Starting phenix.real_space_refine on Fri Jul 3 03:47:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ox0_17251/07_2026/8ox0_17251.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ox0_17251/07_2026/8ox0_17251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ox0_17251/07_2026/8ox0_17251.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ox0_17251/07_2026/8ox0_17251.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ox0_17251/07_2026/8ox0_17251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ox0_17251/07_2026/8ox0_17251.map" } resolution = 2.52 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 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: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 14 5.16 5 C 6773 2.51 5 N 2308 2.21 5 O 2886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 12271 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 847 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 774 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 847 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 774 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "J" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 3064 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "I" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2881 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "J" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.81, per 1000 atoms: 0.23 Number of scatterers: 12271 At special positions: 0 Unit cell: (92.71, 118.99, 125.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 290 15.00 O 2886 8.00 N 2308 7.00 C 6773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 372.9 milliseconds 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1470 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 70.8% alpha, 3.0% beta 143 base pairs and 278 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.712A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.519A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.490A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.530A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.524A pdb=" N SER D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.624A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.009A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.852A 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 49 through 76 removed outlier: 3.802A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.512A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) 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 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 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 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.899A 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 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.567A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.089A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.657A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.836A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.113A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 409 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 355 hydrogen bonds 706 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 278 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1694 1.33 - 1.45: 4763 1.45 - 1.57: 5960 1.57 - 1.69: 578 1.69 - 1.81: 24 Bond restraints: 13019 Sorted by residual: bond pdb=" C ARG F 95 " pdb=" O ARG F 95 " ideal model delta sigma weight residual 1.233 1.203 0.030 1.15e-02 7.56e+03 7.02e+00 bond pdb=" CA GLU E 105 " pdb=" C GLU E 105 " ideal model delta sigma weight residual 1.524 1.557 -0.033 1.27e-02 6.20e+03 6.83e+00 bond pdb=" CA LYS F 31 " pdb=" C LYS F 31 " ideal model delta sigma weight residual 1.520 1.550 -0.029 1.23e-02 6.61e+03 5.75e+00 bond pdb=" C PRO G 26 " pdb=" O PRO G 26 " ideal model delta sigma weight residual 1.235 1.217 0.018 7.90e-03 1.60e+04 4.96e+00 bond pdb=" CA GLU A 105 " pdb=" C GLU A 105 " ideal model delta sigma weight residual 1.524 1.551 -0.028 1.27e-02 6.20e+03 4.74e+00 ... (remaining 13014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 16569 1.30 - 2.60: 1917 2.60 - 3.89: 293 3.89 - 5.19: 19 5.19 - 6.49: 6 Bond angle restraints: 