Starting phenix.real_space_refine on Fri Aug 7 10:30:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9z_64893/08_2026/9v9z_64893.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9z_64893/08_2026/9v9z_64893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v9z_64893/08_2026/9v9z_64893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9z_64893/08_2026/9v9z_64893.map" model { file = "/net/cci-nas-00/data/ceres_data/9v9z_64893/08_2026/9v9z_64893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9z_64893/08_2026/9v9z_64893.cif" } resolution = 3.0 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= 0.003 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 11107 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 263 5.49 5 S 18 5.16 5 C 6828 2.51 5 N 2280 2.21 5 O 2787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 12177 Number of models: 1 Model: "" Number of chains: 13 Chain: "N" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 252 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "A" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 795 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2671 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "J" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2721 Classifications: {'DNA': 132} Link IDs: {'rna3p': 131} Chain: "O" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 39 SG CYS N 27 42.069 66.209 44.223 1.00 81.07 S ATOM 58 SG CYS N 30 41.155 66.871 40.663 1.00 80.06 S ATOM 146 SG CYS N 41 38.729 64.765 42.789 1.00 76.37 S ATOM 166 SG CYS N 44 41.877 63.286 41.707 1.00 80.28 S Time building chain proxies: 2.44, per 1000 atoms: 0.20 Number of scatterers: 12177 At special positions: 0 Unit cell: (126.5, 96.8, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 18 16.00 P 263 15.00 O 2787 8.00 N 2280 7.00 C 6828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 331.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 44 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 30 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 41 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 27 " Number of angles added : 6 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1606 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 12 sheets defined 65.1% alpha, 4.1% beta 127 base pairs and 216 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.575A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.604A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.752A 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 'B' and resid 24 through 29 removed outlier: 3.729A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.897A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.675A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.504A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 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 97 removed outlier: 3.746A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.618A pdb=" N SER D 57 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 4.182A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.513A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.727A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.556A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.930A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.514A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.493A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 4.020A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 34 Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'O' and resid 55 through 59 removed outlier: 3.764A pdb=" N ASP O 58 " --> pdb=" O THR O 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.038A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.658A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.136A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA8, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.918A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.163A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'O' and resid 4 through 7 removed outlier: 6.914A pdb=" N PHE O 4 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU O 69 " --> pdb=" O PHE O 4 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS O 6 " --> pdb=" O LEU O 69 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU O 71 " --> pdb=" O LYS O 6 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL O 70 " --> pdb=" O ARG O 42 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG O 42 " --> pdb=" O VAL O 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'O' and resid 44 through 