Starting phenix.real_space_refine on Sun Aug 24 04:45:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjw_60158/08_2025/8zjw_60158.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjw_60158/08_2025/8zjw_60158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zjw_60158/08_2025/8zjw_60158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjw_60158/08_2025/8zjw_60158.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zjw_60158/08_2025/8zjw_60158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjw_60158/08_2025/8zjw_60158.map" } resolution = 2.35 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= 0.083 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 3388 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: 5 Type Number sf(0) Gaussians Mg 42 5.21 5 S 70 5.16 5 C 10332 2.51 5 N 2030 2.21 5 O 2128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14602 Number of models: 1 Model: "" Number of chains: 56 Chain: "B" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "A" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "E" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "F" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "I" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "J" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "K" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "N" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "Q" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "R" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "S" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "T" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "U" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "V" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "Y" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "a" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "b" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "c" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "d" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "e" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "f" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "g" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "h" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "i" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "j" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "C" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 176 Unusual residues: {'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 176 Unusual residues: {'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 176 Unusual residues: {'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 176 Unusual residues: {'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 176 Unusual residues: {'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "i" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 176 Unusual residues: {'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 176 Unusual residues: {'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.85, per 1000 atoms: 0.20 Number of scatterers: 14602 At special positions: 0 Unit cell: (116.48, 115.44, 75.92, 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 70 16.00 Mg 42 11.99 O 2128 8.00 N 2030 7.00 C 10332 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=42, symmetry=0 Number of additional bonds: simple=42, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 395.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 65.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 14 through 47 Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 13 through 38 Processing helix chain 'D' and resid 14 through 47 removed outlier: 3.588A pdb=" N VAL D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 11 Processing helix chain 'E' and resid 13 through 38 Processing helix chain 'F' and resid 14 through 47 removed outlier: 3.556A pdb=" N VAL F 24 " --> pdb=" O GLU F 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 11 Processing helix chain 'G' and resid 13 through 38 Processing helix chain 'I' and resid 14 through 47 Processing helix chain 'J' and resid 5 through 11 Processing helix chain 'J' and resid 13 through 38 Processing helix chain 'K' and resid 14 through 47 Processing helix chain 'N' and resid 5 through 11 Processing helix chain 'N' and resid 13 through 38 Processing helix chain 'Q' and resid 14 through 47 Processing helix chain 'R' and resid 5 through 11 Processing helix chain 'R' and resid 13 through 38 Processing helix chain 'S' and resid 14 through 47 Processing helix chain 'T' and resid 5 through 11 Processing helix chain 'T' and resid 13 through 38 Processing helix chain 'U' and resid 14 through 47 Processing helix chain 'V' and resid 5 