonds : bond 0.04341 / 2.86 ( 699) hydrogen bonds : angle 5.18523 / 3.64 ( 1944) metal coordination : bond 0.01412 / 0.93 ( 8) metal coordination : angle 2.40873 / 1.42 ( 4) *********************** 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 314 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 254 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 SER cc_start: 0.9338 (t) cc_final: 0.8965 (m) REVERT: A 578 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7315 (t80) REVERT: A 675 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7405 (mtp85) REVERT: A 677 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8588 (tp) REVERT: A 680 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7979 (mtm) REVERT: A 774 GLU cc_start: 0.8090 (pp20) cc_final: 0.7816 (pp20) REVERT: A 795 ARG cc_start: 0.8195 (ttp80) cc_final: 0.7474 (ttp80) REVERT: A 863 MET cc_start: 0.8018 (mmm) cc_final: 0.7706 (mmm) REVERT: A 894 SER cc_start: 0.8829 (t) cc_final: 0.8176 (p) REVERT: A 902 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7892 (mt) REVERT: A 905 MET cc_start: 0.8510 (tpp) cc_final: 0.7772 (tpp) REVERT: A 940 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8510 (p0) REVERT: A 945 MET cc_start: 0.7806 (mmm) cc_final: 0.7567 (mmm) REVERT: A 984 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7627 (tp30) REVERT: B 34 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7957 (ttmt) REVERT: B 61 SER cc_start: 0.8653 (m) cc_final: 0.8429 (p) REVERT: B 62 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7217 (t80) REVERT: B 80 PHE cc_start: 0.8374 (t80) cc_final: 0.7597 (t80) REVERT: B 113 SER cc_start: 0.8555 (p) cc_final: 0.8271 (p) REVERT: B 177 ASP cc_start: 0.8504 (m-30) cc_final: 0.8238 (m-30) REVERT: B 186 ASP cc_start: 0.7904 (t0) cc_final: 0.7412 (t0) REVERT: B 189 PHE cc_start: 0.6359 (m-10) cc_final: 0.6037 (m-10) REVERT: B 195 HIS cc_start: 0.7526 (m-70) cc_final: 0.7161 (m-70) REVERT: B 233 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8255 (mp) REVERT: B 235 ARG cc_start: 0.6748 (ttt90) cc_final: 0.6310 (ttt90) REVERT: B 285 MET cc_start: 0.8573 (mmt) cc_final: 0.8052 (mmm) REVERT: C 528 GLU cc_start: 0.8310 (tt0) cc_final: 0.8082 (tm-30) REVERT: C 548 SER cc_start: 0.9287 (t) cc_final: 0.8909 (m) REVERT: C 587 LYS cc_start: 0.8655 (tptm) cc_final: 0.8293 (tptp) REVERT: C 594 MET cc_start: 0.7939 (mmm) cc_final: 0.7481 (mmm) REVERT: C 595 GLU cc_start: 0.8488 (tm-30) cc_final: 0.7647 (tm-30) REVERT: C 598 ARG cc_start: 0.8292 (ttp-170) cc_final: 0.7860 (ptm-80) REVERT: C 660 ILE cc_start: 0.8785 (mp) cc_final: 0.8484 (tt) REVERT: C 680 MET cc_start: 0.8501 (mtm) cc_final: 0.8052 (mtp) REVERT: C 765 LEU cc_start: 0.8859 (tp) cc_final: 0.8593 (mp) REVERT: C 880 MET cc_start: 0.7835 (tpp) cc_final: 0.7532 (mmt) REVERT: D 117 ASN cc_start: 0.6514 (m-40) cc_final: 0.6027 (p0) REVERT: D 186 ASP cc_start: 0.7850 (t0) cc_final: 0.7465 (t0) REVERT: D 202 ASP cc_start: 0.6235 (t70) cc_final: 0.5968 (t0) REVERT: D 269 HIS cc_start: 0.7442 (OUTLIER) cc_final: 0.7221 (t70) outliers start: 60 outliers final: 41 residues processed: 294 average time/residue: 0.1204 time to fit residues: 54.9766 Evaluate side-chains 297 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 246 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 590 GLU Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 656 GLU 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 813 LEU Chi-restraints excluded: chain A residue 902 LEU 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 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 273 ILE 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 542 LEU Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 656 GLU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 716 LEU 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 844 SER Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 924 CYS 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 120 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 269 HIS Chi-restraints excluded: chain D residue 272 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 83 optimal weight: 0.2980 chunk 155 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 298 HIS D 170 GLN ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.142520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.116900 restraints weight = 26158.656| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.39 r_work: 0.3389 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17276 Z= 0.140 Angle : 0.688 13.147 23832 Z= 0.372 Chirality : 0.044 0.350 2600 Planarity : 0.005 0.069 2682 Dihedral : 22.108 154.978 3248 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.29 % Favored : 95.60 % Rotamer: Outliers : 3.47 % Allowed : 24.31 % Favored : 72.22 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.19), residues: 1794 helix: 0.35 (0.22), residues: 538 sheet: 0.11 (0.27), residues: 372 loop : -1.19 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 148 TYR 0.025 0.002 TYR C 504 PHE 0.030 0.001 PHE D 350 TRP 0.012 0.001 TRP D 317 HIS 0.005 0.001 HIS B 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (17268) covalent geometry : angle 0.68703 / 0.37 (23828) hydrogen bonds : bond 0.04261 / 2.81 ( 699) hydrogen bonds : angle 5.17066 / 3.63 ( 1944) metal coordination : bond 0.01206 / 0.81 ( 