45 removed outlier: 3.573A pdb=" N PHE O 45 " --> pdb=" O LYS O 48 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 329 hydrogen bonds 658 hydrogen bond angles 0 basepair planarities 127 basepair parallelities 216 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2638 1.34 - 1.45: 3845 1.45 - 1.57: 5886 1.57 - 1.69: 524 1.69 - 1.81: 29 Bond restraints: 12922 Sorted by residual: bond pdb=" C3' DT J 57 " pdb=" C2' DT J 57 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DC I 53 " pdb=" C2' DC I 53 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DG I 33 " pdb=" C2' DG I 33 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DG I 44 " pdb=" C2' DG I 44 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 12917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 17102 1.21 - 2.43: 1268 2.43 - 3.64: 183 3.64 - 4.86: 16 4.86 - 6.07: 5 Bond angle restraints: 18574 Sorted by residual: angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT I 75 " pdb=" C4 DT I 75 " pdb=" O4 DT I 75 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT J 105 " pdb=" C4 DT J 105 " pdb=" O4 DT J 105 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT I 57 " pdb=" C4 DT I 57 " pdb=" O4 DT I 57 " 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 I 127 " pdb=" C4 DT I 127 " pdb=" O4 DT I 127 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 18569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 5922 35.31 - 70.62: 1166 70.62 - 105.93: 16 105.93 - 141.24: 0 141.24 - 176.55: 2 Dihedral angle restraints: 7106 sinusoidal: 4625 harmonic: 2481 Sorted by residual: dihedral pdb=" CA GLU O 34 " pdb=" C GLU O 34 " pdb=" N GLY O 35 " pdb=" CA GLY O 35 " ideal model delta harmonic sigma weight residual -180.00 -159.40 -20.60 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C4' DT J 57 " pdb=" C3' DT J 57 " pdb=" O3' DT J 57 " pdb=" P DT J 58 " ideal model delta sinusoidal sigma weight residual -140.00 36.55 -176.55 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 75.66 144.34 1 3.50e+01 8.16e-04 1.42e+01 ... (remaining 7103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1168 0.029 - 0.058: 642 0.058 - 0.087: 195 0.087 - 0.115: 111 0.115 - 0.144: 8 Chirality restraints: 2124 Sorted by residual: chirality pdb=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE O 3 " pdb=" N ILE O 3 " pdb=" C ILE O 3 " pdb=" CB ILE O 3 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 2121 not shown) Planarity restraints: 1438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 80 " -0.015 2.00e-02 2.50e+03 1.02e-02 2.09e+00 pdb=" CG TYR H 80 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR H 80 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR H 80 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR H 80 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR H 80 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR H 80 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR H 80 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO G 80 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 104 " -0.008 2.00e-02 2.50e+03 1.01e-02 1.79e+00 pdb=" CG PHE E 104 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE E 104 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE E 104 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE E 104 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 104 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE E 104 " -0.000 2.00e-02 2.50e+03 ... (remaining 1435 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 799 2.74 - 3.28: 10710 3.28 - 3.82: 22647 3.82 - 4.36: 26655 4.36 - 4.90: 39909 Nonbonded interactions: 100720 Sorted by model distance: nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.294 3.040 nonbonded pdb=" O ASP O 39 " pdb=" NH1 ARG O 72 " model vdw 2.310 3.120 nonbonded pdb=" OH TYR G 39 " pdb=" OE1 GLU H 68 " model vdw 2.321 3.040 nonbonded pdb=" NE2 GLN O 2 " pdb=" O LYS O 63 " model vdw 2.357 3.120 ... (remaining 100715 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 39 through 133) selection = (chain 'E' and resid 39 through 133) } ncs_group { reference = (chain 'B' and resid 22 through 100) selection = (chain 'F' and resid 22 through 100) } ncs_group { reference = (chain 'C' and resid 14 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 30 through 120) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.240 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 0.039 12926 Z= 0.480 Angle : 0.677 6.452 18580 Z= 0.610 Chirality : 0.041 0.144 2124 Planarity : 0.003 0.037 1438 Dihedral : 26.087 176.551 5500 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 2.72 (0.30), residues: 834 helix: 2.95 (0.23), residues: 537 sheet: -1.29 (1.18), residues: 19 loop : -0.34 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 76 TYR 0.024 0.001 TYR H 80 PHE 0.023 0.001 PHE E 104 TRP 0.003 0.001 TRP N 25 HIS 0.004 0.000 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.48 (12922) covalent geometry : angle 0.67378 / 0.61 (18574) hydrogen bonds : bond 0.11046 / 7.33 ( 725) hydrogen bonds : angle 3.62146 / 2.73 ( 1831) metal coordination : bond 0.00300 / 0.15 ( 4) metal coordination : angle 3.71515 / 2.