Starting phenix.real_space_refine on Sun May 18 13:42:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjw_60158/05_2025/8zjw_60158.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjw_60158/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zjw_60158/05_2025/8zjw_60158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjw_60158/05_2025/8zjw_60158.map" model { file = "/net/cci-nas-00/data/ceres_data/8zjw_60158/05_2025/8zjw_60158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjw_60158/05_2025/8zjw_60158.cif" } resolution = 2.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.85, per 1000 atoms: 0.81 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: 4.50 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 0.88 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: 3.59 Time building geometry restraints manager: 5.10 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 57 or resid 101)) selection = chain 'F' selection = (chain 'I' and (resid 9 through 57 or resid 101)) selection = chain 'K' selection = chain 'Q' selection = (chain 'S' and (resid 9 through 57 or resid 101)) selection = (chain 'U' and (resid 9 through 57 or resid 101)) selection = (chain 'Y' and (resid 9 through 57 or resid 101)) selection = chain 'a' selection = (chain 'c' and (resid 9 through 57 or resid 101)) selection = chain 'e' selection = chain 'g' selection = (chain 'i' and (resid 9 through 57 or resid 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: 12.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 36.270 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.440 ------------------------------------------------------------------------------- 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 : 13.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.002 TRP A 9 HIS 0.006 0.002 HIS G 33 PHE 0.021 0.003 PHE B 21 TYR 0.007 0.002 TYR Q 25 ARG 0.003 0.000 ARG J 41 Details of bonding type rmsd hydrogen bonds : bond 0.12205 ( 780) hydrogen bonds : angle 3.36143 ( 2178) covalent geometry : bond 0.02429 (15316) covalent geometry : angle 2.27971 (21434) 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 : 1.315 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: 1.5811 time to fit residues: 359.6666 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 : 1.275 ------------------------------------------------------------------------------- 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 106 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 98 optimal weight: 30.0000 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.143309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.125157 restraints weight = 9665.770| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 0.52 r_work: 0.3143 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.444 15358 Z= 0.167 Angle : 1.003 16.586 21434 Z= 0.330 Chirality : 0.040 0.211 2086 Planarity : 0.005 0.065 2604 Dihedral : 16.864 120.643 2722 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.16 % Allowed : 12.23 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.03 (0.21), residues: 1372 helix: 3.44 (0.15), residues: 840 sheet: None (None), residues: 0 loop : 1.51 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 9 HIS 0.006 0.002 HIS I 40 PHE 0.017 0.002 PHE N 42 TYR 0.008 0.002 TYR i 25 ARG 0.003 0.001 ARG j 41 Details of bonding type rmsd hydrogen bonds : bond 0.04582 ( 780) hydrogen bonds : angle 3.19027 ( 2178) covalent geometry : bond 0.00380 (15316) covalent geometry : angle 1.00251 (21434) Misc. bond : bond 0.18319 ( 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 215 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 1.454 Fit side-chains REVERT: B 19 LYS cc_start: 0.7960 (ttpt) cc_final: 0.7743 (ttmt) REVERT: E 7 LYS cc_start: 0.8113 (mttm) cc_final: 0.7864 (mtpt) REVERT: S 20 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6854 (pp20) REVERT: Y 20 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6811 (pp20) outliers start: 13 outliers final: 2 residues processed: 207 average time/residue: 1.5953 time to fit residues: 356.2899 Evaluate side-chains 203 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 199 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain Y residue 20 GLU Chi-restraints excluded: chain c residue 33 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 49 optimal weight: 8.9990 chunk 100 optimal weight: 0.0870 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 U 27 GLN a 27 GLN c 27 GLN d 48 ASN e 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.144206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.126032 restraints weight = 9701.887| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 0.53 r_work: 0.3153 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.444 15358 Z= 0.152 Angle : 0.952 15.999 21434 Z= 0.312 Chirality : 0.038 0.214 2086 Planarity : 0.005 0.056 2604 Dihedral : 15.821 120.574 2704 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.98 % Allowed : 12.68 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.98 (0.20), residues: 1372 helix: 3.60 