Starting phenix.real_space_refine on Sun Jun 15 07:21:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjw_60158/06_2025/8zjw_60158.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjw_60158/06_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_60158/06_2025/8zjw_60158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjw_60158/06_2025/8zjw_60158.map" model { file = "/net/cci-nas-00/data/ceres_data/8zjw_60158/06_2025/8zjw_60158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjw_60158/06_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-5710/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: 11.43, per 1000 atoms: 0.78 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: 6.66 Conformation dependent library (CDL) restraints added in 1.8 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: 1.74 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: 4.69 Time building geometry restraints manager: 6.36 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: 537.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 40.140 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.080 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:22.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 602.850 ------------------------------------------------------------------------------- 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 : 1.479 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: 2.0052 time to fit residues: 454.8261 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 : 1.454 ------------------------------------------------------------------------------- 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 = 58)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.125139 restraints weight = 9665.770| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 0.52 r_work: 0.3142 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 : 1.324 Fit side-chains REVERT: B 19 LYS cc_start: 0.7950 (ttpt) cc_final: 0.7732 (ttmt) REVERT: E 7 LYS cc_start: 0.8101 (mttm) cc_final: 0.7850 (mtpt) REVERT: S 20 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6843 (pp20) REVERT: Y 20 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6799 (pp20) outliers start: 13 outliers final: 2 residues processed: 207 average time/residue: 1.6409 time to fit residues: 365.6447 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 : 1.472 ------------------------------------------------------------------------------- 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: 2.9990 chunk 65 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.144715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.126841 restraints weight = 9697.911| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 0.51 r_work: 0.3158 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.441 15358 Z= 0.148 Angle : 0.937 15.242 21434 Z= 0.308 Chirality : 0.038 0.213 2086 Planarity : 0.005 0.055 2604 Dihedral : 15.795 120.296 2704 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.89 % Allowed : 12.77 % 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: 4.01 (0.20), residues: 1372 helix: 3.64 (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 0.015 0.002 PHE I 21 TYR 0.007 0.002 TYR B 25 ARG 0.003 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 780) hydrogen bonds : angle 3.10890 ( 2178) covalent geometry : bond 0.00334 (15316) covalent geometry : angle 0.93694 (21434) Misc. bond : bond 0.17546 ( 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: 10 poor density : 203 time to evaluate : 1.505 Fit side-chains REVERT: E 7 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7806 (mtpt) REVERT: S 20 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6801 (pp20) REVERT: Y 20 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6807 (pp20) REVERT: b 7 LYS cc_start: 0.8112 (mttm) cc_final: 0.7871 (mtpt) REVERT: C 1 MET cc_start: 0.7515 (ttm) cc_final: 0.7212 (ttm) outliers start: 10 outliers final: 2 residues processed: 206 average time/residue: 1.6134 time to fit residues: 357.9782 Evaluate side-chains 203 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 198 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 LYS 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 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: 6.9990 chunk 96 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.172436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.160090 restraints weight = 