through 11 removed outlier: 3.548A pdb=" N VAL V 8 " --> pdb=" O THR V 5 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP V 9 " --> pdb=" O HIS V 6 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 38 Processing helix chain 'Y' and resid 14 through 47 Processing helix chain 'a' and resid 14 through 47 Processing helix chain 'b' and resid 5 through 11 Processing helix chain 'b' and resid 13 through 38 Processing helix chain 'c' and resid 14 through 47 Processing helix chain 'd' and resid 5 through 11 Processing helix chain 'd' and resid 13 through 38 Processing helix chain 'e' and resid 14 through 47 Processing helix chain 'f' and resid 5 through 11 Processing helix chain 'f' and resid 13 through 38 Processing helix chain 'g' and resid 14 through 47 Processing helix chain 'h' and resid 5 through 11 Processing helix chain 'h' and resid 13 through 38 Processing helix chain 'i' and resid 14 through 47 Processing helix chain 'j' and resid 5 through 11 Processing helix chain 'j' and resid 13 through 38 Processing helix chain 'C' and resid 5 through 11 Processing helix chain 'C' and resid 13 through 38 780 hydrogen bonds defined for protein. 2178 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.35: 4020 1.35 - 1.53: 10746 1.53 - 1.72: 270 1.72 - 1.90: 112 1.90 - 2.09: 168 Bond restraints: 15316 Sorted by residual: bond pdb=" NA BCL j 102 " pdb="MG BCL j 102 " ideal model delta sigma weight residual 2.170 2.004 0.166 2.40e-02 1.74e+03 4.80e+01 bond pdb=" NA BCL G 101 " pdb="MG BCL G 101 " ideal model delta sigma weight residual 2.170 2.005 0.165 2.40e-02 1.74e+03 4.74e+01 bond pdb=" NA BCL d 101 " pdb="MG BCL d 101 " ideal model delta sigma weight residual 2.170 2.007 0.163 2.40e-02 1.74e+03 4.64e+01 bond pdb=" NA BCL R 101 " pdb="MG BCL R 101 " ideal model delta sigma weight residual 2.170 2.008 0.162 2.40e-02 1.74e+03 4.54e+01 bond pdb=" NA BCL f 101 " pdb="MG BCL f 101 " ideal model delta sigma weight residual 2.170 2.009 0.161 2.40e-02 1.74e+03 4.53e+01 ... (remaining 15311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 19177 3.77 - 7.53: 1885 7.53 - 11.30: 295 11.30 - 15.07: 48 15.07 - 18.83: 29 Bond angle restraints: 21434 Sorted by residual: angle pdb=" C1D BCL E 101 " pdb=" C2D BCL E 101 " pdb=" CMD BCL E 101 " ideal model delta sigma weight residual 125.57 138.74 -13.16 1.83e+00 2.99e-01 5.19e+01 angle pdb=" C1D BCL b 101 " pdb=" C2D BCL b 101 " pdb=" CMD BCL b 101 " ideal model delta sigma weight residual 125.57 138.70 -13.13 1.83e+00 2.99e-01 5.16e+01 angle pdb=" C1D BCL d 101 " pdb=" C2D BCL d 101 " pdb=" CMD BCL d 101 " ideal model delta sigma weight residual 125.57 138.15 -12.58 1.83e+00 2.99e-01 4.73e+01 angle pdb=" C1D BCL h 102 " pdb=" C2D BCL h 102 " pdb=" CMD BCL h 102 " ideal model delta sigma weight residual 125.57 138.11 -12.54 1.83e+00 2.99e-01 4.70e+01 angle pdb=" C1D BCL R 101 " pdb=" C2D BCL R 101 " pdb=" CMD BCL R 101 " ideal model delta sigma weight residual 125.57 138.10 -12.53 1.83e+00 2.99e-01 4.69e+01 ... (remaining 21429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 7132 35.42 - 70.84: 480 70.84 - 106.26: 41 106.26 - 141.68: 4 141.68 - 177.10: 1 Dihedral angle restraints: 7658 sinusoidal: 3556 harmonic: 4102 Sorted by residual: dihedral pdb=" C1 BCL b 101 " pdb=" CGA BCL b 101 " pdb=" O2A BCL b 101 " pdb=" CBA BCL b 101 " ideal model delta sinusoidal sigma weight residual 180.00 96.00 84.00 1 6.00e+00 2.78e-02 2.39e+02 dihedral pdb=" CBD BCL j 102 " pdb=" CGD BCL j 102 " pdb=" O2D BCL j 102 " pdb=" CED BCL j 102 " ideal model delta sinusoidal sigma weight residual 180.00 119.91 60.09 1 5.00e+00 4.00e-02 1.93e+02 dihedral pdb=" CBD BCL G 101 " pdb=" CGD BCL G 101 " pdb=" O2D BCL G 101 " pdb=" CED BCL G 101 " ideal model delta sinusoidal sigma weight residual 180.00 123.13 56.87 1 5.00e+00 4.00e-02 1.74e+02 ... (remaining 7655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1775 0.069 - 0.138: 184 0.138 - 0.207: 105 0.207 - 0.276: 21 0.276 - 0.345: 1 Chirality restraints: 2086 Sorted by residual: chirality pdb=" CA ALA A 51 " pdb=" N ALA A 51 " pdb=" C ALA A 51 " pdb=" CB ALA A 51 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA ALA A 50 " pdb=" N ALA A 50 " pdb=" C ALA A 50 " pdb=" CB ALA A 50 " both_signs ideal model delta sigma weight residual False 2.48 2.23 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CBD BCL Q 101 " pdb=" CAD BCL Q 101 " pdb=" CGD BCL Q 101 " pdb=" CHA BCL Q 101 " both_signs ideal model delta sigma weight residual False 2.62 2.38 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2083 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL b 101 " -0.389 3.00e-02 1.11e+03 3.21e-01 5.73e+02 pdb=" CBA BCL b 101 " -0.142 