Starting phenix.real_space_refine on Wed Mar 4 02:10:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ze8_14685/03_2026/7ze8_14685.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ze8_14685/03_2026/7ze8_14685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ze8_14685/03_2026/7ze8_14685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ze8_14685/03_2026/7ze8_14685.map" model { file = "/net/cci-nas-00/data/ceres_data/7ze8_14685/03_2026/7ze8_14685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ze8_14685/03_2026/7ze8_14685.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 33 5.21 5 S 9 5.16 5 C 7166 2.51 5 N 1374 2.21 5 O 1486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10068 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 371 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "C" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 371 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "E" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 371 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "G" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 371 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "I" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 371 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "K" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 371 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 371 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "O" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 371 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "Q" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 371 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "S" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 744 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PCIS': 6, 'TRANS': 87} Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" 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: "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: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "M" 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: "N" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "O" 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: "P" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" 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: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 396 Unusual residues: {'BCL': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 2.34, per 1000 atoms: 0.23 Number of scatterers: 10068 At special positions: 0 Unit cell: (95.55, 104, 76.05, 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 9 16.00 Mg 33 11.99 O 1486 8.00 N 1374 7.00 C 7166 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=33, symmetry=0 Number of additional bonds: simple=33, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 323.2 milliseconds 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 73.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 11 through 38 Proline residue: A 17 - end of helix Processing helix chain 'A' and resid 38 through 47 removed outlier: 3.637A pdb=" N SER A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP A 45 " --> pdb=" O PHE A 41 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 43 removed outlier: 4.089A pdb=" N HIS B 20 " --> pdb=" O GLU B 16 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 11 through 38 Proline residue: C 17 - end of helix Processing helix chain 'C' and resid 38 through 47 removed outlier: 3.855A pdb=" N SER C 42 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 43 removed outlier: 3.942A pdb=" N HIS D 20 " --> pdb=" O GLU D 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 9 removed outlier: 4.112A pdb=" N GLY E 4 " --> pdb=" O CXM E 1 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG E 5 " --> pdb=" O ASN E 2 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TRP E 7 " --> pdb=" O GLY E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 38 Proline residue: E 17 - end of helix Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.795A pdb=" N SER E 42 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP E 45 " --> pdb=" O PHE E 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 43 removed outlier: 3.821A pdb=" N HIS F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 11 through 37 Proline residue: G 17 - end of helix Processing helix chain 'G' and resid 38 through 47 removed outlier: 3.775A pdb=" N SER G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP G 45 " --> pdb=" O PHE G 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 42 removed outlier: 3.905A pdb=" N HIS H 20 " --> pdb=" O GLU H 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 9 Processing helix chain 'I' and resid 11 through 37 Proline residue: I 17 - end of helix Processing helix chain 'I' and resid 38 through 47 removed outlier: 3.836A pdb=" N SER I 42 " --> pdb=" O THR I 38 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 42 removed outlier: 3.757A pdb=" N HIS J 20 " --> pdb=" O GLU J 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 9 Processing helix chain 'K' and