18804 Sorted by residual: angle pdb=" O5' DG J -35 " pdb=" C5' DG J -35 " pdb=" C4' DG J -35 " ideal model delta sigma weight residual 109.40 113.29 -3.89 8.00e-01 1.56e+00 2.36e+01 angle pdb=" O5' DA J -24 " pdb=" C5' DA J -24 " pdb=" C4' DA J -24 " ideal model delta sigma weight residual 109.40 112.18 -2.78 8.00e-01 1.56e+00 1.21e+01 angle pdb=" C4' DG J 68 " pdb=" O4' DG J 68 " pdb=" C1' DG J 68 " ideal model delta sigma weight residual 110.10 106.64 3.46 1.00e+00 1.00e+00 1.19e+01 angle pdb=" C3' DA I 14 " pdb=" C2' DA I 14 " pdb=" C1' DA I 14 " ideal model delta sigma weight residual 102.50 98.52 3.98 1.20e+00 6.94e-01 1.10e+01 angle pdb=" O5' DG J 57 " pdb=" C5' DG J 57 " pdb=" C4' DG J 57 " ideal model delta sigma weight residual 109.40 111.99 -2.59 8.00e-01 1.56e+00 1.05e+01 ... (remaining 18799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 5747 35.46 - 70.92: 1401 70.92 - 106.38: 4 106.38 - 141.83: 0 141.83 - 177.29: 3 Dihedral angle restraints: 7155 sinusoidal: 4876 harmonic: 2279 Sorted by residual: dihedral pdb=" C4' DT I -18 " pdb=" C3' DT I -18 " pdb=" O3' DT I -18 " pdb=" P DA I -17 " ideal model delta sinusoidal sigma weight residual 220.00 42.71 177.29 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA J -71 " pdb=" C3' DA J -71 " pdb=" O3' DA J -71 " pdb=" P DT J -70 " ideal model delta sinusoidal sigma weight residual 220.00 43.55 176.45 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC I 22 " pdb=" C3' DC I 22 " pdb=" O3' DC I 22 " pdb=" P DC I 23 " ideal model delta sinusoidal sigma weight residual 220.00 64.11 155.89 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 7152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1528 0.062 - 0.124: 527 0.124 - 0.187: 65 0.187 - 0.249: 6 0.249 - 0.311: 3 Chirality restraints: 2129 Sorted by residual: chirality pdb=" C3' DC I 22 " pdb=" C4' DC I 22 " pdb=" O3' DC I 22 " pdb=" C2' DC I 22 " both_signs ideal model delta sigma weight residual False -2.73 -2.42 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C3' DA J -71 " pdb=" C4' DA J -71 " pdb=" O3' DA J -71 " pdb=" C2' DA J -71 " both_signs ideal model delta sigma weight residual False -2.73 -2.43 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C3' DT I -18 " pdb=" C4' DT I -18 " pdb=" O3' DT I -18 " pdb=" C2' DT I -18 " both_signs ideal model delta sigma weight residual False -2.73 -2.45 -0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 2126 not shown) Planarity restraints: 1375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J -35 " -0.034 2.00e-02 2.50e+03 1.43e-02 6.12e+00 pdb=" N9 DG J -35 " 0.032 2.00e-02 2.50e+03 pdb=" C8 DG J -35 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG J -35 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG J -35 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG J -35 " -0.005 2.00e-02 2.50e+03 pdb=" O6 DG J -35 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DG J -35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG J -35 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG J -35 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG J -35 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG J -35 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 15 " -0.033 2.00e-02 2.50e+03 1.38e-02 5.74e+00 pdb=" N9 DG J 15 " 0.028 2.00e-02 2.50e+03 pdb=" C8 DG J 15 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG J 15 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DG J 15 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DG J 15 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG J 15 " -0.015 2.00e-02 2.50e+03 pdb=" N1 DG J 15 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG J 15 " 0.007 2.00e-02 2.50e+03 pdb=" N2 DG J 15 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG J 15 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG J 15 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 64 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C ASN B 64 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN B 64 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 65 " -0.013 2.00e-02 2.50e+03 ... (remaining 1372 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 424 2.70 - 3.25: 10392 3.25 - 3.80: 22837 3.80 - 4.35: 29973 4.35 - 4.90: 41615 Nonbonded