Starting phenix.real_space_refine on Sun Aug 9 13:59:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v6x_64809/08_2026/9v6x_64809.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v6x_64809/08_2026/9v6x_64809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v6x_64809/08_2026/9v6x_64809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v6x_64809/08_2026/9v6x_64809.map" model { file = "/net/cci-nas-00/data/ceres_data/9v6x_64809/08_2026/9v6x_64809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v6x_64809/08_2026/9v6x_64809.cif" } resolution = 4.0 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= 0.001 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 9009 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 4 6.06 5 P 368 5.49 5 S 33 5.16 5 C 8475 2.51 5 N 2839 2.21 5 O 3600 1.98 5 H 12243 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27562 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1635 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "G" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1735 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "E" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1608 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1466 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1735 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1466 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1348 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "F" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1348 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "I" Number of atoms: 5820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 5820 Classifications: {'DNA': 184} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 183} Chain: "J" Number of atoms: 5859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 5859 Classifications: {'DNA': 184} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 183} Chain: "M" Number of atoms: 1935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1935 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "N" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1603 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24266 SG CYS M 18 60.468 111.942 101.285 1.00550.68 S ATOM 24311 SG CYS M 21 61.506 114.922 99.254 1.00569.34 S ATOM 24575 SG CYS M 39 60.627 111.569 97.563 1.00517.96 S ATOM 24621 SG CYS M 42 63.916 112.023 99.447 1.00508.30 S ATOM 24498 SG CYS M 34 56.919 100.924 107.739 1.00424.39 S ATOM 24813 SG CYS M 53 59.735 103.294 108.934 1.00429.11 S ATOM 24856 SG CYS M 56 58.038 100.888 111.377 1.00433.93 S ATOM 26523 SG CYS N 51 39.375 92.837 94.265 1.00507.23 S ATOM 26566 SG CYS N 54 35.690 93.819 94.344 1.00494.14 S ATOM 26865 SG CYS N 72 38.002 94.496 97.356 1.00467.17 S ATOM 26897 SG CYS N 75 36.849 90.933 96.385 1.00446.04 S ATOM 26775 SG CYS N 67 51.203 90.711 94.124 1.00429.75 S ATOM 27081 SG CYS N 87 48.542 88.627 92.345 1.00425.10 S ATOM 27119 SG CYS N 90 51.963 89.038 90.728 1.00434.77 S Time building chain proxies: 4.28, per 1000 atoms: 0.16 Number of scatterers: 27562 At special positions: 0 Unit cell: (125.4, 136.4, 170.5, 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 4 29.99 S 33 16.00 P 368 15.00 O 3600 8.00 N 2839 7.00 C 8475 6.00 H 12243 1.00 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: 2.30 Conformation dependent library (CDL) restraints added in 487.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 21 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 39 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 42 " pdb=" ZN M 402 " pdb="ZN ZN M 402 " - pdb=" ND1 HIS M 36 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 34 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 56 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 53 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 51 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 54 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 75 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 72 " pdb=" ZN N 402 " pdb="ZN ZN N 402 " - pdb=" ND1 HIS N 69 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 87 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 90 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 67 " Number of angles added : 18 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 11 sheets defined 64.1% alpha, 3.6% beta 178 base pairs and 283 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.615A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.704A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.855A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.691A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.582A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.947A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 