Starting phenix.real_space_refine on Mon Jul 6 12:37:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v6x_64809/07_2026/9v6x_64809.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v6x_64809/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9v6x_64809/07_2026/9v6x_64809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v6x_64809/07_2026/9v6x_64809.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v6x_64809/07_2026/9v6x_64809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v6x_64809/07_2026/9v6x_64809.map" } 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-dev-6108/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: 3.92, per 1000 atoms: 0.14 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: 1.59 Conformation dependent library (CDL) restraints added in 474.6 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: 4.38 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: 5.07 Time building geometry restraints manager: 2.28 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: 46176 1.11 - 2.23: 4789 2.23 - 3.34: 829 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.150 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 29.710 Find NCS groups from input model: 0.130 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.760 ------------------------------------------------------------------------------- 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 : 0.729 5.572 23675 Z= 0.639 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 0.72722 / 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 : 0.568 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: 0.2437 time to fit residues: 35.7409 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 : 0.392 ------------------------------------------------------------------------------- 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: 20.0000 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 = 0.3825 r_free = 0.3825 target = 0.066063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.044847 restraints weight = 474974.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.045275 restraints weight = 257226.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.045620 restraints weight = 203450.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.045345 restraints weight = 183458.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.045363 restraints weight = 170048.791| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16357 Z= 0.207 Angle : 0.611 8.486 23675 Z= 0.392 Chirality : 0.039 0.207 2699 Planarity : 0.004 0.058 1716 Dihedral : 30.183 160.041 5120 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: 1.42 (0.28), residues: 961 helix: 2.10 (0.21), residues: 606 sheet: None (None), residues: 0 loop : -1.18 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.008 0.001 TYR G 57 PHE 0.008 0.001 PHE M 87 TRP 0.002 0.001 TRP N 17 HIS 0.003 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.21 (16341) covalent geometry : angle 0.60702 / 0.39 (23657) hydrogen bonds : bond 0.06120 / 4.18 ( 897) hydrogen bonds : angle 3.76180 / 2.80 ( 2208) metal coordination : bond 0.00740 / 0.51 ( 16) metal coordination : angle 2.52712 / 1.98 ( 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 89 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.373 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: 0.8611 (m-30) cc_final: 0.8329 (m-30) REVERT: M 70 ARG cc_start: 0.8703 (ptt180) cc_final: 0.8436 (ptp90) REVERT: N 64 THR cc_start: 0.7504 (p) cc_final: 0.7219 (t) outliers start: 2 outliers final: 2 residues processed: 88 average time/residue: 0.2718 time to fit residues: 34.3138 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 : 0.432 ------------------------------------------------------------------------------- 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: 10.0000 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 40.0000 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 101 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 76 GLN ** 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 = 0.3803 r_free = 0.3803 target = 0.065191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.045034 restraints weight = 476683.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.044395 restraints weight = 246494.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.044594 restraints weight = 184166.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.044611 restraints weight = 164226.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.044605 restraints weight = 160342.003| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16357 Z= 0.192 Angle : 0.583 7.280 23675 Z= 0.378 Chirality : 0.038 0.199 2699 Planarity : 0.005 0.079 1716 Dihedral : 30.462 160.841 5120 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.36 % Allowed : 7.31 % Favored : 92.33 % 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: 1.06 (0.27), residues: 961 helix: 1.86 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -1.45 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 45 TYR 0.012 0.001 TYR M 46 PHE 0.025 0.001 PHE M 87 TRP 0.002 0.000 TRP N 17 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.19 (16341) covalent geometry : angle 0.57876 / 0.38 (23657) hydrogen bonds : bond 0.06058 / 4.12 ( 897) hydrogen bonds : angle 3.60448 / 2.66 ( 2208) metal coordination : bond 0.00897 / 0.64 ( 16) metal coordination : angle 2.47802 / 1.86 ( 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 86 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.577 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: A 105 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7891 (tm-30) REVERT: E 106 ASP cc_start: 0.8711 (m-30) cc_final: 0.8424 (m-30) outliers start: 3 outliers final: 2 residues processed: 84 average time/residue: 0.2631 time to fit residues: 32.9836 Evaluate side-chains 84 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU 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: 9.9990 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: 0.8980 chunk 51 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 45 optimal weight: 0.1980 chunk 118 optimal weight: 30.0000 chunk 49 optimal weight: 4.