interactions: 105241 Sorted by model distance: nonbonded pdb=" O ARG F 23 " pdb=" OD1 ASP F 24 " model vdw 2.156 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.316 3.040 nonbonded pdb=" NH2 ARG B 35 " pdb=" OP2 DG J 8 " model vdw 2.336 3.120 nonbonded pdb=" N2 DG J 21 " pdb=" O2 DC I -21 " model vdw 2.340 2.496 ... (remaining 105236 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 37 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 17 through 102) 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 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.700 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.007 0.035 13019 Z= 0.440 Angle : 0.866 6.490 18804 Z= 0.616 Chirality : 0.060 0.311 2129 Planarity : 0.005 0.042 1375 Dihedral : 27.178 177.293 5685 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 1.78 (0.28), residues: 771 helix: 1.92 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.55 (0.32), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 42 TYR 0.018 0.004 TYR B 51 PHE 0.019 0.004 PHE H 67 HIS 0.006 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.44 (13019) covalent geometry : angle 0.86566 / 0.62 (18804) hydrogen bonds : bond 0.12714 / 8.37 ( 764) hydrogen bonds : angle 3.90005 / 2.82 ( 1909) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8164 (ttt180) cc_final: 0.7737 (ttp-110) REVERT: A 64 LYS cc_start: 0.7812 (mttt) cc_final: 0.7605 (mttp) REVERT: B 91 LYS cc_start: 0.7694 (tttp) cc_final: 0.7174 (ttpt) REVERT: C 90 ASP cc_start: 0.7168 (t0) cc_final: 0.6927 (t70) REVERT: C 91 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7506 (mp0) REVERT: D 48 ASP cc_start: 0.8654 (m-30) cc_final: 0.8277 (OUTLIER) REVERT: D 96 ARG cc_start: 0.7629 (mtm180) cc_final: 0.7230 (mtt90) REVERT: E 68 GLN cc_start: 0.7502 (tt0) cc_final: 0.7122 (tt0) REVERT: F 93 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7141 (mp10) REVERT: G 15 LYS cc_start: 0.7822 (mtmm) cc_final: 0.7282 (mtpt) REVERT: G 73 ASN cc_start: 0.7834 (m110) cc_final: 0.7588 (m110) REVERT: G 75 LYS cc_start: 0.8046 (mttt) cc_final: 0.7783 (mtpp) REVERT: G 90 ASP cc_start: 0.7528 (t0) cc_final: 0.7269 (t0) REVERT: G 95 LYS cc_start: 0.8030 (tttt) cc_final: 0.7660 (tppt) REVERT: G 99 ARG cc_start: 0.7726 (mmm160) cc_final: 0.7242 (mpt180) REVERT: H 31 LYS cc_start: 0.8126 (mtpp) cc_final: 0.7752 (mttp) REVERT: H 105 LYS cc_start: 0.7467 (ttpt) cc_final: 0.7063 (mmtm) outliers start: 0 outliers final: 1 residues processed: 148 average time/residue: 0.9955 time to fit residues: 155.0118 Evaluate side-chains 129 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 24 GLN H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.090409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.071506 restraints weight = 21984.097| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.26 r_work: 0.3023 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13019 Z= 0.161 Angle : 0.698 7.235 18804 Z= 0.401 Chirality : 0.052 0.229 2129 Planarity : 0.004 0.042 1375 Dihedral : 31.014 179.102 4095 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.37 % Allowed : 9.01 % Favored : 89.62 % 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: 2.35 (0.29), residues: 771 helix: 2.34 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.48 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 30 TYR 0.011 0.002 TYR H 37 PHE 0.011 0.002 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.16 (13019) covalent geometry : angle 0.69835 / 0.40 (18804) hydrogen bonds : bond 0.06644 / 4.34 ( 764) hydrogen bonds : angle 3.29254 / 2.39 ( 1909) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9021 (mttt) cc_final: 0.8721 (mttp) REVERT: A 115 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8830 (mtpt) REVERT: B 91 LYS cc_start: 0.8748 (tttp) cc_final: 0.8267 (ttpt) REVERT: E 59 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8566 (pm20) REVERT: E 64 LYS cc_start: 0.8565 (mtmm) cc_final: 0.8286 (mtmm) REVERT: E 68 GLN cc_start: 0.8684 (tt0) cc_final: 0.8196 (tt0) REVERT: E 133 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: G 15 LYS cc_start: 0.8732 (mtmm) cc_final: 0.8155 (mtpt) REVERT: G 73 ASN cc_start: 0.8515 (m110) cc_final: 0.8235 (m110) REVERT: G 95 LYS cc_start: 0.9018 (tttt) cc_final: 