9731.713| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 0.34 r_work: 0.3517 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.466 15358 Z= 0.255 Angle : 1.139 19.366 21434 Z= 0.386 Chirality : 0.048 0.250 2086 Planarity : 0.007 0.055 2604 Dihedral : 16.084 114.113 2702 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.52 % Allowed : 12.59 % 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: 3.40 (0.21), residues: 1372 helix: 2.96 (0.15), residues: 840 sheet: None (None), residues: 0 loop : 1.22 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 9 HIS 0.009 0.003 HIS I 40 PHE 0.023 0.004 PHE I 21 TYR 0.007 0.002 TYR Q 25 ARG 0.006 0.001 ARG E 41 Details of bonding type rmsd hydrogen bonds : bond 0.05231 ( 780) hydrogen bonds : angle 3.39025 ( 2178) covalent geometry : bond 0.00598 (15316) covalent geometry : angle 1.13877 (21434) Misc. bond : bond 0.19196 ( 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 211 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 1.332 Fit side-chains REVERT: N 13 ASP cc_start: 0.8467 (t70) cc_final: 0.8172 (t70) REVERT: S 20 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7227 (pp20) REVERT: Y 20 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7233 (pp20) REVERT: a 20 GLU cc_start: 0.7882 (pt0) cc_final: 0.7010 (pp20) outliers start: 17 outliers final: 7 residues processed: 201 average time/residue: 1.6584 time to fit residues: 358.4059 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 : 1.380 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 2 optimal weight: 4.9990 chunk 109 optimal weight: 0.0870 chunk 104 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 122 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 4 optimal weight: 0.4980 overall best weight: 0.5962 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.144155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.126167 restraints weight = 9720.479| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 0.51 r_work: 0.3153 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 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 : 0.010 0.433 15358 Z= 0.149 Angle : 0.930 15.953 21434 Z= 0.307 Chirality : 0.038 0.208 2086 Planarity : 0.005 0.050 2604 Dihedral : 15.665 107.509 2702 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.07 % Allowed : 13.48 % Favored : 85.45 % 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 (0.20), residues: 1372 helix: 3.47 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.19 (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 V 41 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 780) hydrogen bonds : angle 3.13810 ( 2178) covalent geometry : bond 0.00336 (15316) covalent geometry : angle 0.93019 (21434) Misc. bond : bond 0.17880 ( 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 215 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 1.341 Fit side-chains REVERT: E 7 LYS cc_start: 0.8051 (mttm) cc_final: 0.7805 (mtpt) REVERT: N 13 ASP cc_start: 0.8262 (t70) cc_final: 0.7932 (t70) REVERT: S 15 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: Y 20 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6797 (pp20) REVERT: b 7 LYS cc_start: 0.8132 (mttm) cc_final: 0.7905 (mtpt) REVERT: f 7 LYS cc_start: 0.8099 (mtpt) cc_final: 0.7842 (mtpm) outliers start: 12 outliers final: 4 residues processed: 209 average time/residue: 1.6014 time to fit residues: 360.1383 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 : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 15 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 118 optimal weight: 4.9990 chunk 121 optimal weight: 0.0040 chunk 83 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.202745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.191474 restraints weight = 9845.190| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 0.31 r_work: 0.3843 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1212 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= 0.156 Angle : 0.948 16.913 21434 Z= 0.313 Chirality : 0.038 0.208 2086 Planarity : 0.005 0.049 2604 Dihedral : 15.496 107.015 2702 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.07 % Allowed : 13.21 % 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: 3.83 (0.20), residues: 1372 helix: 3.46 (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 0.013 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 G 41 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 780) hydrogen bonds : angle 