3.00e-02 1.11e+03 pdb=" CGA BCL b 101 " 0.097 3.00e-02 1.11e+03 pdb=" O1A BCL b 101 " -0.129 3.00e-02 1.11e+03 pdb=" O2A BCL b 101 " 0.564 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL R 101 " -0.312 3.00e-02 1.11e+03 2.57e-01 3.68e+02 pdb=" CBA BCL R 101 " -0.176 3.00e-02 1.11e+03 pdb=" CGA BCL R 101 " 0.068 3.00e-02 1.11e+03 pdb=" O1A BCL R 101 " -0.024 3.00e-02 1.11e+03 pdb=" O2A BCL R 101 " 0.444 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL N 101 " -0.301 3.00e-02 1.11e+03 2.39e-01 3.16e+02 pdb=" CBA BCL N 101 " -0.196 3.00e-02 1.11e+03 pdb=" CGA BCL N 101 " 0.079 3.00e-02 1.11e+03 pdb=" O1A BCL N 101 " 0.033 3.00e-02 1.11e+03 pdb=" O2A BCL N 101 " 0.385 3.00e-02 1.11e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3255 2.81 - 3.34: 13154 3.34 - 3.86: 30628 3.86 - 4.38: 34438 4.38 - 4.90: 53964 Nonbonded interactions: 135439 Sorted by model distance: nonbonded pdb=" O MET h 11 " pdb=" NH1 ARG j 15 " model vdw 2.292 3.120 nonbonded pdb=" O LEU V 37 " pdb=" ND2 ASN V 43 " model vdw 2.383 3.120 nonbonded pdb=" O ASP j 13 " pdb=" OG1 THR j 17 " model vdw 2.394 3.040 nonbonded pdb=" NH1 ARG B 47 " pdb=" O ARG A 41 " model vdw 2.399 3.120 nonbonded pdb=" NH2 ARG B 47 " pdb=" O ASN A 48 " model vdw 2.402 3.120 ... (remaining 135434 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 1 through 53 or resid 102)) selection = (chain 'C' and (resid 1 through 53 or resid 102)) selection = (chain 'E' and (resid 1 through 53 or resid 102)) selection = (chain 'G' and (resid 1 through 53 or resid 102)) selection = (chain 'J' and (resid 1 through 53 or resid 102)) selection = (chain 'N' and (resid 1 through 53 or resid 102)) selection = (chain 'R' and (resid 1 through 53 or resid 102)) selection = (chain 'T' and (resid 1 through 53 or resid 102)) selection = (chain 'V' and (resid 1 through 53 or resid 102)) selection = (chain 'b' and (resid 1 through 53 or resid 102)) selection = (chain 'd' and (resid 1 through 53 or resid 102)) selection = (chain 'f' and (resid 1 through 53 or resid 102)) selection = (chain 'h' and (resid 1 through 53 or resid 102)) selection = (chain 'j' and (resid 1 through 53 or resid 102)) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 9 through 101) selection = chain 'F' selection = (chain 'I' and resid 9 through 101) selection = chain 'K' selection = chain 'Q' selection = (chain 'S' and resid 9 through 101) selection = (chain 'U' and resid 9 through 101) selection = (chain 'Y' and resid 9 through 101) selection = chain 'a' selection = (chain 'c' and resid 9 through 101) selection = chain 'e' selection = chain 'g' selection = (chain 'i' and resid 9 through 101) } 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: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.350 Find NCS groups from input model: 0.350 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: 0.010 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 : 0.026 0.439 15358 Z= 1.465 Angle : 2.280 18.835 21434 Z= 1.004 Chirality : 0.062 0.345 2086 Planarity : 0.025 0.321 2604 Dihedral : 20.978 177.098 4970 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.54 % Allowed : 11.88 % Favored : 87.59 % Cbeta Deviations : 0.07 % 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 aren not related in a simple way. whole: 3.96 (0.21), residues: 1372 helix: 3.58 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.25 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 41 TYR 0.007 0.002 TYR Q 25 PHE 0.021 0.003 PHE B 21 TRP 0.011 0.002 TRP A 9 HIS 0.006 0.002 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.02429 (15316) covalent geometry : angle 2.27971 (21434) hydrogen bonds : bond 0.12205 ( 780) hydrogen bonds : angle 3.36143 ( 2178) Misc. bond : bond 0.20328 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 205 time to evaluate : 0.317 Fit side-chains REVERT: N 53 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7858 (mptt) REVERT: f 1 MET cc_start: 0.7604 (mtm) cc_final: 0.7328 (mtp) REVERT: f 53 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7852 (mptt) REVERT: C 53 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7902 (mmmt) outliers start: 6 outliers final: 4 residues processed: 211 average time/residue: 0.6690 time to fit residues: 151.9628 Evaluate side-chains 202 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 195 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain N residue 53 LYS Chi-restraints excluded: chain U residue 19 LYS Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain f residue 53 LYS Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 53 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 27 GLN K 27 GLN Q 27 GLN U 27 GLN a 27 GLN c 27 GLN e 