0.8685 (tppt) REVERT: H 31 LYS cc_start: 0.8571 (mtpp) cc_final: 0.8300 (mttp) REVERT: H 105 LYS cc_start: 0.8470 (ttpt) cc_final: 0.8110 (mmmm) REVERT: H 113 LYS cc_start: 0.8766 (ttmm) cc_final: 0.8508 (ttmt) outliers start: 9 outliers final: 4 residues processed: 137 average time/residue: 0.9867 time to fit residues: 142.3136 Evaluate side-chains 135 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 74 optimal weight: 30.0000 chunk 16 optimal weight: 3.9990 chunk 84 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 chunk 75 optimal weight: 30.0000 chunk 41 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.090071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.071164 restraints weight = 22254.261| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.27 r_work: 0.3012 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13019 Z= 0.199 Angle : 0.689 7.377 18804 Z= 0.396 Chirality : 0.051 0.228 2129 Planarity : 0.004 0.038 1375 Dihedral : 31.089 177.829 4095 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.83 % Allowed : 10.84 % Favored : 87.33 % 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: 2.42 (0.29), residues: 771 helix: 2.42 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.53 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 30 TYR 0.010 0.002 TYR E 54 PHE 0.009 0.002 PHE A 67 HIS 0.002 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.20 (13019) covalent geometry : angle 0.68881 / 0.40 (18804) hydrogen bonds : bond 0.06514 / 4.26 ( 764) hydrogen bonds : angle 3.14383 / 2.28 ( 1909) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9032 (mttt) cc_final: 0.8727 (mttp) REVERT: B 91 LYS cc_start: 0.8794 (tttp) cc_final: 0.8317 (ttpt) REVERT: E 64 LYS cc_start: 0.8618 (mtmm) cc_final: 0.8345 (mtmm) REVERT: E 68 GLN cc_start: 0.8723 (tt0) cc_final: 0.8315 (tt0) REVERT: E 133 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7992 (mt-10) REVERT: F 93 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7101 (mp10) REVERT: G 15 LYS cc_start: 0.8720 (mtmm) cc_final: 0.8160 (mtpt) REVERT: G 73 ASN cc_start: 0.8472 (m110) cc_final: 0.8174 (m110) REVERT: G 95 LYS cc_start: 0.9024 (tttt) cc_final: 0.8690 (tppt) REVERT: H 31 LYS cc_start: 0.8588 (mtpp) cc_final: 0.8314 (mttp) REVERT: H 105 LYS cc_start: 0.8526 (ttpt) cc_final: 0.8135 (mmtm) outliers start: 12 outliers final: 6 residues processed: 128 average time/residue: 0.9620 time to fit residues: 129.9608 Evaluate side-chains 132 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 32 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.0970 chunk 62 optimal weight: 4.9990 chunk 89 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.090513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.071626 restraints weight = 22195.450| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.26 r_work: 0.3025 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13019 Z= 0.155 Angle : 0.659 7.350 18804 Z= 0.384 Chirality : 0.049 0.235 2129 Planarity : 0.004 0.037 1375 Dihedral : 31.083 178.079 4095 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.37 % Allowed : 11.45 % Favored : 87.18 % 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: 2.58 (0.29), residues: 771 helix: 2.55 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.51 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 30 TYR 0.010 0.001 TYR H 37 PHE 0.009 0.001 PHE A 67 HIS 0.002 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 (13019) covalent geometry : angle 0.65949 / 0.38 (18804) hydrogen bonds : bond 0.06113 / 4.00 ( 764) hydrogen bonds : angle 3.12465 / 2.27 ( 1909) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9022 (mttt) cc_final: 0.8718 (mttp) REVERT: B 91 LYS cc_start: 0.8783 (tttp) cc_final: 0.8321 (ttpt) REVERT: E 64 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8323 (mtmm) REVERT: E 68 GLN cc_start: 0.8693 (tt0) cc_final: 0.8235 (tt0) REVERT: E 133 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7982 (mt-10) REVERT: F 93 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7004 (mp10) REVERT: G 15 LYS cc_start: 0.8711 (mtmm) cc_final: 0.8158 (mtpt) REVERT: G 73 ASN cc_start: 0.8451 (m110) cc_final: 0.8162 (m110) REVERT: G 95 LYS cc_start: 0.9011 (tttt) cc_final: 0.8668 (tppt) REVERT: H 31 LYS cc_start: 