3.14591 ( 2178) covalent geometry : bond 0.00353 (15316) covalent geometry : angle 0.94755 (21434) Misc. bond : bond 0.17676 ( 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 210 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 198 time to evaluate : 1.448 Fit side-chains REVERT: E 7 LYS cc_start: 0.8260 (mttm) cc_final: 0.8049 (mtpt) REVERT: N 13 ASP cc_start: 0.8529 (t70) cc_final: 0.8219 (t70) REVERT: U 19 LYS cc_start: 0.8306 (ttpt) cc_final: 0.8085 (ttmt) REVERT: b 7 LYS cc_start: 0.8308 (mttm) cc_final: 0.8098 (mtpt) REVERT: f 1 MET cc_start: 0.7864 (mtm) cc_final: 0.7465 (mtp) REVERT: f 13 ASP cc_start: 0.8533 (t70) cc_final: 0.8198 (t70) outliers start: 12 outliers final: 5 residues processed: 205 average time/residue: 1.6907 time to fit residues: 373.1647 Evaluate side-chains 204 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 199 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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 i residue 19 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 43 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 111 optimal weight: 0.0870 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.176830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.164823 restraints weight = 9731.486| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 0.33 r_work: 0.3569 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.421 15358 Z= 0.153 Angle : 0.935 16.573 21434 Z= 0.310 Chirality : 0.038 0.209 2086 Planarity : 0.005 0.048 2604 Dihedral : 15.468 106.613 2702 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.89 % Allowed : 13.39 % 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: 3.85 (0.21), residues: 1372 helix: 3.48 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.23 (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 0.015 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 0.04320 ( 780) hydrogen bonds : angle 3.13403 ( 2178) covalent geometry : bond 0.00347 (15316) covalent geometry : angle 0.93466 (21434) Misc. bond : bond 0.17533 ( 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 211 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 201 time to evaluate : 1.329 Fit side-chains REVERT: E 7 LYS cc_start: 0.8212 (mttm) cc_final: 0.7987 (mtpt) REVERT: N 13 ASP cc_start: 0.8415 (t70) cc_final: 0.8098 (t70) REVERT: U 19 LYS cc_start: 0.8230 (ttpt) cc_final: 0.8009 (ttmt) REVERT: b 7 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.8028 (mtpt) REVERT: f 13 ASP cc_start: 0.8468 (t70) cc_final: 0.8144 (t70) outliers start: 10 outliers final: 6 residues processed: 206 average time/residue: 1.6354 time to fit residues: 362.8353 Evaluate side-chains 205 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 198 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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 b residue 7 LYS 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=2.00 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.5980 chunk 27 optimal weight: 7.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.173359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.161081 restraints weight = 9751.589| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 0.34 r_work: 0.3512 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 0.445 15358 Z= 0.224 Angle : 1.078 18.390 21434 Z= 0.365 Chirality : 0.045 0.238 2086 Planarity : 0.006 0.050 2604 Dihedral : 15.652 105.318 2702 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.89 % Allowed : 13.48 % 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: 3.50 (0.21), residues: 1372 helix: 3.16 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.13 (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 g 40 PHE 0.021 0.003 PHE I 21 TYR 0.007 0.002 TYR i 25 ARG 0.004 0.001 ARG E 41 Details of bonding type rmsd hydrogen bonds : bond 0.04975 ( 780) hydrogen bonds : angle 3.33071 ( 2178) covalent geometry : bond 0.00520 (15316) covalent geometry : angle 1.07827 (21434) Misc. bond : bond 0.18489 ( 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 : 1.356 Fit side-chains REVERT: N 13 ASP cc_start: 0.8487 (t70) cc_final: 0.8187 (t70) REVERT: Q 54 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7877 (mm-30) REVERT: U 19 LYS cc_start: 0.8293 (ttpt) cc_final: 0.8033 (ttmt) REVERT: a 20 GLU cc_start: 0.7871 (pt0) cc_final: 0.6970 (pp20) REVERT: c 54 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7866 (mm-30) REVERT: f 1 MET