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: B 63 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7221 (mt-10) REVERT: C 95 LYS cc_start: 0.8656 (tttt) cc_final: 0.8376 (tppt) REVERT: D 59 MET cc_start: 0.8372 (mmm) cc_final: 0.7881 (mmm) REVERT: E 59 GLU cc_start: 0.7817 (pm20) cc_final: 0.7478 (pm20) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.8202 time to fit residues: 120.0009 Evaluate side-chains 113 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 50.0000 chunk 106 optimal weight: 0.4980 chunk 38 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN E 125 GLN G 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.161999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.117469 restraints weight = 16094.606| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.25 r_work: 0.3187 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12926 Z= 0.154 Angle : 0.594 6.314 18580 Z= 0.356 Chirality : 0.044 0.251 2124 Planarity : 0.004 0.037 1438 Dihedral : 29.561 176.356 3805 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.05 % Allowed : 9.00 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.59 (0.29), residues: 834 helix: 2.86 (0.22), residues: 546 sheet: -0.99 (1.18), residues: 19 loop : -0.57 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 129 TYR 0.011 0.001 TYR H 118 PHE 0.016 0.001 PHE E 104 TRP 0.009 0.003 TRP N 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (12922) covalent geometry : angle 0.59133 / 0.36 (18574) hydrogen bonds : bond 0.05583 / 3.65 ( 725) hydrogen bonds : angle 2.75973 / 2.03 ( 1831) metal coordination : bond 0.00270 / 0.13 ( 4) metal coordination : angle 3.11706 / 2.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: B 63 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7618 (mt-10) REVERT: C 95 LYS cc_start: 0.8823 (tttt) cc_final: 0.8492 (tppt) REVERT: D 30 ARG cc_start: 0.5554 (mtt180) cc_final: 0.5329 (mtt180) REVERT: D 68 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8284 (tp30) REVERT: D 102 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7089 (mm-30) REVERT: E 59 GLU cc_start: 0.8332 (pm20) cc_final: 0.8019 (pm20) REVERT: G 36 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7992 (mttt) REVERT: G 95 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.7977 (tmtm) REVERT: H 32 GLU cc_start: 0.6254 (OUTLIER) cc_final: 0.5973 (pm20) outliers start: 22 outliers final: 7 residues processed: 124 average time/residue: 0.7952 time to fit residues: 104.1280 Evaluate side-chains 121 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 32 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 0.0370 chunk 63 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 99 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN D 60 ASN E 125 GLN H 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.157034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111662 restraints weight = 16113.080| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.16 r_work: 0.3059 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12926 Z= 0.185 Angle : 0.636 6.507 18580 Z= 0.369 Chirality : 0.046 0.245 2124 Planarity : 0.005 0.044 1438 Dihedral : 29.970 178.836 3805 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.74 % Allowed : 10.94 % Favored : 85.32 % 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: 2.13 (0.29), residues: 834 helix: 2.56 (0.22), residues: 548 sheet: -2.13 (1.71), residues: 9 loop : -0.91 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 129 TYR 0.015 0.002 TYR G 50 PHE 0.013 0.002 PHE D 62 TRP 0.006 0.002 TRP N 25 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (12922) covalent geometry : angle 0.63289 / 0.37 (18574) hydrogen bonds : bond 0.06772 / 4.51 ( 725) hydrogen bonds : angle 2.83707 / 2.08 ( 1831) metal coordination : bond 0.00373 / 0.19 ( 4) metal coordination : angle 3.73406 / 2.