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.064771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.044403 restraints weight = 473952.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.043905 restraints weight = 245884.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.044030 restraints weight = 184149.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.044099 restraints weight = 166368.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.044296 restraints weight = 161004.398| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1758 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= 0.180 Angle : 0.576 7.612 23675 Z= 0.372 Chirality : 0.038 0.200 2699 Planarity : 0.004 0.053 1716 Dihedral : 30.584 160.664 5120 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.72 % Allowed : 8.15 % Favored : 91.13 % 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: 1.14 (0.27), residues: 961 helix: 1.94 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -1.45 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 70 TYR 0.009 0.001 TYR G 57 PHE 0.008 0.001 PHE M 87 TRP 0.003 0.001 TRP N 17 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.18 (16341) covalent geometry : angle 0.57215 / 0.37 (23657) hydrogen bonds : bond 0.05846 / 4.02 ( 897) hydrogen bonds : angle 3.48791 / 2.58 ( 2208) metal coordination : bond 0.00808 / 0.58 ( 16) metal coordination : angle 2.52967 / 1.85 ( 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 90 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.583 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: A 105 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7821 (tm-30) REVERT: E 106 ASP cc_start: 0.8637 (m-30) cc_final: 0.8355 (m-30) outliers start: 6 outliers final: 6 residues processed: 85 average time/residue: 0.2775 time to fit residues: 34.6792 Evaluate side-chains 86 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU 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 43 ILE 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: 3.9990 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 50.0000 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 92 optimal weight: 30.0000 chunk 72 optimal weight: 50.0000 chunk 15 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.064869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.044622 restraints weight = 472407.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.044302 restraints weight = 246527.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.044475 restraints weight = 181451.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.044555 restraints weight = 162534.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.044544 restraints weight = 158795.615| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16357 Z= 0.154 Angle : 0.565 7.379 23675 Z= 0.365 Chirality : 0.037 0.198 2699 Planarity : 0.004 0.046 1716 Dihedral : 30.647 160.742 5120 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.72 % Allowed : 8.99 % Favored : 90.29 % 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: 1.18 (0.27), residues: 961 helix: 2.01 (0.21), residues: 607 sheet: -0.48 (1.95), residues: 10 loop : -1.51 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 45 TYR 0.011 0.001 TYR M 46 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 0.00241 / 0.15 (16341) covalent geometry : angle 0.56060 / 0.36 (23657) hydrogen bonds : bond 0.05137 / 3.51 ( 897) hydrogen bonds : angle 3.37829 / 2.50 ( 2208) metal coordination : bond 0.00730 / 0.54 ( 16) metal coordination : angle 2.56157 / 1.92 ( 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: 6 poor density : 85 time to evaluate : 0.583 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: A 105 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7918 (tm-30) REVERT: E 106 ASP cc_start: 0.8651 (m-30) cc_final: 0.8360 (m-30) REVERT: H 71 GLU cc_start: 0.8617 (tt0) cc_final: 0.8106 (tm-30) outliers start: 6 outliers final: 6 residues processed: 86 average time/residue: 0.2511 time to fit residues: 32.4458 Evaluate side-chains 89 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU 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 Chi-restraints excluded: chain N residue 25 GLN 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: 5.9990 chunk 71 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 86 optimal weight: 40.0000 chunk 125 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.064220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.044116 restraints weight = 478865.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.043318 restraints weight = 247611.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.043479 restraints weight = 187646.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.043668 restraints weight = 166538.