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.143733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.125483 restraints weight = 9673.604| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 0.53 r_work: 0.3148 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.442 15358 Z= 0.162 Angle : 0.993 16.796 21434 Z= 0.325 Chirality : 0.039 0.207 2086 Planarity : 0.005 0.064 2604 Dihedral : 16.870 120.746 2722 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.16 % Allowed : 12.14 % Favored : 86.70 % 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 aren not related in a simple way. whole: 4.07 (0.21), residues: 1372 helix: 3.47 (0.15), residues: 840 sheet: None (None), residues: 0 loop : 1.53 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 41 TYR 0.009 0.002 TYR i 25 PHE 0.016 0.002 PHE N 42 TRP 0.012 0.002 TRP A 9 HIS 0.006 0.002 HIS I 40 Details of bonding type rmsd covalent geometry : bond 0.00367 (15316) covalent geometry : angle 0.99317 (21434) hydrogen bonds : bond 0.04509 ( 780) hydrogen bonds : angle 3.17593 ( 2178) Misc. bond : bond 0.18262 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.333 Fit side-chains REVERT: B 19 LYS cc_start: 0.7947 (ttpt) cc_final: 0.7730 (ttmt) REVERT: E 7 LYS cc_start: 0.8203 (mttm) cc_final: 0.7950 (mtpt) REVERT: S 20 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6749 (pp20) outliers start: 13 outliers final: 1 residues processed: 208 average time/residue: 0.6859 time to fit residues: 153.5159 Evaluate side-chains 203 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain T residue 26 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 64 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 27 optimal weight: 0.1980 chunk 70 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 27 GLN K 27 GLN Q 27 GLN U 27 GLN a 27 GLN c 27 GLN d 48 ASN e 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.144115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.126170 restraints weight = 9761.154| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 0.51 r_work: 0.3155 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.445 15358 Z= 0.152 Angle : 0.950 15.969 21434 Z= 0.312 Chirality : 0.038 0.215 2086 Planarity : 0.005 0.055 2604 Dihedral : 15.765 120.784 2702 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.98 % Allowed : 12.59 % Favored : 86.43 % 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 aren not related in a simple way. whole: 3.98 (0.20), residues: 1372 helix: 3.60 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.27 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 41 TYR 0.007 0.002 TYR B 25 PHE 0.016 0.002 PHE I 21 TRP 0.012 0.002 TRP A 9 HIS 0.006 0.002 HIS I 40 Details of bonding type rmsd covalent geometry : bond 0.00345 (15316) covalent geometry : angle 0.95005 (21434) hydrogen bonds : bond 0.04352 ( 780) hydrogen bonds : angle 3.13289 ( 2178) Misc. bond : bond 0.17772 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 0.370 Fit side-chains REVERT: E 7 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7815 (mtpt) REVERT: b 7 LYS cc_start: 0.8119 (mttm) cc_final: 0.7875 (mtpt) outliers start: 11 outliers final: 3 residues processed: 206 average time/residue: 0.6709 time to fit residues: 148.8839 Evaluate side-chains 202 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 198 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain c residue 33 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 27 GLN K 27 GLN Q 27 GLN U 27 GLN a 27 GLN c 27 GLN d 48 ASN e 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.173658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.161389 restraints weight = 9741.099| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 0.34 r_work: 0.3518 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.456 15358 Z= 0.212 Angle : 1.065 18.919 21434 Z= 0.357 Chirality : 0.044 0.238 2086 Planarity : 0.006 0.054 2604 Dihedral : 15.808 110.856 2702 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.61 % Allowed : 12.14 % Favored : 86.25 % 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 aren not related in a simple way. whole: 3.61 (0.21), residues: 1372 helix: 3.13 (0.15), residues: 840 sheet: None (None), residues: 0 loop : 1.29 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG b 41 TYR 0.007 0.002 TYR i 25 PHE 0.021 0.003 PHE I 21 TRP 0.015 0.002 TRP A 9 HIS 0.008 0.002 HIS I 40 Details of bonding type rmsd covalent geometry : bond 0.00492 (15316) covalent geometry : angle 1.06474 (21434) hydrogen bonds : bond 0.04915 ( 780) hydrogen bonds : angle 3.30121 ( 2178) Misc. bond : bond 0.18664 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.296 Fit side-chains