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.199 Fit side-chains REVERT: A 129 ARG cc_start: 0.8113 (tmt170) cc_final: 0.7785 (ttp80) REVERT: B 63 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7860 (mt-10) REVERT: D 30 ARG cc_start: 0.5599 (mtt180) cc_final: 0.5316 (mtt180) REVERT: D 68 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8422 (tp30) REVERT: D 102 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7286 (mm-30) REVERT: E 59 GLU cc_start: 0.8310 (pm20) cc_final: 0.7952 (pm20) REVERT: E 131 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8616 (mtp85) REVERT: G 36 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8010 (mttt) REVERT: G 56 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: G 95 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8005 (tmtm) REVERT: H 32 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.6117 (pm20) outliers start: 27 outliers final: 10 residues processed: 125 average time/residue: 0.7794 time to fit residues: 102.8272 Evaluate side-chains 126 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 32 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 0.3980 chunk 99 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.158096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.113146 restraints weight = 16045.726| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.19 r_work: 0.3079 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12926 Z= 0.149 Angle : 0.602 5.954 18580 Z= 0.351 Chirality : 0.044 0.226 2124 Planarity : 0.004 0.039 1438 Dihedral : 30.015 177.513 3805 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.77 % Allowed : 13.85 % Favored : 83.38 % 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: 2.27 (0.29), residues: 834 helix: 2.74 (0.22), residues: 545 sheet: -2.13 (1.70), residues: 9 loop : -0.98 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 96 TYR 0.012 0.001 TYR H 118 PHE 0.008 0.001 PHE B 61 TRP 0.007 0.002 TRP N 25 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (12922) covalent geometry : angle 0.59909 / 0.35 (18574) hydrogen bonds : bond 0.05892 / 3.92 ( 725) hydrogen bonds : angle 2.76464 / 2.02 ( 1831) metal coordination : bond 0.00298 / 0.15 ( 4) metal coordination : angle 3.15952 / 2.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8142 (tmt170) cc_final: 0.7895 (ttp80) REVERT: B 63 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7821 (mt-10) REVERT: C 91 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: D 30 ARG cc_start: 0.5523 (mtt180) cc_final: 0.5247 (mtt180) REVERT: D 59 MET cc_start: 0.8815 (mmm) cc_final: 0.8402 (mmm) REVERT: D 102 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7228 (mm-30) REVERT: E 59 GLU cc_start: 0.8284 (pm20) cc_final: 0.8016 (pm20) REVERT: E 133 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6217 (mp0) REVERT: G 95 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.7991 (tmtm) REVERT: H 32 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.6094 (pm20) outliers start: 20 outliers final: 11 residues processed: 115 average time/residue: 0.8490 time to fit residues: 103.1975 Evaluate side-chains 122 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 32 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 0.0000 chunk 107 optimal weight: 30.0000 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 0.0970 chunk 3 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 79 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.160015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.115443 restraints weight = 16225.980| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.28 r_work: 0.3154 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12926 Z= 0.128 Angle : 0.563 5.867 18580 Z= 0.333 Chirality : 0.042 0.227 2124 Planarity : 0.003 0.038 1438 Dihedral : 30.042 176.442 3805 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.05 % Allowed : 13.85 % Favored : 83.10 % 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: 2.51 (0.29), residues: 834 helix: 2.92 (0.22), residues: 547 sheet: -2.12 (1.70), residues: 9 loop : -0.88 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 71 TYR 0.012 0.001 TYR F 88 PHE 0.007 0.001 PHE B 61 TRP 0.007 0.001 TRP N 25 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.13 (12922) covalent geometry : angle 0.56084 / 0.33 (18574) hydrogen bonds : bond 0.05043 / 3.36 ( 725) hydrogen bonds : angle 2.63172 / 1.92 ( 1831) metal coordination : bond 0.00262 / 0.13 ( 4) metal coordination : angle 3.08583 / 2.