0.8593 (mtpp) cc_final: 0.8318 (mttp) REVERT: H 105 LYS cc_start: 0.8494 (ttpt) cc_final: 0.8117 (mmtm) outliers start: 9 outliers final: 7 residues processed: 128 average time/residue: 0.9531 time to fit residues: 128.6756 Evaluate side-chains 134 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 0.0060 chunk 90 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 88 optimal weight: 30.0000 chunk 51 optimal weight: 8.9990 overall best weight: 5.8006 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.088556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.069631 restraints weight = 22357.104| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.29 r_work: 0.2980 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 13019 Z= 0.290 Angle : 0.748 7.936 18804 Z= 0.415 Chirality : 0.054 0.242 2129 Planarity : 0.005 0.043 1375 Dihedral : 31.516 177.023 4095 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.83 % Allowed : 11.45 % Favored : 86.72 % 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: 2.32 (0.29), residues: 771 helix: 2.38 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.67 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 30 TYR 0.015 0.002 TYR E 54 PHE 0.015 0.002 PHE A 104 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.29 (13019) covalent geometry : angle 0.74767 / 0.42 (18804) hydrogen bonds : bond 0.07180 / 4.77 ( 764) hydrogen bonds : angle 3.10849 / 2.26 ( 1909) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8518 (pm20) cc_final: 0.8298 (pm20) REVERT: A 64 LYS cc_start: 0.9048 (mttt) cc_final: 0.8738 (mttp) REVERT: B 91 LYS cc_start: 0.8791 (tttp) cc_final: 0.8315 (ttpt) REVERT: E 133 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7961 (mt-10) REVERT: F 93 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7157 (mp10) REVERT: G 15 LYS cc_start: 0.8722 (mtmm) cc_final: 0.8169 (mtpt) REVERT: G 95 LYS cc_start: 0.9018 (tttt) cc_final: 0.8691 (tppt) REVERT: H 31 LYS cc_start: 0.8640 (mtpp) cc_final: 0.8366 (mttp) REVERT: H 105 LYS cc_start: 0.8581 (ttpt) cc_final: 0.8144 (mmtm) outliers start: 12 outliers final: 6 residues processed: 125 average time/residue: 0.9545 time to fit residues: 126.0297 Evaluate side-chains 128 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 67 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 44 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.089370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.070488 restraints weight = 22220.538| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.26 r_work: 0.2996 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13019 Z= 0.173 Angle : 0.706 7.744 18804 Z= 0.397 Chirality : 0.052 0.237 2129 Planarity : 0.004 0.038 1375 Dihedral : 31.516 177.553 4095 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.83 % Allowed : 11.60 % Favored : 86.56 % 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: 2.42 (0.29), residues: 771 helix: 2.46 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.64 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 30 TYR 0.013 0.002 TYR H 37 PHE 0.011 0.002 PHE A 104 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (13019) covalent geometry : angle 0.70580 / 0.40 (18804) hydrogen bonds : bond 0.06522 / 4.33 ( 764) hydrogen bonds : angle 3.09132 / 2.25 ( 1909) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9021 (mttt) cc_final: 0.8716 (mttm) REVERT: B 91 LYS cc_start: 0.8766 (tttp) cc_final: 0.8490 (ttmm) REVERT: E 68 GLN cc_start: 0.8713 (tt0) cc_final: 0.8243 (tt0) REVERT: E 133 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: F 93 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7242 (mp10) REVERT: G 15 LYS cc_start: 0.8703 (mtmm) cc_final: 0.8175 (mtpt) REVERT: G 90 ASP cc_start: 0.8345 (t70) cc_final: 0.7905 (t0) REVERT: G 95 LYS cc_start: 0.9001 (tttt) cc_final: 0.8669 (tppt) REVERT: H 31 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8348 (mttp) REVERT: H 105 LYS cc_start: 0.8535 (ttpt) cc_final: 0.8093 (mmtm) outliers start: 12 outliers final: 8 residues processed: 128 average time/residue: 0.9454 time to fit residues: 127.7696 Evaluate side-chains 133 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.089168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.070268 restraints