REVERT: N 13 ASP cc_start: 0.8464 (t70) cc_final: 0.8147 (t70) REVERT: S 20 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7186 (pp20) REVERT: Y 20 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7215 (pp20) REVERT: a 20 GLU cc_start: 0.7857 (pt0) cc_final: 0.6972 (pp20) outliers start: 18 outliers final: 8 residues processed: 201 average time/residue: 0.6962 time to fit residues: 150.5403 Evaluate side-chains 203 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 193 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain Y residue 20 GLU Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain f residue 26 VAL Chi-restraints excluded: chain i residue 19 LYS Chi-restraints excluded: chain C residue 26 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 69 optimal weight: 0.1980 chunk 71 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 27 GLN K 27 GLN Q 27 GLN U 27 GLN a 27 GLN c 27 GLN e 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.201896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.190632 restraints weight = 9810.075| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 0.31 r_work: 0.3834 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.442 15358 Z= 0.167 Angle : 0.970 17.068 21434 Z= 0.321 Chirality : 0.040 0.218 2086 Planarity : 0.005 0.051 2604 Dihedral : 15.654 108.423 2702 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.98 % Allowed : 13.30 % Favored : 85.71 % 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 aren not related in a simple way. whole: 3.73 (0.20), residues: 1372 helix: 3.40 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.16 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG T 41 TYR 0.007 0.002 TYR i 25 PHE 0.017 0.002 PHE I 21 TRP 0.013 0.002 TRP A 9 HIS 0.006 0.002 HIS I 40 Details of bonding type rmsd covalent geometry : bond 0.00382 (15316) covalent geometry : angle 0.97026 (21434) hydrogen bonds : bond 0.04492 ( 780) hydrogen bonds : angle 3.17919 ( 2178) Misc. bond : bond 0.18113 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 0.370 Fit side-chains REVERT: E 7 LYS cc_start: 0.8296 (mttm) cc_final: 0.8095 (mtpt) REVERT: N 13 ASP cc_start: 0.8541 (t70) cc_final: 0.8213 (t70) REVERT: f 1 MET cc_start: 0.7887 (mtm) cc_final: 0.7510 (mtp) REVERT: f 13 ASP cc_start: 0.8538 (t70) cc_final: 0.8203 (t70) outliers start: 11 outliers final: 6 residues processed: 205 average time/residue: 0.7161 time to fit residues: 157.9756 Evaluate side-chains 204 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 198 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain f residue 26 VAL Chi-restraints excluded: chain i residue 19 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 109 optimal weight: 0.0870 chunk 10 optimal weight: 1.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 27 GLN K 27 GLN Q 27 GLN U 27 GLN a 27 GLN c 27 GLN d 48 ASN e 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.199887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.189665 restraints weight = 9692.603| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 0.27 r_work: 0.3871 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.451 15358 Z= 0.203 Angle : 1.042 18.271 21434 Z= 0.350 Chirality : 0.043 0.234 2086 Planarity : 0.006 0.051 2604 Dihedral : 15.694 106.561 2702 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.25 % Allowed : 13.04 % Favored : 85.71 % 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 aren not related in a simple way. whole: 3.56 (0.21), residues: 1372 helix: 3.10 (0.15), residues: 840 sheet: None (None), residues: 0 loop : 1.24 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG j 41 TYR 0.006 0.002 TYR i 25 PHE 0.020 0.003 PHE I 21 TRP 0.015 0.002 TRP A 9 HIS 0.007 0.002 HIS g 40 Details of bonding type rmsd covalent geometry : bond 0.00470 (15316) covalent geometry : angle 1.04231 (21434) hydrogen bonds : bond 0.04827 ( 780) hydrogen bonds : angle 3.28141 ( 2178) Misc. bond : bond 0.18583 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.500 Fit side-chains REVERT: N 13 ASP cc_start: 0.8530 (t70) cc_final: 0.8211 (t70) REVERT: S 15 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: S 17 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8061 (mt-10) REVERT: S 20 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7193 (pp20) REVERT: U 19 LYS cc_start: 0.8339 (ttpt) cc_final: 0.8127 (ttmt) REVERT: Y 20 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7208 (pp20) REVERT: a 20 GLU cc_start: 0.8009 (pt0) cc_final: 0.7153 (pp20) REVERT: f 13 ASP cc_start: 0.8597 (t70) cc_final: 0.8295 (t70) outliers start: 14 outliers final: 7 residues processed: 202 average time/residue: 0.8097 time to fit