4.206A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.662A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.550A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.631A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.921A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'M' and resid 9 through 13 Processing helix chain 'M' and resid 40 through 47 Processing helix chain 'M' and resid 64 through 67 Processing helix chain 'M' and resid 72 through 83 removed outlier: 3.763A pdb=" N GLN M 76 " --> pdb=" O ASP M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 99 removed outlier: 3.530A pdb=" N ASN M 89 " --> pdb=" O GLY M 85 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU M 90 " --> pdb=" O LEU M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 115 Processing helix chain 'N' and resid 20 through 25 removed outlier: 4.139A pdb=" N GLN N 25 " --> pdb=" O LEU N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 83 Processing helix chain 'N' and resid 96 through 100 removed outlier: 3.706A pdb=" N SER N 99 " --> pdb=" O SER N 96 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 114 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.074A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.484A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'G' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.622A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 88 through 89 removed outlier: 3.731A pdb=" N ILE D 89 " --> pdb=" O ARG C 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA8, first strand: chain 'M' and resid 5 through 7 removed outlier: 3.568A pdb=" N THR M 5 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL N 40 " --> pdb=" O THR M 5 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE M 7 " --> pdb=" O ILE N 38 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE N 38 " --> pdb=" O ILE M 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'M' and resid 36 through 39 removed outlier: 3.936A pdb=" N HIS M 36 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG M 70 " --> pdb=" O THR M 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 50 through 51 removed outlier: 3.773A pdb=" N ASP N 56 " --> pdb=" O CYS N 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 70 through 72 447 hydrogen bonds defined for protein. 1308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 450 hydrogen bonds 900 hydrogen bond angles 0 basepair planarities 178 basepair parallelities 283 stacking parallelities Total time for adding SS restraints: 5.94 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12239 1.03 - 1.23: 177 1.23 - 1.43: 7346 1.43 - 1.62: 8774 1.62 - 1.82: 48 Bond restraints: 28584 Sorted by residual: bond pdb=" C1' DT I -47 " pdb=" N1 DT I -47 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.40e+01 bond pdb=" C1' DT J 54 " pdb=" N1 DT J 54 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" C1' DT I -26 " pdb=" N1 DT I -26 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.13e+01 bond pdb=" C1' DC I 6 " pdb=" N1 DC I 6 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.07e+01 bond pdb=" C1' DT J -16 " pdb=" N1 DT J -16 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.02e+01 ... (remaining 28579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 46145 1.11 - 2.23: 4818 2.23 - 3.34: 831 3.34 - 4.46: 47 4.46 - 5.57: 8 Bond angle restraints: 51849 Sorted by residual: angle pdb=" N3 DT I -26 " pdb=" C4 DT I -26 " pdb=" O4 DT I -26 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT I -28 " pdb=" C4 DT I -28 " pdb=" O4 DT I -28 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT J -82 " pdb=" C4 DT J -82 " pdb=" O4 DT J -82 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT I -88 " pdb=" C4 DT I -88 " pdb=" O4 DT I -88 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 ... (remaining 51844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.49: 9817 31.49 - 62.99: 2032 62.99 - 94.48: 66 94.48 - 125.97: 0 125.97 - 157.46: 3 Dihedral angle restraints: 11918 sinusoidal: 8729 harmonic: 3189 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 62.54 157.46 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 64.74 155.26 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" CA ILE M 32 " pdb=" C ILE M 32 " pdb=" N GLU M 33 " pdb=" CA GLU M 33 " ideal model delta harmonic sigma weight residual 180.00 161.33 18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 11915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1690 0.032 - 0.064: 515 0.064 - 0.096: 103 0.096 - 0.128: 165 0.128 - 0.160: 226 Chirality restraints: 2699 Sorted by residual: chirality pdb=" C3' DC I 80 " pdb=" C4' DC I 80 " pdb=" O3' DC I 80 " pdb=" C2' DC I 80 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" C3' DA I -69 " pdb=" C4' DA I -69 " pdb=" O3' DA I -69 " pdb=" C2' DA I -69 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" C3' DG I -60 " pdb=" C4' DG I -60 " pdb=" O3' DG I -60 " pdb=" C2' DG I -60 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 2696 not shown) Planarity restraints: 2936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP M 27 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C ASP M 27 " 0.028 2.00e-02 2.50e+03 pdb=" O ASP M 27 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA M 28 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG M 64 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO M 65 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO M 65 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO M 65 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 36 " 0.018 2.00e-02 2.50e+03 8.20e-03 1.85e+00 pdb=" N1 DC I 36 " -0.018 2.00e-02 2.50e+03 pdb=" C2 DC I 36 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DC I 36 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DC I 36 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 36 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 36 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DC I 36 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC I 36 " -0.001 2.00e-02 2.50e+03 pdb=" H5 DC I 36 " 0.001 2.00e-02 2.50e+03 pdb=" H6 DC I 36 " -0.003 2.00e-02 2.50e+03 ... (remaining 2933 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 654 2.13 - 2.75: 42106 2.75 - 3.36: 73435 3.36 - 3.98: 99065 3.98 - 4.60: 146068 Nonbonded interactions: 361328 Sorted by model distance: nonbonded pdb=" HE1 HIS M 36 " pdb="ZN ZN M 402 " model vdw 1.512 1.408 nonbonded pdb=" H THR H 90 " pdb=" OE2 GLU H 93 " model vdw 1.591 2.450 nonbonded pdb=" O CYS M 18 " pdb=" H GLY M 22 " model vdw 1.604 2.450 nonbonded pdb=" HG SER H 56 " pdb=" OP1 DA I -54 " model vdw 1.613 2.450 nonbonded pdb=" OE1 GLU E 59 " pdb=" H GLU E 59 " model vdw 1.616 2.450 ... (remaining 361323 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 40 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ E or name HH11 or name HH12 or name HH21 or name HH22)) or resid 41 through 134) \ ) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.150 Extract box with map and model: 0.420 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 32.490 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16357 Z= 0.490 Angle : 0.734 5.572 23675 Z= 0.643 Chirality : 0.057 0.160 2699 Planarity : 0.003 0.040 1716 Dihedral : 27.043 157.463 7065 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.28), residues: 961 helix: 2.46 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -0.76 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 101 TYR 0.009 0.001 TYR F 98 PHE 0.015 0.001 PHE M 87 TRP 0.001 0.000 TRP N 17 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.49 (16341) covalent geometry : angle 0.73238 / 0.64 (23657) hydrogen bonds : bond 0.10943 / 7.00 ( 897) hydrogen bonds : angle 3.90736 / 2.95 ( 2208) metal coordination : bond 0.00426 / 0.25 ( 16) metal coordination : angle 2.02039 / 1.45 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.552 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 106 ASP cc_start: 0.8550 (m-30) cc_final: 0.8325 (m-30) REVERT: M 46 TYR cc_start: 0.9522 (t80) cc_final: 0.9163 (t80) REVERT: M 51 LYS cc_start: 0.7340 (pttm) cc_final: 0.6958 (mptt) REVERT: M 87 PHE cc_start: 0.8644 (p90) cc_final: 0.8255 (p90) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2622 time to fit residues: 39.0697 Evaluate side-chains 89 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 50.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 50.0000 chunk 55 optimal weight: 0.9980 chunk 129 optimal weight: 20.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 13 ASN ** N 25 GLN ** 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 = 0.3821 r_free = 0.3821 target = 0.065871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.045849 restraints weight = 475488.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.045578 restraints weight = 246006.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.045768 restraints weight = 179061.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.045750 restraints weight = 159109.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.045750 restraints weight = 155451.229| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16357 Z= 0.213 Angle : 0.618 8.758 23675 Z= 0.392 Chirality : 0.039 0.206 2699 Planarity : 0.004 0.064 1716 Dihedral : 30.201 160.107 5120 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.24 % Allowed : 5.64 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.28), residues: 961 helix: 2.05 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -1.18 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 67 TYR 0.007 0.001 TYR G 57 PHE 0.008 0.001 PHE F 100 TRP 0.002 0.001 TRP N 17 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.21 (16341) covalent geometry : angle 0.61544 / 0.39 (23657) hydrogen bonds : bond 0.06384 / 4.37 ( 897) hydrogen bonds : angle 3.71819 / 2.77 ( 2208) metal coordination : bond 0.00614 / 0.49 ( 16) metal coordination : angle 2.27532 / 1.83 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.599 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 106 ASP cc_start: 0.8632 (m-30) cc_final: 0.8333 (m-30) REVERT: M 46 TYR cc_start: 0.9166 (t80) cc_final: 0.8905 (t80) REVERT: M 70 ARG cc_start: 0.8770 (ptt180) cc_final: 0.8364 (ptp90) outliers start: 2 outliers final: 2 residues processed: 89 average time/residue: 0.2941 time to fit residues: 37.4179 Evaluate side-chains 83 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 58 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 94 optimal weight: 40.0000 chunk 52 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 86 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 25 GLN ** 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 = 0.3813 r_free = 0.3813 target = 0.065560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.045014 restraints weight = 476125.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.045153 restraints weight = 264810.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.045355 restraints weight = 206903.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.044887 restraints weight = 187587.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.045064 restraints weight = 167584.282| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16357 Z= 0.174 Angle : 0.567 6.973 23675 Z= 0.371 Chirality : 0.037 0.212 2699 Planarity : 0.004 0.053 1716 Dihedral : 30.369 160.308 5120 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.36 % Allowed : 7.07 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.27), residues: 961 helix: 1.98 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -1.39 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 45 TYR 0.010 0.001 TYR G 57 PHE 0.017 0.001 PHE M 87 TRP 0.002 0.001 TRP N 17 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.17 (16341) covalent geometry : angle 0.56346 / 0.37 (23657) hydrogen bonds : bond 0.05642 / 3.83 ( 897) hydrogen bonds : angle 3.57237 / 2.65 ( 2208) metal coordination : bond 0.00718 / 0.50 ( 16) metal coordination : angle 2.43771 / 1.85 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.604 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 106 ASP cc_start: 0.8632 (m-30) cc_final: 0.8352 (m-30) REVERT: M 46 TYR cc_start: 0.8990 (t80) cc_final: 0.8749 (t80) outliers start: 3 outliers final: 1 residues processed: 83 average time/residue: 0.2731 time to fit residues: 33.8883 Evaluate side-chains 81 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 66 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 55 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 118 optimal weight: 30.0000 chunk 49 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN ** N 25 GLN ** 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 = 0.3760 r_free = 0.3760 target = 0.063572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.042905 restraints weight = 484764.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 80)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.042373 restraints weight = 271681.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.042523 restraints weight = 201434.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.042563 restraints weight = 180518.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.042563 restraints weight = 175010.350| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16357 Z= 0.280 Angle : 0.675 12.620 23675 Z= 0.414 Chirality : 0.041 0.194 2699 Planarity : 0.005 0.069 1716 Dihedral : 30.688 161.681 5120 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.60 % Allowed : 8.03 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.26), residues: 961 helix: 1.25 (0.20), residues: 608 sheet: None (None), residues: 0 loop : -1.73 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 92 TYR 0.013 0.002 TYR D 42 PHE 0.012 0.001 PHE M 87 TRP 0.004 0.001 TRP N 17 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.28 (16341) covalent geometry : angle 0.67092 / 0.41 (23657) hydrogen bonds : bond 0.09311 / 6.33 ( 897) hydrogen bonds : angle 3.93961 / 2.90 ( 2208) metal coordination : bond 0.01464 / 1.01 ( 16) metal coordination : angle 2.91300 / 2.15 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.749 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 106 ASP cc_start: 0.8699 (m-30) cc_final: 0.8423 (m-30) REVERT: H 71 GLU cc_start: 0.8611 (tt0) cc_final: 0.8139 (tm-30) REVERT: M 46 TYR cc_start: 0.8912 (t80) cc_final: 0.8705 (t80) outliers start: 5 outliers final: 4 residues processed: 85 average time/residue: 0.2792 time to fit residues: 35.1331 Evaluate side-chains 82 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain M residue 66 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 87 optimal weight: 40.0000 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 92 optimal weight: 30.0000 chunk 72 optimal weight: 50.0000 chunk 15 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 25 GLN ** 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 = 0.3772 r_free = 0.3772 target = 0.064341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.043971 restraints weight = 473226.