8) metal coordination : angle 2.70686 / 1.54 ( 4) ********************** 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 323 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 268 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 SER cc_start: 0.9325 (t) cc_final: 0.8973 (m) REVERT: A 578 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.7195 (t80) REVERT: A 675 ARG cc_start: 0.8097 (mtp85) cc_final: 0.7442 (mtp85) REVERT: A 677 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8557 (tp) REVERT: A 680 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8151 (mtm) REVERT: A 774 GLU cc_start: 0.8073 (pp20) cc_final: 0.7789 (pp20) REVERT: A 795 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7519 (ttp80) REVERT: A 863 MET cc_start: 0.7991 (mmm) cc_final: 0.7575 (mmm) REVERT: A 894 SER cc_start: 0.8877 (t) cc_final: 0.8228 (p) REVERT: A 902 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7978 (mt) REVERT: A 905 MET cc_start: 0.8521 (tpp) cc_final: 0.7785 (tpp) REVERT: A 940 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.7838 (m-30) REVERT: A 945 MET cc_start: 0.7853 (mmm) cc_final: 0.7617 (mmm) REVERT: A 950 TYR cc_start: 0.7912 (m-80) cc_final: 0.7401 (m-80) REVERT: A 984 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7637 (tp30) REVERT: B 34 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7958 (ttmt) REVERT: B 61 SER cc_start: 0.8574 (m) cc_final: 0.8341 (p) REVERT: B 62 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7036 (t80) REVERT: B 113 SER cc_start: 0.8568 (p) cc_final: 0.8295 (p) REVERT: B 145 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7649 (pp) REVERT: B 177 ASP cc_start: 0.8508 (m-30) cc_final: 0.8233 (m-30) REVERT: B 186 ASP cc_start: 0.7873 (t0) cc_final: 0.7423 (t0) REVERT: B 189 PHE cc_start: 0.6436 (m-10) cc_final: 0.6092 (m-10) REVERT: B 285 MET cc_start: 0.8555 (mmt) cc_final: 0.8024 (mmm) REVERT: C 528 GLU cc_start: 0.8277 (tt0) cc_final: 0.8075 (tm-30) REVERT: C 548 SER cc_start: 0.9283 (t) cc_final: 0.8910 (m) REVERT: C 587 LYS cc_start: 0.8633 (tptm) cc_final: 0.8304 (tptp) REVERT: C 594 MET cc_start: 0.7950 (mmm) cc_final: 0.7482 (mmm) REVERT: C 598 ARG cc_start: 0.8283 (ttp-170) cc_final: 0.7851 (ptm-80) REVERT: C 660 ILE cc_start: 0.8786 (mp) cc_final: 0.8500 (tt) REVERT: C 680 MET cc_start: 0.8443 (mtm) cc_final: 0.8018 (mtp) REVERT: C 765 LEU cc_start: 0.8821 (tp) cc_final: 0.8569 (mp) REVERT: D 117 ASN cc_start: 0.6521 (m-40) cc_final: 0.5997 (p0) REVERT: D 186 ASP cc_start: 0.7839 (t0) cc_final: 0.7456 (t0) REVERT: D 202 ASP cc_start: 0.6243 (t70) cc_final: 0.5967 (t0) REVERT: D 269 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.7248 (t70) REVERT: D 346 TYR cc_start: 0.8271 (m-10) cc_final: 0.7786 (m-10) outliers start: 55 outliers final: 35 residues processed: 302 average time/residue: 0.1299 time to fit residues: 60.2492 Evaluate side-chains 294 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 249 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 590 GLU Chi-restraints excluded: chain A residue 598 ARG 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 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 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 141 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 295 VAL 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 542 LEU Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 656 GLU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 716 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 924 CYS 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 141 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 269 HIS Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 294 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 171 optimal weight: 8.9990 chunk 67 optimal weight: 0.2980 chunk 96 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 173 optimal weight: 8.9990 chunk 79 optimal weight: 0.0000 chunk 10 optimal weight: 0.9980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 822 ASN B 298 HIS C 822 ASN D 171 ASN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.142103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116200 restraints weight = 26327.391| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.44 r_work: 0.3368 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17276 Z= 0.144 Angle : 0.696 13.225 23832 Z= 0.375 Chirality : 0.045 0.338 2600 Planarity : 0.005 0.073 2682 Dihedral : 22.006 154.121 3241 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.18 % Favored : 95.71 % Rotamer: Outliers : 3.35 % Allowed : 24.75 % Favored : 71.91 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.19), residues: 1794 helix: 0.37 (0.22), residues: 538 sheet: 0.12 (0.27), residues: 372 loop : -1.20 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 148 TYR 0.022 0.002 TYR C 500 PHE 0.012 0.001 PHE B 62 TRP 0.013 0.001 TRP A 915 HIS 0.005 0.001 HIS B 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (17268) covalent geometry : angle 0.69529 / 0.38 (23828) hydrogen bonds : bond 0.04218 / 2.80 ( 699) hydrogen bonds : angle 5.14885 / 3.61 ( 1944) metal coordination : bond 0.01184 / 0.79 ( 8) metal coordination : angle 2.63233 / 1.42 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3390.30 seconds wall clock time: 59 minutes 11.18 seconds (3551.18 seconds total)