residues: 175.4145 Evaluate side-chains 204 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain S residue 15 GLU Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain Y residue 20 GLU Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain f residue 26 VAL Chi-restraints excluded: chain i residue 19 LYS Chi-restraints excluded: chain C residue 26 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 21 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 40 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 27 GLN K 27 GLN Q 27 GLN T 48 ASN U 27 GLN a 27 GLN c 27 GLN e 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.202778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.191554 restraints weight = 9716.998| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 0.30 r_work: 0.3883 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3774 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.430 15358 Z= 0.157 Angle : 0.944 16.638 21434 Z= 0.314 Chirality : 0.038 0.211 2086 Planarity : 0.005 0.049 2604 Dihedral : 15.560 106.774 2702 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.71 % Allowed : 13.30 % Favored : 85.98 % 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 aren not related in a simple way. whole: 3.80 (0.21), residues: 1372 helix: 3.46 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.17 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 41 TYR 0.007 0.002 TYR B 25 PHE 0.016 0.002 PHE I 21 TRP 0.013 0.002 TRP A 9 HIS 0.005 0.002 HIS I 40 Details of bonding type rmsd covalent geometry : bond 0.00355 (15316) covalent geometry : angle 0.94417 (21434) hydrogen bonds : bond 0.04371 ( 780) hydrogen bonds : angle 3.15377 ( 2178) Misc. bond : bond 0.17877 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 198 time to evaluate : 0.500 Fit side-chains REVERT: N 13 ASP cc_start: 0.8483 (t70) cc_final: 0.8146 (t70) REVERT: U 19 LYS cc_start: 0.8287 (ttpt) cc_final: 0.8062 (ttmt) REVERT: f 1 MET cc_start: 0.7864 (mtm) cc_final: 0.7538 (mtp) REVERT: f 13 ASP cc_start: 0.8530 (t70) cc_final: 0.8182 (t70) outliers start: 8 outliers final: 6 residues processed: 204 average time/residue: 0.7335 time to fit residues: 160.9561 Evaluate side-chains 203 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 197 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain f residue 26 VAL Chi-restraints excluded: chain C residue 26 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 chunk 111 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 36 optimal weight: 0.3980 chunk 53 optimal weight: 0.4980 chunk 112 optimal weight: 0.0040 overall best weight: 0.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 27 GLN K 27 GLN Q 27 GLN U 27 GLN a 27 GLN c 27 GLN d 48 ASN e 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.209235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.198455 restraints weight = 9738.585| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 0.30 r_work: 0.3879 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.401 15358 Z= 0.121 Angle : 0.829 12.294 21434 Z= 0.279 Chirality : 0.035 0.190 2086 Planarity : 0.004 0.046 2604 Dihedral : 15.433 106.131 2702 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.36 % Allowed : 13.57 % Favored : 86.07 % 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 aren not related in a simple way. whole: 4.12 (0.21), residues: 1372 helix: 3.75 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.25 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 41 TYR 0.008 0.002 TYR i 25 PHE 0.011 0.002 PHE f 42 TRP 0.011 0.001 TRP G 9 HIS 0.004 0.001 HIS I 40 Details of bonding type rmsd covalent geometry : bond 0.00270 (15316) covalent geometry : angle 0.82950 (21434) hydrogen bonds : bond 0.03858 ( 780) hydrogen bonds : angle 2.97437 ( 2178) Misc. bond : bond 0.15872 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 211 time to evaluate : 0.506 Fit side-chains REVERT: D 54 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7920 (mm-30) REVERT: N 13 ASP cc_start: 0.8495 (t70) cc_final: 0.8180 (t70) REVERT: Y 20 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7303 (pp20) REVERT: a 54 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7841 (mm-30) REVERT: f 1 MET cc_start: 0.7899 (mtm) cc_final: 0.7547 (mtp) outliers start: 4 outliers final: 1 residues processed: 211 average time/residue: 0.7857 time to fit residues: 178.5103 Evaluate side-chains 210 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 208 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 20 GLU Chi-restraints excluded: chain Y residue 33 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 69 optimal weight: 0.2980 chunk 87 