cc_start: 0.7913 (mtm) cc_final: 0.7600 (mtp) REVERT: f 13 ASP cc_start: 0.8573 (t70) cc_final: 0.8213 (t70) outliers start: 10 outliers final: 6 residues processed: 200 average time/residue: 1.6658 time to fit residues: 357.9790 Evaluate side-chains 199 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 193 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 53 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 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 = 0.3516 r_free = 0.3516 target = 0.143576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.125485 restraints weight = 9721.523| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 0.52 r_work: 0.3144 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1272 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 : 0.943 16.571 21434 Z= 0.315 Chirality : 0.038 0.213 2086 Planarity : 0.005 0.048 2604 Dihedral : 15.451 105.849 2702 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.54 % Allowed : 13.66 % Favored : 85.80 % 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: 3.78 (0.21), residues: 1372 helix: 3.43 (0.15), residues: 812 sheet: None (None), residues: 0 loop : 1.21 (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 B 25 ARG 0.003 0.000 ARG V 41 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 780) hydrogen bonds : angle 3.16416 ( 2178) covalent geometry : bond 0.00359 (15316) covalent geometry : angle 0.94284 (21434) Misc. bond : bond 0.17777 ( 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 203 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 197 time to evaluate : 1.761 Fit side-chains REVERT: N 13 ASP cc_start: 0.8271 (t70) cc_final: 0.7935 (t70) REVERT: U 19 LYS cc_start: 0.7994 (ttpt) cc_final: 0.7748 (ttmt) REVERT: b 7 LYS cc_start: 0.8093 (mttm) cc_final: 0.7863 (mtpt) REVERT: f 1 MET cc_start: 0.7641 (mtm) cc_final: 0.7322 (mtp) REVERT: f 13 ASP cc_start: 0.8298 (t70) cc_final: 0.7953 (t70) outliers start: 6 outliers final: 5 residues processed: 202 average time/residue: 1.6623 time to fit residues: 361.3033 Evaluate side-chains 202 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 197 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.8833 > 50: distance: 62 - 63: 9.520 distance: 63 - 64: 11.041 distance: 63 - 66: 4.878 distance: 64 - 65: 9.244 distance: 64 - 70: 43.829 distance: 65 - 231: 36.174 distance: 66 - 67: 27.555 distance: 67 - 68: 19.220 distance: 68 - 69: 36.588 distance: 70 - 71: 14.934 distance: 71 - 72: 8.831 distance: 71 - 74: 16.632 distance: 72 - 73: 10.056 distance: 72 - 77: 20.768 distance: 74 - 75: 11.990 distance: 74 - 76: 57.035 distance: 77 - 78: 18.619 distance: 78 - 79: 21.006 distance: 78 - 81: 56.236 distance: 79 - 80: 18.776 distance: 79 - 88: 44.528 distance: 81 - 82: 56.396 distance: 82 - 84: 41.889 distance: 84 - 86: 40.763 distance: 86 - 87: 15.713 distance: 88 - 89: 39.645 distance: 89 - 90: 51.137 distance: 89 - 92: 38.954 distance: 90 - 91: 44.374 distance: 90 - 94: 29.125 distance: 94 - 95: 24.953 distance: 95 - 96: 12.227 distance: 95 - 98: 31.177 distance: 96 - 97: 44.363 distance: 96 - 101: 34.421 distance: 97 - 120: 15.842 distance: 98 - 99: 5.968 distance: 98 - 100: 24.330 distance: 101 - 102: 34.943 distance: 102 - 103: 21.563 distance: 102 - 105: 46.515 distance: 103 - 104: 5.827 distance: 103 - 111: 12.260 distance: 104 - 127: 14.680 distance: 105 - 106: 39.502 distance: 106 - 107: 48.359 distance: 106 - 108: 23.160 distance: 107 - 109: 19.054 distance: 108 - 110: 14.911 distance: 109 - 110: 20.574 distance: 111 - 112: 29.990 distance: 112 - 113: 40.548 distance: 112 - 115: 27.011 distance: 113 - 114: 35.736 distance: 113 - 120: 36.344 distance: 114 - 141: 26.967 distance: 115 - 116: 21.634 distance: 116 - 117: 34.735 distance: 117 - 118: 29.600 distance: 118 - 119: 15.729 distance: 120 - 121: 20.430 distance: 121 - 122: 43.816 distance: 121 - 124: 20.480 distance: 122 - 123: 15.750 distance: 122 - 127: 17.135 distance: 123 - 149: 34.629 distance: 124 - 125: 4.540 distance: 124 - 126: 47.126 distance: 127 - 128: 18.388 distance: 128 - 129: 24.843 distance: 128 - 131: 13.628 distance: 129 - 130: 17.335 distance: 129 - 141: 20.500 distance: 131 - 132: 11.699 distance: 132 - 133: 26.013 distance: 132 - 134: 14.462 distance: 133 - 135: 3.310 distance: 134 - 136: 17.361 distance: 134 - 137: 5.184 distance: 135 - 136: 24.915 distance: 136 - 138: 10.623 distance: 137 - 139: 14.769 distance: 138 - 140: 11.711 distance: 139 - 140: 4.259