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8172 (tmt170) cc_final: 0.7909 (ttp80) REVERT: C 91 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7455 (mt-10) REVERT: D 30 ARG cc_start: 0.5523 (mtt180) cc_final: 0.5275 (mtt180) REVERT: D 59 MET cc_start: 0.8766 (mmm) cc_final: 0.8367 (mmm) REVERT: D 90 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: D 102 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7047 (mm-30) REVERT: E 59 GLU cc_start: 0.8118 (pm20) cc_final: 0.7866 (pm20) REVERT: G 36 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7929 (mttt) REVERT: H 32 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5985 (pm20) outliers start: 22 outliers final: 10 residues processed: 118 average time/residue: 0.8523 time to fit residues: 106.1170 Evaluate side-chains 121 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 0.2980 chunk 19 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 75 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 60 ASN E 125 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.154916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.105580 restraints weight = 15998.176| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.18 r_work: 0.3045 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12926 Z= 0.218 Angle : 0.682 6.598 18580 Z= 0.386 Chirality : 0.049 0.253 2124 Planarity : 0.006 0.045 1438 Dihedral : 30.197 179.016 3805 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.60 % Allowed : 15.10 % Favored : 81.30 % 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: 1.71 (0.29), residues: 834 helix: 2.31 (0.22), residues: 548 sheet: -2.69 (1.47), residues: 9 loop : -1.21 (0.32), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 53 TYR 0.015 0.002 TYR H 118 PHE 0.014 0.002 PHE D 62 TRP 0.008 0.002 TRP N 25 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.22 (12922) covalent geometry : angle 0.67870 / 0.39 (18574) hydrogen bonds : bond 0.07524 / 5.02 ( 725) hydrogen bonds : angle 2.94729 / 2.15 ( 1831) metal coordination : bond 0.00403 / 0.20 ( 4) metal coordination : angle 3.78143 / 2.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.316 Fit side-chains REVERT: C 91 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: D 30 ARG cc_start: 0.5652 (mtt180) cc_final: 0.5382 (mtt180) REVERT: D 68 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8413 (tp30) REVERT: D 73 GLU cc_start: 0.8759 (tp30) cc_final: 0.8495 (tp30) REVERT: D 102 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7326 (mm-30) REVERT: E 59 GLU cc_start: 0.8148 (pm20) cc_final: 0.7842 (pm20) REVERT: E 60 LEU cc_start: 0.8954 (mt) cc_final: 0.8750 (mt) REVERT: E 133 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6252 (mp0) REVERT: G 36 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8107 (mttt) REVERT: G 56 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: G 95 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.7996 (tmtm) REVERT: H 32 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.6065 (pm20) outliers start: 26 outliers final: 10 residues processed: 123 average time/residue: 0.8055 time to fit residues: 104.5550 Evaluate side-chains 127 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 86 optimal weight: 30.0000 chunk 35 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 17 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 60 ASN H 44 GLN H 60 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.156523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107437 restraints weight = 15953.023| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.17 r_work: 0.3080 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12926 Z= 0.146 Angle : 0.618 5.847 18580 Z= 0.356 Chirality : 0.046 0.227 2124 Planarity : 0.004 0.047 1438 Dihedral : 30.198 178.779 3805 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.19 % Allowed : 15.37 % Favored : 81.44 % 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: 1.96 (0.29), residues: 834 helix: 2.51 (0.22), residues: 548 sheet: -2.79 (1.43), residues: 9 loop : -1.15 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 53 TYR 0.015 0.001 TYR F 88 PHE 0.008 0.001 PHE B 61 TRP 0.009 0.002 TRP N 25 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (12922) covalent geometry : angle 0.61502 / 0.36 (18574) hydrogen bonds : bond 0.06128 / 4.09 ( 725) hydrogen bonds : angle 2.81935 / 2.07 ( 1831) metal coordination : bond 0.00383 / 0.20 ( 4) metal coordination : angle 3.44786 / 2.