weight = 22086.644| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.27 r_work: 0.2996 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13019 Z= 0.228 Angle : 0.711 7.767 18804 Z= 0.398 Chirality : 0.052 0.249 2129 Planarity : 0.004 0.039 1375 Dihedral : 31.521 177.400 4095 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.83 % Allowed : 11.76 % Favored : 86.41 % 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: 2.42 (0.29), residues: 771 helix: 2.46 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.66 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 30 TYR 0.012 0.002 TYR E 54 PHE 0.010 0.002 PHE A 104 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.23 (13019) covalent geometry : angle 0.71069 / 0.40 (18804) hydrogen bonds : bond 0.06544 / 4.34 ( 764) hydrogen bonds : angle 3.04387 / 2.21 ( 1909) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9026 (mttt) cc_final: 0.8722 (mttm) REVERT: B 91 LYS cc_start: 0.8775 (tttp) cc_final: 0.8308 (ttpt) REVERT: E 133 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: F 93 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7423 (mp10) REVERT: G 15 LYS cc_start: 0.8719 (mtmm) cc_final: 0.8190 (mtpt) REVERT: G 90 ASP cc_start: 0.8363 (t70) cc_final: 0.7944 (t0) REVERT: G 95 LYS cc_start: 0.9017 (tttt) cc_final: 0.8672 (tppt) REVERT: H 31 LYS cc_start: 0.8624 (mtpp) cc_final: 0.8354 (mttp) REVERT: H 105 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8124 (mmtm) outliers start: 12 outliers final: 8 residues processed: 127 average time/residue: 0.9451 time to fit residues: 126.7651 Evaluate side-chains 130 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 93 optimal weight: 20.0000 chunk 74 optimal weight: 40.0000 chunk 96 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.089574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.070716 restraints weight = 22136.219| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.25 r_work: 0.3006 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13019 Z= 0.166 Angle : 0.692 7.631 18804 Z= 0.391 Chirality : 0.051 0.241 2129 Planarity : 0.004 0.038 1375 Dihedral : 31.514 177.622 4095 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.68 % Allowed : 11.45 % Favored : 86.87 % 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: 2.48 (0.29), residues: 771 helix: 2.51 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.64 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 30 TYR 0.011 0.002 TYR H 37 PHE 0.010 0.002 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.17 (13019) covalent geometry : angle 0.69163 / 0.39 (18804) hydrogen bonds : bond 0.06245 / 4.14 ( 764) hydrogen bonds : angle 3.04314 / 2.21 ( 1909) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.353 Fit side-chains REVERT: A 64 LYS cc_start: 0.9019 (mttt) cc_final: 0.8720 (mttp) REVERT: B 91 LYS cc_start: 0.8769 (tttp) cc_final: 0.8494 (ttmm) REVERT: E 68 GLN cc_start: 0.8709 (tt0) cc_final: 0.8245 (tt0) REVERT: E 133 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: F 93 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7426 (mp10) REVERT: G 15 LYS cc_start: 0.8709 (mtmm) cc_final: 0.8185 (mtpt) REVERT: G 90 ASP cc_start: 0.8343 (t70) cc_final: 0.7990 (t0) REVERT: G 95 LYS cc_start: 0.9006 (tttt) cc_final: 0.8671 (tppt) REVERT: H 31 LYS cc_start: 0.8618 (mtpp) cc_final: 0.8346 (mttp) REVERT: H 105 LYS cc_start: 0.8548 (ttpt) cc_final: 0.8109 (mmtm) outliers start: 11 outliers final: 8 residues processed: 126 average time/residue: 0.9429 time to fit residues: 125.4316 Evaluate side-chains 133 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 75 optimal weight: 30.0000 chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 82 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.090070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.071162 restraints weight = 22232.957| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.27 r_work: 0.3013 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 13019 Z= 0.141 Angle : 0.686 13.392 18804 Z= 0.389 Chirality : 0.050 0.242 2129 Planarity : 0.004 0.039 1375 Dihedral : 31.487 177.917 4095 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.14 % Allowed : 11.30 % Favored : 86.56 % 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: 