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.043681 restraints weight = 159107.718| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 16357 Z= 0.210 Angle : 0.598 11.334 23675 Z= 0.380 Chirality : 0.038 0.190 2699 Planarity : 0.004 0.048 1716 Dihedral : 30.713 161.228 5120 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.96 % Allowed : 10.07 % 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: 0.96 (0.27), residues: 961 helix: 1.82 (0.21), residues: 607 sheet: -0.62 (2.05), residues: 10 loop : -1.58 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 45 TYR 0.009 0.001 TYR M 46 PHE 0.008 0.001 PHE F 61 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 0.00369 / 0.21 (16341) covalent geometry : angle 0.59409 / 0.38 (23657) hydrogen bonds : bond 0.06246 / 4.26 ( 897) hydrogen bonds : angle 3.54895 / 2.62 ( 2208) metal coordination : bond 0.00958 / 0.63 ( 16) metal coordination : angle 2.54866 / 1.85 ( 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 94 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.572 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: A 105 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7898 (tm-30) REVERT: E 106 ASP cc_start: 0.8666 (m-30) cc_final: 0.8385 (m-30) REVERT: H 71 GLU cc_start: 0.8624 (tt0) cc_final: 0.8149 (tm-30) outliers start: 8 outliers final: 8 residues processed: 88 average time/residue: 0.2672 time to fit residues: 35.0083 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 : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU 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 25 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 62 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 94 optimal weight: 30.0000 chunk 113 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 107 optimal weight: 50.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.064675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.043996 restraints weight = 473307.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.043698 restraints weight = 253228.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.043907 restraints weight = 190096.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.043941 restraints weight = 169177.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.043948 restraints weight = 162354.488| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16357 Z= 0.148 Angle : 0.571 7.916 23675 Z= 0.366 Chirality : 0.038 0.199 2699 Planarity : 0.004 0.060 1716 Dihedral : 30.743 161.073 5120 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.84 % Allowed : 11.27 % Favored : 87.89 % 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: 1.09 (0.27), residues: 961 helix: 1.96 (0.21), residues: 607 sheet: -0.97 (1.92), residues: 10 loop : -1.58 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 45 TYR 0.007 0.001 TYR B 51 PHE 0.008 0.001 PHE F 100 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 0.00228 / 0.15 (16341) covalent geometry : angle 0.56590 / 0.37 (23657) hydrogen bonds : bond 0.05007 / 3.42 ( 897) hydrogen bonds : angle 3.32854 / 2.45 ( 2208) metal coordination : bond 0.00647 / 0.44 ( 16) metal coordination : angle 2.71393 / 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 94 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.586 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: A 105 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7944 (tm-30) REVERT: E 106 ASP cc_start: 0.8625 (m-30) cc_final: 0.8343 (m-30) REVERT: H 71 GLU cc_start: 0.8576 (tt0) cc_final: 0.8109 (tm-30) outliers start: 7 outliers final: 7 residues processed: 88 average time/residue: 0.2686 time to fit residues: 34.9453 Evaluate side-chains 94 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU 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 F residue 68 ASP 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: 0.3980 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 30.0000 chunk 120 optimal weight: 30.0000 chunk 15 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 106 optimal weight: 40.0000 chunk 62 optimal weight: 8.9990 chunk 125 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 61 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.064494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.043798 restraints weight = 475076.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.043709 restraints weight = 256480.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.043643 restraints weight = 187996.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.043716 restraints weight = 172247.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.043711 restraints weight = 165247.605| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16357 Z= 0.162 Angle : 0.581 9.078 23675 Z= 0.369 Chirality : 0.037 0.192 2699 Planarity : 0.004 0.054 1716 Dihedral : 30.754 160.976 5120 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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: 1.08 (0.27), residues: 961 helix: 1.96 (0.21), residues: 607 sheet: -1.19 (1.89), residues: 10 loop : -1.60 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 45 TYR 0.008 0.001 TYR F 98 PHE 0.009 0.001 PHE M 87 TRP 0.001 0.000 TRP N 17 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.16 (16341) covalent geometry : angle 0.57600 / 0.37 (23657) hydrogen bonds : bond 0.05253 / 3.58 ( 897) hydrogen bonds : angle 3.33676 / 2.46 ( 2208) metal coordination : bond 0.00761 / 0.50 ( 16) metal coordination : angle 2.73940 / 1.98 ( 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 93 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.603 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: 0.8630 (m-30) cc_final: 0.8356 (m-30) REVERT: H 71 GLU cc_start: 0.8581 (tt0) cc_final: 0.8118 (tm-30) outliers start: 7 outliers final: 7 residues processed: 87 average time/residue: 0.2782 time to fit residues: 35.1523 Evaluate side-chains 93 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU 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 F residue 68 ASP Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 66 LEU 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: 30.0000 chunk 58 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 30.0000 chunk 111 optimal weight: 40.0000 chunk 36 optimal weight: 9.9990 chunk 83 optimal weight: 30.0000 chunk 90 optimal weight: 50.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.063497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.043092 restraints weight = 479008.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.042614 restraints weight = 256373.