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8093 (tmt170) cc_final: 0.7858 (ttp80) REVERT: C 91 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: D 30 ARG cc_start: 0.5639 (mtt180) cc_final: 0.5347 (mtt180) REVERT: D 68 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8421 (tp30) REVERT: D 73 GLU cc_start: 0.8722 (tp30) cc_final: 0.8467 (tp30) REVERT: D 102 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7224 (mm-30) REVERT: E 59 GLU cc_start: 0.8140 (pm20) cc_final: 0.7803 (pm20) REVERT: E 131 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8384 (mtp85) REVERT: G 36 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7933 (mttt) REVERT: G 95 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.7971 (tmtm) REVERT: H 32 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.6064 (pm20) outliers start: 23 outliers final: 10 residues processed: 119 average time/residue: 0.8694 time to fit residues: 109.0050 Evaluate side-chains 125 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 32 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 30.0000 chunk 66 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 88 optimal weight: 50.0000 chunk 104 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 46 HIS D 60 ASN E 125 GLN G 89 ASN O 31 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.152878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.103394 restraints weight = 15911.907| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.16 r_work: 0.3010 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 12926 Z= 0.280 Angle : 0.751 6.983 18580 Z= 0.418 Chirality : 0.053 0.269 2124 Planarity : 0.007 0.080 1438 Dihedral : 30.338 177.720 3805 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.19 % Allowed : 16.07 % Favored : 80.75 % 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: 1.16 (0.28), residues: 834 helix: 1.90 (0.21), residues: 547 sheet: -2.45 (1.09), residues: 19 loop : -1.43 (0.32), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 63 TYR 0.019 0.003 TYR H 118 PHE 0.014 0.003 PHE D 62 TRP 0.010 0.003 TRP N 25 HIS 0.007 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.28 (12922) covalent geometry : angle 0.74686 / 0.42 (18574) hydrogen bonds : bond 0.08483 / 5.65 ( 725) hydrogen bonds : angle 3.05961 / 2.23 ( 1831) metal coordination : bond 0.00602 / 0.30 ( 4) metal coordination : angle 4.35029 / 3.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.302 Fit side-chains REVERT: B 29 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9053 (mm) REVERT: B 53 GLU cc_start: 0.8010 (tp30) cc_final: 0.7789 (tp30) REVERT: C 72 ASP cc_start: 0.8139 (t0) cc_final: 0.7673 (t0) REVERT: C 91 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: D 30 ARG cc_start: 0.5663 (mtt180) cc_final: 0.5369 (mtt180) REVERT: D 73 GLU cc_start: 0.8733 (tp30) cc_final: 0.8501 (tp30) REVERT: D 102 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7385 (mm-30) REVERT: E 59 GLU cc_start: 0.8207 (pm20) cc_final: 0.7890 (pm20) REVERT: E 131 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8128 (mtp180) REVERT: E 133 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6315 (mp0) REVERT: G 36 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8075 (mttt) REVERT: H 32 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.6017 (pm20) REVERT: H 39 TYR cc_start: 0.8472 (t80) cc_final: 0.8263 (t80) outliers start: 23 outliers final: 11 residues processed: 125 average time/residue: 0.8776 time to fit residues: 115.6865 Evaluate side-chains 127 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 0.0060 chunk 9 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 99 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 60 ASN E 125 GLN H 44 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.156044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.107236 restraints weight = 16039.809| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.17 r_work: 0.3065 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12926 Z= 0.151 Angle : 0.637 7.068 18580 Z= 0.363 Chirality : 0.046 0.241 2124 Planarity : 0.005 0.048 1438 Dihedral : 30.293 179.978 3805 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.63 % Allowed : 17.17 % Favored : 80.19 % 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: 1.78 (0.29), residues: 834 helix: 2.43 (0.22), residues: 545 sheet: -2.09 (1.13), residues: 19 loop : -1.29 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 53 TYR 0.013 0.002 TYR H 118 PHE 0.008 0.001 PHE B 61 TRP 0.010 0.002 TRP N 25 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (12922) covalent geometry : angle 0.63367 / 0.36 (18574) hydrogen bonds : bond 0.06192 / 4.14 ( 725) hydrogen bonds : angle 2.83871 / 2.08 ( 1831) metal coordination : bond 0.00351 / 0.18 ( 4) metal coordination : angle 3.85878 / 2.