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.25 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 9 HIS 0.006 0.002 HIS I 40 PHE 0.016 0.002 PHE I 21 TYR 0.008 0.002 TYR i 25 ARG 0.003 0.000 ARG T 41 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 780) hydrogen bonds : angle 3.12882 ( 2178) covalent geometry : bond 0.00344 (15316) covalent geometry : angle 0.95225 (21434) Misc. bond : bond 0.17689 ( 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 : 1.514 Fit side-chains REVERT: E 7 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7815 (mtpt) REVERT: Y 20 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6814 (pp20) REVERT: b 7 LYS cc_start: 0.8116 (mttm) cc_final: 0.7875 (mtpt) REVERT: C 1 MET cc_start: 0.7524 (ttm) cc_final: 0.7217 (ttm) outliers start: 11 outliers final: 2 residues processed: 205 average time/residue: 1.6305 time to fit residues: 359.8381 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 : 1.326 ------------------------------------------------------------------------------- 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 20 GLU Chi-restraints excluded: chain Y residue 33 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 70 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.141828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.123538 restraints weight = 9715.816| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 0.52 r_work: 0.3121 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.454 15358 Z= 0.193 Angle : 1.031 18.513 21434 Z= 0.343 Chirality : 0.042 0.227 2086 Planarity : 0.006 0.053 2604 Dihedral : 15.723 111.775 2702 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.34 % Allowed : 12.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.68 (0.20), residues: 1372 helix: 3.35 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.15 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 9 HIS 0.008 0.002 HIS I 40 PHE 0.019 0.003 PHE I 21 TYR 0.007 0.002 TYR i 25 ARG 0.003 0.001 ARG G 41 Details of bonding type rmsd hydrogen bonds : bond 0.04753 ( 780) hydrogen bonds : angle 3.25697 ( 2178) covalent geometry : bond 0.00445 (15316) covalent geometry : angle 1.03061 (21434) Misc. bond : bond 0.18587 ( 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 210 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 1.388 Fit side-chains REVERT: E 7 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7872 (mtpt) REVERT: N 13 ASP cc_start: 0.8327 (t70) cc_final: 0.7999 (t70) REVERT: S 20 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6834 (pp20) REVERT: Y 20 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6840 (pp20) REVERT: a 20 GLU cc_start: 0.7478 (pt0) cc_final: 0.6531 (pp20) outliers start: 15 outliers final: 6 residues processed: 201 average time/residue: 1.5534 time to fit residues: 336.2854 Evaluate side-chains 203 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 194 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 103 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 109 optimal weight: 0.0980 chunk 104 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 24 optimal weight: 0.0970 chunk 122 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.203847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.192715 restraints weight = 9780.306| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 0.30 r_work: 0.3903 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1245 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= 0.146 Angle : 0.916 15.691 21434 Z= 0.303 Chirality : 0.037 0.204 2086 Planarity : 0.005 0.050 2604 Dihedral : 15.605 106.825 2702 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.98 % Allowed : 13.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.90 (0.20), residues: 1372 helix: 3.56 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.18 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 9 HIS 0.005 0.002 HIS I 40 PHE 0.015 0.002 PHE I 21 TYR 0.007 0.002 TYR B 25 ARG 0.003 0.000 ARG V 41 Details of bonding type rmsd hydrogen bonds : bond 0.04245 ( 780) hydrogen bonds : angle 3.11333 ( 2178) covalent geometry : bond 0.00328 (15316) covalent geometry : angle 0.91609 (21434) Misc. bond : bond 0.17705 ( 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 213 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 1.274 Fit side-chains REVERT: E 7 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8044 (mtpt) REVERT: N 13 ASP cc_start: 0.8477 (t70) cc_final: 0.8160 (t70) REVERT: S 20 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7156 (pp20) REVERT: U 19 LYS cc_start: 0.8264 (ttpt) cc_final: 0.8048 (ttmt) REVERT: Y 20 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7211 (pp20) REVERT: f 1 MET cc_start: 0.7882 (mtm) cc_final: 0.7541 (mtp) REVERT: f 13 ASP cc_start: 0.8527 (t70) cc_final: 0.8177 (t70) outliers start: 11 outliers final: 3 residues processed: 206 average time/residue: 1.5423 time to fit residues: 342.4655 Evaluate side-chains 207 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 201 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 LYS 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 118 optimal weight: 3.9990 chunk 121 optimal weight: 0.0470 chunk 83 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.202778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.191449 restraints weight = 9848.142| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 0.31 r_work: 0.3834 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.428 15358 Z= 0.158 Angle : 0.947 17.005 21434 Z= 0.314 Chirality : 0.039 0.211 2086 Planarity : 0.005 0.049 2604 Dihedral : 15.465 105.992 2702 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.25 % Allowed : 12.