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.043459 restraints weight = 245192.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.043616 restraints weight = 184437.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.043672 restraints weight = 165432.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.043671 restraints weight = 159399.059| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16357 Z= 0.149 Angle : 0.573 7.569 23675 Z= 0.368 Chirality : 0.038 0.221 2699 Planarity : 0.004 0.051 1716 Dihedral : 30.749 161.499 5120 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.60 % Allowed : 10.43 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.27), residues: 961 helix: 1.77 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -1.67 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 77 TYR 0.009 0.001 TYR F 51 PHE 0.011 0.001 PHE F 61 TRP 0.002 0.001 TRP N 17 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.15 (16341) covalent geometry : angle 0.56828 / 0.37 (23657) hydrogen bonds : bond 0.05437 / 3.71 ( 897) hydrogen bonds : angle 3.51155 / 2.59 ( 2208) metal coordination : bond 0.00739 / 0.51 ( 16) metal coordination : angle 2.68943 / 1.94 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.636 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 106 ASP cc_start: 0.8655 (m-30) cc_final: 0.8361 (m-30) REVERT: H 71 GLU cc_start: 0.8593 (tt0) cc_final: 0.8113 (tm-30) REVERT: M 46 TYR cc_start: 0.9083 (t80) cc_final: 0.8824 (t80) outliers start: 5 outliers final: 5 residues processed: 88 average time/residue: 0.2791 time to fit residues: 36.1553 Evaluate side-chains 87 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain M residue 66 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 78 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 86 optimal weight: 40.0000 chunk 125 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 61 HIS ** N 25 GLN ** 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 = 0.3748 r_free = 0.3748 target = 0.063509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.043503 restraints weight = 480127.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.042897 restraints weight = 243895.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.042988 restraints weight = 187562.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.043019 restraints weight = 166549.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.043025 restraints weight = 163426.083| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16357 Z= 0.226 Angle : 0.623 8.339 23675 Z= 0.388 Chirality : 0.039 0.196 2699 Planarity : 0.004 0.051 1716 Dihedral : 30.804 161.666 5120 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.72 % Allowed : 10.91 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.26), residues: 961 helix: 1.52 (0.20), residues: 607 sheet: -0.84 (1.96), residues: 10 loop : -1.80 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 83 TYR 0.009 0.001 TYR D 42 PHE 0.008 0.001 PHE F 61 TRP 0.002 0.001 TRP N 17 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.23 (16341) covalent geometry : angle 0.61877 / 0.39 (23657) hydrogen bonds : bond 0.07181 / 4.88 ( 897) hydrogen bonds : angle 3.70265 / 2.73 ( 2208) metal coordination : bond 0.01134 / 0.73 ( 16) metal coordination : angle 2.74959 / 1.98 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.523 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 106 ASP cc_start: 0.8674 (m-30) cc_final: 0.8396 (m-30) REVERT: H 71 GLU cc_start: 0.8635 (tt0) cc_final: 0.8212 (tm-30) REVERT: M 46 TYR cc_start: 0.9161 (t80) cc_final: 0.8904 (t80) outliers start: 6 outliers final: 6 residues processed: 85 average time/residue: 0.2581 time to fit residues: 32.9549 Evaluate side-chains 85 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 66 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 62 optimal weight: 0.6980 chunk 15 optimal weight: 0.0870 chunk 50 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 94 optimal weight: 30.0000 chunk 113 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 107 optimal weight: 50.0000 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.064406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.043890 restraints weight = 471410.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 80)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.043296 restraints weight = 247928.