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.383 Fit side-chains REVERT: A 129 ARG cc_start: 0.8100 (tmt170) cc_final: 0.7881 (ttp80) REVERT: C 91 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: D 30 ARG cc_start: 0.5721 (mtt180) cc_final: 0.5445 (mtt180) REVERT: D 73 GLU cc_start: 0.8737 (tp30) cc_final: 0.8512 (tp30) REVERT: D 90 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: D 102 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7264 (mm-30) REVERT: E 59 GLU cc_start: 0.8214 (pm20) cc_final: 0.7904 (pm20) REVERT: G 95 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8003 (tmtm) REVERT: H 32 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.6061 (pm20) REVERT: H 39 TYR cc_start: 0.8420 (t80) cc_final: 0.8209 (t80) outliers start: 19 outliers final: 9 residues processed: 118 average time/residue: 0.9576 time to fit residues: 119.2674 Evaluate side-chains 123 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 89 optimal weight: 40.0000 chunk 14 optimal weight: 0.0470 chunk 64 optimal weight: 4.9990 chunk 85 optimal weight: 30.0000 chunk 37 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 77 optimal weight: 30.0000 chunk 95 optimal weight: 20.0000 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 60 ASN E 125 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.153833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.104601 restraints weight = 15943.275| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.16 r_work: 0.3032 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12926 Z= 0.235 Angle : 0.698 7.430 18580 Z= 0.392 Chirality : 0.050 0.268 2124 Planarity : 0.006 0.066 1438 Dihedral : 30.336 178.589 3805 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.49 % Allowed : 17.31 % Favored : 80.19 % 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: 1.43 (0.29), residues: 834 helix: 2.17 (0.22), residues: 545 sheet: -2.40 (1.10), residues: 19 loop : -1.43 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 71 TYR 0.016 0.002 TYR H 118 PHE 0.011 0.002 PHE A 104 TRP 0.011 0.003 TRP N 25 HIS 0.006 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.24 (12922) covalent geometry : angle 0.69403 / 0.39 (18574) hydrogen bonds : bond 0.07534 / 5.03 ( 725) hydrogen bonds : angle 2.94829 / 2.16 ( 1831) metal coordination : bond 0.00441 / 0.22 ( 4) metal coordination : angle 4.26359 / 3.00 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.369 Fit side-chains REVERT: C 91 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7489 (mt-10) REVERT: D 30 ARG cc_start: 0.5666 (mtt180) cc_final: 0.5349 (mtt180) REVERT: D 73 GLU cc_start: 0.8751 (tp30) cc_final: 0.8522 (tp30) REVERT: D 102 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7328 (mm-30) REVERT: E 59 GLU cc_start: 0.8239 (pm20) cc_final: 0.7906 (pm20) REVERT: E 131 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8286 (mtp85) REVERT: G 36 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8163 (mttt) REVERT: G 95 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.7997 (tmtm) REVERT: H 32 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.6111 (pm20) REVERT: H 39 TYR cc_start: 0.8452 (t80) cc_final: 0.8248 (t80) outliers start: 18 outliers final: 10 residues processed: 118 average time/residue: 0.9280 time to fit residues: 115.5823 Evaluate side-chains 126 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 89 optimal weight: 40.0000 chunk 59 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 60 ASN E 125 GLN H 44 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.156047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.107305 restraints weight = 15917.234| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.15 r_work: 0.3070 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 12926 Z= 0.143 Angle : 0.641 7.390 18580 Z= 0.366 Chirality : 0.047 0.234 2124 Planarity : 0.004 0.052 1438 Dihedral : 30.300 178.992 3805 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.35 % Allowed : 17.59 % Favored : 80.06 % 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: 1.83 (0.29), residues: 834 helix: 2.50 (0.22), residues: 545 sheet: -2.30 (1.14), residues: 19 loop : -1.32 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 71 TYR 0.021 0.002 TYR F 88 PHE 0.009 0.001 PHE B 61 TRP 0.011 0.002 TRP N 25 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (12922) covalent geometry : angle 0.63740 / 0.37 (18574) hydrogen bonds : bond 0.06025 / 4.02 ( 725) hydrogen bonds : angle 2.88119 / 2.11 ( 1831) metal coordination : bond 0.00414 / 0.21 ( 4) metal coordination : angle 3.91675 / 2.81 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4135.83 seconds wall clock time: 70 minutes 53.45 seconds (4253.45 seconds total)