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.20), residues: 1372 helix: 3.48 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.20 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 9 HIS 0.006 0.002 HIS I 40 PHE 0.016 0.002 PHE I 21 TYR 0.007 0.002 TYR i 25 ARG 0.003 0.000 ARG j 41 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 780) hydrogen bonds : angle 3.14497 ( 2178) covalent geometry : bond 0.00357 (15316) covalent geometry : angle 0.94685 (21434) Misc. bond : bond 0.17738 ( 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 213 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 1.321 Fit side-chains REVERT: E 7 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8090 (mtpt) REVERT: N 13 ASP cc_start: 0.8522 (t70) cc_final: 0.8211 (t70) REVERT: U 19 LYS cc_start: 0.8295 (ttpt) cc_final: 0.8075 (ttmt) REVERT: f 13 ASP cc_start: 0.8549 (t70) cc_final: 0.8216 (t70) outliers start: 14 outliers final: 6 residues processed: 206 average time/residue: 1.6240 time to fit residues: 360.5855 Evaluate side-chains 206 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 199 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 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 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 43 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 108 optimal weight: 0.0970 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.176770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.164727 restraints weight = 9763.282| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 0.34 r_work: 0.3564 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.424 15358 Z= 0.153 Angle : 0.930 16.560 21434 Z= 0.309 Chirality : 0.038 0.206 2086 Planarity : 0.005 0.048 2604 Dihedral : 15.447 106.045 2702 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.71 % Allowed : 13.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.20), residues: 1372 helix: 3.50 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.22 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 9 HIS 0.006 0.002 HIS I 40 PHE 0.015 0.002 PHE I 21 TYR 0.007 0.002 TYR i 25 ARG 0.003 0.000 ARG G 41 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 780) hydrogen bonds : angle 3.12826 ( 2178) covalent geometry : bond 0.00346 (15316) covalent geometry : angle 0.93046 (21434) Misc. bond : bond 0.17519 ( 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 207 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 1.322 Fit side-chains REVERT: E 7 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8018 (mtpt) REVERT: N 13 ASP cc_start: 0.8471 (t70) cc_final: 0.8148 (t70) REVERT: U 19 LYS cc_start: 0.8236 (ttpt) cc_final: 0.8001 (ttmt) REVERT: f 13 ASP cc_start: 0.8467 (t70) cc_final: 0.8144 (t70) outliers start: 8 outliers final: 6 residues processed: 204 average time/residue: 1.5762 time to fit residues: 346.5366 Evaluate side-chains 204 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 197 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain E residue 7 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.173322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.161036 restraints weight = 9739.864| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 0.34 r_work: 0.3524 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.460 15358 Z= 0.228 Angle : 1.085 18.366 21434 Z= 0.367 Chirality : 0.045 0.241 2086 Planarity : 0.006 0.050 2604 Dihedral : 15.641 105.368 2702 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.89 % Allowed : 13.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.49 (0.21), residues: 1372 helix: 3.17 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.12 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 9 HIS 0.009 0.003 HIS B 40 PHE 0.021 0.003 PHE I 21 TYR 0.007 0.002 TYR i 25 ARG 0.004 0.001 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.05002 ( 780) hydrogen bonds : angle 3.33391 ( 2178) covalent geometry : bond 0.00530 (15316) covalent geometry : angle 1.08484 (21434) Misc. bond : bond 0.18703 ( 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 204 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 1.601 Fit side-chains REVERT: N 13 ASP cc_start: 0.8486 (t70) cc_final: 0.8182 (t70) REVERT: U 19 LYS cc_start: 0.8272 (ttpt) cc_final: 0.8009 (ttmt) REVERT: a 20 GLU cc_start: 0.7869 (pt0) cc_final: 0.7004 (pp20) REVERT: f 13 ASP cc_start: 0.8521 (t70) cc_final: 0.8208 (t70) outliers start: 10 outliers final: 7 residues