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.042714 restraints weight = 194352.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.042946 restraints weight = 172542.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.042891 restraints weight = 164083.528| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16357 Z= 0.230 Angle : 0.633 10.296 23675 Z= 0.392 Chirality : 0.038 0.179 2699 Planarity : 0.004 0.051 1716 Dihedral : 30.905 162.282 5120 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.96 % Allowed : 12.35 % Favored : 86.69 % 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: 0.57 (0.27), residues: 961 helix: 1.53 (0.20), residues: 607 sheet: -1.39 (1.88), residues: 10 loop : -1.73 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 92 TYR 0.012 0.002 TYR F 98 PHE 0.011 0.002 PHE A 78 TRP 0.002 0.001 TRP N 17 HIS 0.006 0.001 HIS M 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.23 (16341) covalent geometry : angle 0.62856 / 0.39 (23657) hydrogen bonds : bond 0.07558 / 5.13 ( 897) hydrogen bonds : angle 3.66265 / 2.69 ( 2208) metal coordination : bond 0.01332 / 0.87 ( 16) metal coordination : angle 2.81957 / 2.07 ( 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 95 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.790 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: A 105 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7891 (tm-30) REVERT: E 106 ASP cc_start: 0.8663 (m-30) cc_final: 0.8381 (m-30) REVERT: H 71 GLU cc_start: 0.8631 (tt0) cc_final: 0.8247 (tm-30) outliers start: 8 outliers final: 6 residues processed: 90 average time/residue: 0.2807 time to fit residues: 37.0008 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 : 0.507 ------------------------------------------------------------------------------- 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 F residue 68 ASP Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 66 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 33 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.064294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.043476 restraints weight = 472671.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.042941 restraints weight = 257554.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.043088 restraints weight = 193323.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.043140 restraints weight = 173745.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.043400 restraints weight = 168246.796| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16357 Z= 0.144 Angle : 0.587 9.733 23675 Z= 0.371 Chirality : 0.037 0.199 2699 Planarity : 0.004 0.047 1716 Dihedral : 30.906 161.660 5120 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.72 % Allowed : 12.59 % Favored : 86.69 % 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: 0.95 (0.27), residues: 961 helix: 1.86 (0.21), residues: 607 sheet: -1.52 (1.84), residues: 10 loop : -1.64 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 77 TYR 0.011 0.001 TYR B 51 PHE 0.008 0.001 PHE F 100 TRP 0.004 0.001 TRP N 17 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.14 (16341) covalent geometry : angle 0.58307 / 0.37 (23657) hydrogen bonds : bond 0.05049 / 3.44 ( 897) hydrogen bonds : angle 3.32096 / 2.44 ( 2208) metal coordination : bond 0.00725 / 0.48 ( 16) metal coordination : angle 2.65466 / 2.01 ( 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: 6 poor density : 88 time to evaluate : 0.593 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: A 105 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7877 (tm-30) REVERT: E 106 ASP cc_start: 0.8648 (m-30) cc_final: 0.8364 (m-30) REVERT: H 71 GLU cc_start: 0.8597 (tt0) cc_final: 0.8190 (tm-30) REVERT: M 87 PHE cc_start: 0.7772 (p90) cc_final: 0.7526 (p90) outliers start: 6 outliers final: 6 residues processed: 89 average time/residue: 0.2791 time to fit residues: 36.4529 Evaluate side-chains 92 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 96 optimal weight: 20.0000 chunk 99 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 124 optimal weight: 30.0000 chunk 95 optimal weight: 20.0000 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: 8.9990 chunk 107 optimal weight: 50.0000 overall best weight: 15.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN G 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.061839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.041175 restraints weight = 489487.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.040568 restraints weight = 275807.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.040718 restraints weight = 213201.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.040972 restraints weight = 191818.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.040975 restraints weight = 183328.424| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.008 0.103 16357 Z= 0.444 Angle : 0.856 8.318 23675 Z= 0.499 Chirality : 0.046 0.217 2699 Planarity : 0.006 0.067 1716 Dihedral : 31.216 165.193 5120 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.45 % Favored : 93.44 % Rotamer: Outliers : 0.84 % Allowed : 12.83 % Favored : 86.33 % 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: -1.32 (0.24), residues: 961 helix: -0.08 (0.18), residues: 609 sheet: -0.77 (1.98), residues: 10 loop : -2.27 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 40 TYR 0.017 0.003 TYR A 99 PHE 0.019 0.003 PHE A 78 TRP 0.004 0.001 TRP N 17 HIS 0.010 0.003 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00822 / 0.44 (16341) covalent geometry : angle 0.84998 / 0.50 (23657) hydrogen bonds : bond 0.13495 / 9.13 ( 897) hydrogen bonds : angle 4.73144 / 3.46 ( 2208) metal coordination : bond 0.02527 / 1.65 ( 16) metal coordination : angle 3.84307 / 2.71 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5643.38 seconds wall clock time: 96 minutes 43.90 seconds (5803.90 seconds total)