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.043411 restraints weight = 186657.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.043596 restraints weight = 168824.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.043604 restraints weight = 161066.044| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16357 Z= 0.140 Angle : 0.576 8.273 23675 Z= 0.367 Chirality : 0.038 0.219 2699 Planarity : 0.004 0.046 1716 Dihedral : 30.807 161.082 5120 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.96 % Allowed : 11.75 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.27), residues: 961 helix: 1.91 (0.21), residues: 607 sheet: -1.35 (1.84), residues: 10 loop : -1.68 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 101 TYR 0.008 0.001 TYR B 51 PHE 0.010 0.001 PHE M 87 TRP 0.002 0.001 TRP N 17 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.14 (16341) covalent geometry : angle 0.57147 / 0.37 (23657) hydrogen bonds : bond 0.04860 / 3.32 ( 897) hydrogen bonds : angle 3.35364 / 2.47 ( 2208) metal coordination : bond 0.00601 / 0.39 ( 16) metal coordination : angle 2.71005 / 1.96 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.589 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7854 (tm-30) REVERT: E 106 ASP cc_start: 0.8644 (m-30) cc_final: 0.8368 (m-30) REVERT: H 71 GLU cc_start: 0.8590 (tt0) cc_final: 0.8129 (tm-30) REVERT: M 46 TYR cc_start: 0.8942 (t80) cc_final: 0.8719 (t80) outliers start: 8 outliers final: 7 residues processed: 88 average time/residue: 0.2628 time to fit residues: 34.8112 Evaluate side-chains 91 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 91 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 100 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 120 optimal weight: 30.0000 chunk 15 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 106 optimal weight: 30.0000 chunk 62 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.063980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.043436 restraints weight = 475355.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.043025 restraints weight = 251312.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.043104 restraints weight = 190321.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.043343 restraints weight = 170507.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.043353 restraints weight = 160470.399| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16357 Z= 0.173 Angle : 0.588 9.380 23675 Z= 0.371 Chirality : 0.038 0.197 2699 Planarity : 0.004 0.047 1716 Dihedral : 30.797 160.972 5120 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.84 % Allowed : 12.23 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.27), residues: 961 helix: 1.86 (0.21), residues: 607 sheet: -1.52 (1.92), residues: 10 loop : -1.74 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 83 TYR 0.010 0.001 TYR F 98 PHE 0.007 0.001 PHE F 61 TRP 0.001 0.000 TRP N 17 HIS 0.003 0.001 HIS M 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.17 (16341) covalent geometry : angle 0.58383 / 0.37 (23657) hydrogen bonds : bond 0.05710 / 3.88 ( 897) hydrogen bonds : angle 3.41709 / 2.51 ( 2208) metal coordination : bond 0.00865 / 0.54 ( 16) metal coordination : angle 2.70650 / 2.01 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.617 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 106 ASP cc_start: 0.8621 (m-30) cc_final: 0.8356 (m-30) REVERT: H 71 GLU cc_start: 0.8607 (tt0) cc_final: 0.8195 (tm-30) REVERT: M 46 TYR cc_start: 0.9022 (t80) cc_final: 0.8784 (t80) outliers start: 7 outliers final: 7 residues processed: 85 average time/residue: 0.2636 time to fit residues: 33.1269 Evaluate side-chains 88 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 91 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 40 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 75 optimal weight: 30.0000 chunk 111 optimal weight: 50.0000 chunk 36 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 chunk 90 optimal weight: 50.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.062585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.041948 restraints weight = 484448.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.041466 restraints weight = 282848.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.041547 restraints weight = 212603.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.041835 restraints weight = 187577.