processed: 201 average time/residue: 1.6224 time to fit residues: 350.7083 Evaluate side-chains 200 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 193 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL 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 Chi-restraints excluded: chain C residue 26 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 93 optimal weight: 0.0770 chunk 53 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 overall best weight: 0.6340 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.144237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.126090 restraints weight = 9698.414| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 0.52 r_work: 0.3150 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.429 15358 Z= 0.151 Angle : 0.922 15.953 21434 Z= 0.308 Chirality : 0.038 0.206 2086 Planarity : 0.005 0.048 2604 Dihedral : 15.424 105.717 2702 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.71 % Allowed : 13.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.82 (0.21), residues: 1372 helix: 3.47 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.20 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 9 HIS 0.006 0.002 HIS I 40 PHE 0.015 0.002 PHE I 21 TYR 0.007 0.002 TYR B 25 ARG 0.003 0.000 ARG V 41 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 780) hydrogen bonds : angle 3.13546 ( 2178) covalent geometry : bond 0.00341 (15316) covalent geometry : angle 0.92224 (21434) Misc. bond : bond 0.17606 ( 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 207 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 1.446 Fit side-chains REVERT: E 7 LYS cc_start: 0.8048 (mttm) cc_final: 0.7809 (mtpt) REVERT: N 13 ASP cc_start: 0.8268 (t70) cc_final: 0.7919 (t70) REVERT: f 1 MET cc_start: 0.7536 (mtm) cc_final: 0.7299 (mtp) REVERT: f 13 ASP cc_start: 0.8289 (t70) cc_final: 0.7945 (t70) outliers start: 8 outliers final: 6 residues processed: 205 average time/residue: 1.6365 time to fit residues: 361.3532 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 : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 84 optimal weight: 0.0470 chunk 73 optimal weight: 2.9990 chunk 80 optimal weight: 0.0270 chunk 108 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 overall best weight: 0.5136 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.145342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.127384 restraints weight = 9648.652| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 0.52 r_work: 0.3166 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.391 15358 Z= 0.139 Angle : 0.890 14.979 21434 Z= 0.298 Chirality : 0.037 0.200 2086 Planarity : 0.005 0.047 2604 Dihedral : 15.213 106.033 2702 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.45 % Allowed : 13.93 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.96 (0.21), residues: 1372 helix: 3.58 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.27 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 9 HIS 0.005 0.001 HIS I 40 PHE 0.014 0.002 PHE f 42 TYR 0.007 0.002 TYR B 25 ARG 0.003 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 780) hydrogen bonds : angle 3.08338 ( 2178) covalent geometry : bond 0.00312 (15316) covalent geometry : angle 0.88992 (21434) Misc. bond : bond 0.16393 ( 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 209 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 204 time to evaluate : 4.285 Fit side-chains REVERT: E 7 LYS cc_start: 0.8011 (mttm) cc_final: 0.7770 (mtpt) REVERT: N 13 ASP cc_start: 0.8252 (t70) cc_final: 0.7898 (t70) REVERT: f 1 MET cc_start: 0.7591 (mtm) cc_final: 0.7328 (mtp) REVERT: f 13 ASP cc_start: 0.8300 (t70) cc_final: 0.7956 (t70) outliers start: 5 outliers final: 5 residues processed: 208 average time/residue: 1.6065 time to fit residues: 363.5975 Evaluate side-chains 208 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 203 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 0.0970 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.144178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.126182 restraints weight = 9756.737| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 0.52 r_work: 0.3150 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.416 15358 Z= 0.154 Angle : 0.926 16.618 21434 Z= 0.312 Chirality : 0.038 0.207 2086 Planarity : 0.005 0.048 2604 Dihedral : 15.114 104.439 2702 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.62 % Allowed : 14.11 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.21), residues: 1372 helix: 3.48 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.25 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 9 HIS 0.006 0.002 HIS g 40 PHE 0.016 0.002 PHE I 21 TYR 0.007 0.002 TYR i 25 ARG 0.003 0.000 ARG T 41 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 780) hydrogen bonds : angle 3.14696 ( 2178) covalent geometry : bond 0.00348 (15316) covalent geometry : angle 0.92566 (21434) Misc. bond : bond 0.17056 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10544.75 seconds wall clock time: 183 minutes 24.37 seconds (11004.37 seconds total)