2.57 (0.29), residues: 771 helix: 2.58 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.60 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 30 TYR 0.011 0.001 TYR H 37 PHE 0.010 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.14 (13019) covalent geometry : angle 0.68610 / 0.39 (18804) hydrogen bonds : bond 0.05903 / 3.91 ( 764) hydrogen bonds : angle 3.02348 / 2.20 ( 1909) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.350 Fit side-chains REVERT: A 64 LYS cc_start: 0.9009 (mttt) cc_final: 0.8708 (mttp) REVERT: B 91 LYS cc_start: 0.8757 (tttp) cc_final: 0.8482 (ttmm) REVERT: E 68 GLN cc_start: 0.8680 (tt0) cc_final: 0.8214 (tt0) REVERT: E 133 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7905 (mt-10) REVERT: F 93 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7155 (mp10) REVERT: G 15 LYS cc_start: 0.8699 (mtmm) cc_final: 0.8176 (mtpt) REVERT: G 95 LYS cc_start: 0.9007 (tttt) cc_final: 0.8664 (tppt) REVERT: H 31 LYS cc_start: 0.8637 (mtpp) cc_final: 0.8340 (mttp) REVERT: H 105 LYS cc_start: 0.8525 (ttpt) cc_final: 0.8090 (mmtm) outliers start: 14 outliers final: 7 residues processed: 129 average time/residue: 0.9576 time to fit residues: 130.4202 Evaluate side-chains 132 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.090041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.071107 restraints weight = 22365.958| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.27 r_work: 0.3014 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13019 Z= 0.156 Angle : 0.672 7.437 18804 Z= 0.382 Chirality : 0.050 0.246 2129 Planarity : 0.004 0.039 1375 Dihedral : 31.474 177.866 4095 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.37 % Allowed : 12.06 % Favored : 86.56 % 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: 2.61 (0.29), residues: 771 helix: 2.61 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.59 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 30 TYR 0.011 0.001 TYR H 37 PHE 0.010 0.001 PHE A 78 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.16 (13019) covalent geometry : angle 0.67243 / 0.38 (18804) hydrogen bonds : bond 0.05877 / 3.89 ( 764) hydrogen bonds : angle 2.99120 / 2.17 ( 1909) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.349 Fit side-chains REVERT: A 64 LYS cc_start: 0.9008 (mttt) cc_final: 0.8707 (mttp) REVERT: B 91 LYS cc_start: 0.8764 (tttp) cc_final: 0.8316 (ttpt) REVERT: E 68 GLN cc_start: 0.8687 (tt0) cc_final: 0.8224 (tt0) REVERT: E 133 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: F 93 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7160 (mp10) REVERT: G 15 LYS cc_start: 0.8699 (mtmm) cc_final: 0.8178 (mtpt) REVERT: G 95 LYS cc_start: 0.9013 (tttt) cc_final: 0.8667 (tppt) REVERT: H 31 LYS cc_start: 0.8635 (mtpp) cc_final: 0.8342 (mttp) REVERT: H 105 LYS cc_start: 0.8528 (ttpt) cc_final: 0.8091 (mmtm) outliers start: 9 outliers final: 7 residues processed: 122 average time/residue: 0.9676 time to fit residues: 124.5301 Evaluate side-chains 130 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 99 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 chunk 89 optimal weight: 30.0000 chunk 21 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.090221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.071329 restraints weight = 22167.510| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.26 r_work: 0.3017 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13019 Z= 0.166 Angle : 0.668 7.337 18804 Z= 0.380 Chirality : 0.049 0.252 2129 Planarity : 0.004 0.038 1375 Dihedral : 31.453 177.828 4095 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.37 % Allowed : 12.21 % Favored : 86.41 % 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: 2.66 (0.29), residues: 771 helix: 2.64 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.58 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 30 TYR 0.010 0.001 TYR H 37 PHE 0.009 0.002 PHE A 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 (13019) covalent geometry : angle 0.66766 / 0.38 (18804) hydrogen bonds : bond 0.05799 / 3.83 ( 764) hydrogen bonds : angle 2.96570 / 2.15 ( 1909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5090.38 seconds wall clock time: 87 minutes 21.12 seconds (5241.12 seconds total)