resid 11 through 38 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 38 through 47 removed outlier: 3.903A pdb=" N SER K 42 " --> pdb=" O THR K 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 42 removed outlier: 3.995A pdb=" N HIS L 20 " --> pdb=" O GLU L 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 9 Processing helix chain 'M' and resid 11 through 37 Proline residue: M 17 - end of helix Processing helix chain 'M' and resid 38 through 47 removed outlier: 3.999A pdb=" N SER M 42 " --> pdb=" O THR M 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 42 removed outlier: 3.929A pdb=" N HIS N 20 " --> pdb=" O GLU N 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 9 Processing helix chain 'O' and resid 11 through 37 Proline residue: O 17 - end of helix Processing helix chain 'O' and resid 38 through 47 removed outlier: 3.837A pdb=" N SER O 42 " --> pdb=" O THR O 38 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP O 45 " --> pdb=" O PHE O 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 43 removed outlier: 3.536A pdb=" N HIS P 20 " --> pdb=" O GLU P 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 9 Processing helix chain 'Q' and resid 11 through 37 Proline residue: Q 17 - end of helix Processing helix chain 'Q' and resid 38 through 47 removed outlier: 3.817A pdb=" N SER Q 42 " --> pdb=" O THR Q 38 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP Q 45 " --> pdb=" O PHE Q 41 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN Q 46 " --> pdb=" O SER Q 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 43 removed outlier: 3.879A pdb=" N HIS R 20 " --> pdb=" O GLU R 16 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL R 34 " --> pdb=" O ALA R 30 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.37: 2887 1.37 - 1.57: 7521 1.57 - 1.78: 9 1.78 - 1.98: 9 1.98 - 2.18: 132 Bond restraints: 10558 Sorted by residual: bond pdb=" SD CXM M 1 " pdb=" CE CXM M 1 " ideal model delta sigma weight residual 1.808 1.762 0.046 2.00e-02 2.50e+03 5.22e+00 bond pdb=" SD CXM I 1 " pdb=" CE CXM I 1 " ideal model delta sigma weight residual 1.808 1.762 0.046 2.00e-02 2.50e+03 5.22e+00 bond pdb=" SD CXM O 1 " pdb=" CE CXM O 1 " ideal model delta sigma weight residual 1.808 1.762 0.046 2.00e-02 2.50e+03 5.19e+00 bond pdb=" SD CXM A 1 " pdb=" CE CXM A 1 " ideal model delta sigma weight residual 1.808 1.763 0.045 2.00e-02 2.50e+03 5.09e+00 bond pdb=" SD CXM E 1 " pdb=" CE CXM E 1 " ideal model delta sigma weight residual 1.808 1.763 0.045 2.00e-02 2.50e+03 5.07e+00 ... (remaining 10553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.28: 14810 5.28 - 10.56: 22 10.56 - 15.84: 0 15.84 - 21.13: 2 21.13 - 26.41: 3 Bond angle restraints: 14837 Sorted by residual: angle pdb=" C1 BCL S 105 " pdb=" O2A BCL S 105 " pdb=" CGA BCL S 105 " ideal model delta sigma weight residual 116.11 142.52 -26.41 4.27e+00 5.48e-02 3.82e+01 angle pdb=" C1 BCL S 102 " pdb=" C2 BCL S 102 " pdb=" C3 BCL S 102 " ideal model delta sigma weight residual 123.38 147.16 -23.79 4.41e+00 5.14e-02 2.91e+01 angle pdb=" C1 BCL S 106 " pdb=" O2A BCL S 106 " pdb=" CGA BCL S 106 " ideal model delta sigma weight residual 116.11 137.48 -21.36 4.27e+00 5.48e-02 2.50e+01 angle pdb=" N GLY M 21 " pdb=" CA GLY M 21 " pdb=" C GLY M 21 " ideal model delta sigma weight residual 112.50 117.35 -4.85 1.16e+00 7.43e-01 1.75e+01 angle pdb=" C1 BCL I 101 " pdb=" C2 BCL I 101 " pdb=" C3 BCL I 101 " ideal model delta sigma weight residual 123.38 140.31 -16.93 4.41e+00 5.14e-02 1.48e+01 ... (remaining 14832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.36: 4937 21.36 - 42.71: 314 42.71 - 64.07: 43 64.07 - 85.43: 4 85.43 - 106.78: 7 Dihedral angle restraints: 5305 sinusoidal: 2624 harmonic: 2681 Sorted by residual: dihedral pdb=" C1 BCL S 105 " pdb=" CGA BCL S 105 " pdb=" O2A BCL S 105 " pdb=" CBA BCL S 105 " ideal model delta sinusoidal sigma weight residual -180.00 -147.50 -32.50 1 6.00e+00 2.78e-02 4.18e+01 dihedral pdb=" CA LEU D 46 " pdb=" C LEU D 46 " pdb=" N HIS D 47 " pdb=" CA HIS D 47 " ideal model delta harmonic sigma weight residual 180.00 -151.80 -28.20 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA LEU N 46 " pdb=" C LEU N 46 " pdb=" N HIS N 47 " pdb=" CA HIS N 47 " ideal model delta harmonic sigma weight residual -180.00 -151.82 -28.18 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 5302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1071 0.041 - 0.082: 309 0.082 - 0.123: 92 0.123 - 0.164: 5 0.164 - 0.204: 3 Chirality restraints: 1480 Sorted by residual: chirality pdb=" CBD BCL A 101 " pdb=" CAD BCL A 101 " pdb=" CGD BCL A 101 " pdb=" CHA BCL A 101 " both_signs ideal model delta sigma weight residual False 2.62 2.42 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CBD BCL I 101 " pdb=" CAD BCL I 101 " pdb=" CGD BCL I 101 " pdb=" CHA BCL I 101 " both_signs ideal model delta sigma weight residual False 2.62 2.42 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CBD BCL G 101 " pdb=" CAD BCL G 101 " pdb=" CGD BCL G 101 " pdb=" CHA BCL G 101 " both_signs ideal model delta sigma weight residual