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 27 GLN K 27 GLN Q 27 GLN U 27 GLN a 27 GLN c 27 GLN d 48 ASN e 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.202914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.191712 restraints weight = 9730.564| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 0.30 r_work: 0.3865 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.427 15358 Z= 0.160 Angle : 0.938 16.893 21434 Z= 0.315 Chirality : 0.039 0.210 2086 Planarity : 0.005 0.048 2604 Dihedral : 15.085 104.548 2702 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.62 % Allowed : 13.48 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.91 (0.21), residues: 1372 helix: 3.53 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.26 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG j 41 TYR 0.008 0.002 TYR i 25 PHE 0.016 0.002 PHE I 21 TRP 0.015 0.002 TRP A 9 HIS 0.006 0.002 HIS g 40 Details of bonding type rmsd covalent geometry : bond 0.00363 (15316) covalent geometry : angle 0.93836 (21434) hydrogen bonds : bond 0.04370 ( 780) hydrogen bonds : angle 3.14718 ( 2178) Misc. bond : bond 0.17365 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 203 time to evaluate : 0.429 Fit side-chains REVERT: N 13 ASP cc_start: 0.8543 (t70) cc_final: 0.8221 (t70) REVERT: f 1 MET cc_start: 0.7970 (mtm) cc_final: 0.7574 (mtp) outliers start: 7 outliers final: 3 residues processed: 207 average time/residue: 0.7926 time to fit residues: 176.5605 Evaluate side-chains 203 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 200 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain i residue 19 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 21 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 27 GLN K 27 GLN Q 27 GLN U 27 GLN a 27 GLN c 27 GLN d 48 ASN e 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.201811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.190622 restraints weight = 9693.651| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 0.30 r_work: 0.3876 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.443 15358 Z= 0.173 Angle : 0.968 17.704 21434 Z= 0.327 Chirality : 0.040 0.217 2086 Planarity : 0.005 0.048 2604 Dihedral : 15.139 103.517 2702 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.27 % Allowed : 14.64 % Favored : 85.09 % 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 aren not related in a simple way. whole: 3.74 (0.21), residues: 1372 helix: 3.39 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.19 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 41 TYR 0.007 0.002 TYR i 25 PHE 0.018 0.003 PHE I 21 TRP 0.013 0.002 TRP A 9 HIS 0.007 0.002 HIS g 40 Details of bonding type rmsd covalent geometry : bond 0.00394 (15316) covalent geometry : angle 0.96765 (21434) hydrogen bonds : bond 0.04508 ( 780) hydrogen bonds : angle 3.20621 ( 2178) Misc. bond : bond 0.17844 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 200 time to evaluate : 0.575 Fit side-chains REVERT: N 13 ASP cc_start: 0.8534 (t70) cc_final: 0.8206 (t70) REVERT: f 1 MET cc_start: 0.8042 (mtm) cc_final: 0.7661 (mtp) outliers start: 3 outliers final: 3 residues processed: 202 average time/residue: 0.8714 time to fit residues: 188.9076 Evaluate side-chains 203 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 200 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain i residue 19 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 27 GLN K 27 GLN Q 27 GLN U 27 GLN a 27 GLN c 27 GLN d 48 ASN e 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.201996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.190745 restraints weight = 9746.623| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 0.30 r_work: 0.3839 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.440 15358 Z= 0.171 Angle : 0.966 17.705 21434 Z= 0.327 Chirality : 0.040 0.217 2086 Planarity : 0.005 0.048 2604 Dihedral : 15.138 103.734 2702 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.36 % Allowed : 14.82 % Favored : 84.82 % 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 aren not related in a simple way. whole: 3.69 (0.21), residues: 1372 helix: 3.34 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.19 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG T 41 TYR 0.007 0.002 TYR i 25 PHE 0.017 0.002 PHE I 21 TRP 0.014 0.002 TRP A 9 HIS 0.006 0.002 HIS g 40 Details of bonding type rmsd covalent geometry : bond 0.00390 (15316) covalent geometry : angle 0.96598 (21434) hydrogen bonds : bond 0.04478 ( 780) hydrogen bonds : angle 3.20661 ( 2178) Misc. bond : bond 0.17825 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5009.26 seconds wall clock time: 86 minutes 10.98 seconds (5170.98 seconds total)