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.041806 restraints weight = 175130.596| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16357 Z= 0.308 Angle : 0.713 11.768 23675 Z= 0.428 Chirality : 0.041 0.185 2699 Planarity : 0.005 0.057 1716 Dihedral : 31.050 163.349 5120 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.84 % Allowed : 12.11 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.25), residues: 961 helix: 0.80 (0.19), residues: 608 sheet: -1.52 (1.74), residues: 10 loop : -2.04 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 40 TYR 0.013 0.002 TYR A 99 PHE 0.014 0.002 PHE A 78 TRP 0.004 0.001 TRP N 17 HIS 0.007 0.002 HIS N 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.31 (16341) covalent geometry : angle 0.70741 / 0.43 (23657) hydrogen bonds : bond 0.09947 / 6.73 ( 897) hydrogen bonds : angle 4.15256 / 3.04 ( 2208) metal coordination : bond 0.01725 / 1.12 ( 16) metal coordination : angle 3.29679 / 2.34 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.545 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: symmetry clash revert: symmetry clash REVERT: E 106 ASP cc_start: 0.8689 (m-30) cc_final: 0.8420 (m-30) REVERT: H 71 GLU cc_start: 0.8628 (tt0) cc_final: 0.8314 (tm-30) REVERT: N 70 ARG cc_start: 0.7239 (mmp80) cc_final: 0.6923 (mmp80) outliers start: 7 outliers final: 7 residues processed: 83 average time/residue: 0.2470 time to fit residues: 30.6384 Evaluate side-chains 85 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 91 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 33 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 115 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.063966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.043511 restraints weight = 470715.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.042950 restraints weight = 248089.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.043119 restraints weight = 190842.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.043166 restraints weight = 168348.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.043168 restraints weight = 161544.697| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16357 Z= 0.147 Angle : 0.621 11.773 23675 Z= 0.384 Chirality : 0.039 0.222 2699 Planarity : 0.005 0.077 1716 Dihedral : 31.041 161.994 5120 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.08 % Allowed : 12.71 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.26), residues: 961 helix: 1.58 (0.20), residues: 606 sheet: -1.41 (1.86), residues: 10 loop : -1.87 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 77 TYR 0.015 0.002 TYR M 46 PHE 0.013 0.001 PHE N 106 TRP 0.002 0.001 TRP N 17 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.15 (16341) covalent geometry : angle 0.61536 / 0.38 (23657) hydrogen bonds : bond 0.05153 / 3.51 ( 897) hydrogen bonds : angle 3.44442 / 2.53 ( 2208) metal coordination : bond 0.00707 / 0.46 ( 16) metal coordination : angle 3.06679 / 2.19 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.485 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 106 ASP cc_start: 0.8666 (m-30) cc_final: 0.8377 (m-30) REVERT: H 71 GLU cc_start: 0.8613 (tt0) cc_final: 0.8231 (tm-30) outliers start: 9 outliers final: 8 residues processed: 88 average time/residue: 0.2399 time to fit residues: 31.6439 Evaluate side-chains 92 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain N residue 106 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 96 optimal weight: 30.0000 chunk 99 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 124 optimal weight: 30.0000 chunk 95 optimal weight: 30.0000 chunk 100 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 107 optimal weight: 50.0000 overall best weight: 18.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.061533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.040990 restraints weight = 493688.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.040386 restraints weight = 272555.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.040559 restraints weight = 209916.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.040707 restraints weight = 190640.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.040708 restraints weight = 183553.017| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 16357 Z= 0.488 Angle : 0.901 10.108 23675 Z= 0.516 Chirality : 0.047 0.218 2699 Planarity : 0.007 0.067 1716 Dihedral : 31.295 165.540 5120 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 22.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.18 % Favored : 92.72 % Rotamer: Outliers : 0.84 % Allowed : 13.19 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.24), residues: 961 helix: -0.33 (0.18), residues: 611 sheet: -0.89 (1.95), residues: 10 loop : -2.45 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 40 TYR 0.018 0.003 TYR A 99 PHE 0.021 0.004 PHE A 78 TRP 0.004 0.003 TRP N 17 HIS 0.011 0.003 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00902 / 0.49 (16341) covalent geometry : angle 0.89391 / 0.52 (23657) hydrogen bonds : bond 0.14126 / 9.55 ( 897) hydrogen bonds : angle 4.92224 / 3.59 ( 2208) metal coordination : bond 0.02689 / 1.74 ( 16) metal coordination : angle 4.31568 / 2.93 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5450.59 seconds wall clock time: 93 minutes 17.75 seconds (5597.75 seconds total)