False 2.62 2.45 0.17 2.00e-01 2.50e+01 7.46e-01 ... (remaining 1477 not shown) Planarity restraints: 1772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 IRM P 101 " 0.085 2.00e-02 2.50e+03 7.14e-02 6.37e+01 pdb=" C17 IRM P 101 " -0.106 2.00e-02 2.50e+03 pdb=" C18 IRM P 101 " -0.045 2.00e-02 2.50e+03 pdb=" C19 IRM P 101 " 0.070 2.00e-02 2.50e+03 pdb=" C36 IRM P 101 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 IRM C 103 " 0.083 2.00e-02 2.50e+03 7.04e-02 6.19e+01 pdb=" C17 IRM C 103 " -0.100 2.00e-02 2.50e+03 pdb=" C18 IRM C 103 " -0.052 2.00e-02 2.50e+03 pdb=" C19 IRM C 103 " 0.071 2.00e-02 2.50e+03 pdb=" C36 IRM C 103 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL S 105 " -0.107 3.00e-02 1.11e+03 1.01e-01 5.71e+01 pdb=" CBA BCL S 105 " -0.053 3.00e-02 1.11e+03 pdb=" CGA BCL S 105 " -0.032 3.00e-02 1.11e+03 pdb=" O1A BCL S 105 " 0.002 3.00e-02 1.11e+03 pdb=" O2A BCL S 105 " 0.190 3.00e-02 1.11e+03 ... (remaining 1769 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 710 2.74 - 3.28: 9071 3.28 - 3.82: 16567 3.82 - 4.36: 20774 4.36 - 4.90: 35796 Nonbonded interactions: 82918 Sorted by model distance: nonbonded pdb=" OD2 ASP H 23 " pdb=" OH TYR S 21 " model vdw 2.203 3.040 nonbonded pdb=" OD2 ASP F 23 " pdb=" OH TYR S 5 " model vdw 2.280 3.040 nonbonded pdb=" OD2 ASP N 23 " pdb=" OH TYR S 69 " model vdw 2.289 3.040 nonbonded pdb=" ON2 CXM M 1 " pdb=" NE2 HIS N 18 " model vdw 2.323 3.120 nonbonded pdb=" ON2 CXM C 1 " pdb=" NE2 HIS D 18 " model vdw 2.340 3.120 ... (remaining 82913 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 102) selection = (chain 'C' and resid 1 through 102) selection = chain 'E' selection = (chain 'G' and resid 1 through 102) selection = (chain 'I' and resid 1 through 102) selection = (chain 'K' and resid 1 through 102) selection = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = (chain 'B' and resid 2 through 47) selection = (chain 'D' and resid 2 through 47) selection = (chain 'F' and resid 2 through 47) selection = (chain 'H' and resid 2 through 47) selection = (chain 'J' and resid 2 through 47) selection = (chain 'L' and resid 2 through 47) selection = (chain 'N' and resid 2 through 47) selection = (chain 'P' and resid 2 through 47) selection = (chain 'R' and resid 2 through 47) } 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 group one per residue 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.790 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.010 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.019 0.405 10591 Z= 1.677 Angle : 0.942 26.408 14837 Z= 0.393 Chirality : 0.041 0.204 1480 Planarity : 0.011 0.101 1772 Dihedral : 14.048 106.781 3581 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.25), residues: 893 helix: 0.72 (0.18), residues: 585 sheet: None (None), residues: 0 loop : -0.27 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.005 ARG B 26 TYR 0.032 0.003 TYR S 53 PHE 0.019 0.001 PHE K 32 TRP 0.021 0.002 TRP O 40 HIS 0.003 0.001 HIS N 18 Details of bonding type rmsd covalent geometry : bond 0.00486 (10558) covalent geometry : angle 0.94206 (14837) hydrogen bonds : bond 0.15594 ( 495) hydrogen bonds : angle 6.39498 ( 1428) Misc. bond : bond 0.32342 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.398 Fit side-chains REVERT: D 16 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6783 (tp30) REVERT: G 5 ARG cc_start: 0.7433 (mtt180) cc_final: 0.6978 (mtt180) REVERT: K 46 ASN cc_start: 0.7332 (t0) cc_final: 0.6995 (m-40) REVERT: O 2 ASN cc_start: 0.8977 (m110) cc_final: 0.8451 (m110) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0808 time to fit residues: 7.4059 Evaluate side-chains 39 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.0870 overall best weight: 1.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN C 37 ASN C 46 ASN E 3 GLN H 20 HIS K 3 GLN L 20 HIS ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 20 HIS Q 46 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.108351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.098361 restraints weight = 11281.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.091367 restraints weight = 14824.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.091696 restraints weight = 12125.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.091832 restraints weight = 11391.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.092000 restraints weight = 11074.509| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.407 10591 Z= 0.156 Angle : 0.741 8.381 14837 Z= 0.288 Chirality : 0.038 0.127 1480 Planarity : 0.005 0.036 1772 Dihedral : 14.263 102.062 1988 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.13 % Allowed : 3.80 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.27), residues: 893 helix: 3.21 (0.19), residues: 558 sheet: None (None), residues: 0 loop : -0.46 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 26 TYR 0.007 0.001 TYR Q 44 PHE 0.011 0.001 PHE K 32 TRP 0.017 0.002 TRP C 45 HIS 0.005 0.001 HIS R 36 Details of bonding type rmsd covalent geometry : bond 0.00370 (10558) covalent geometry : angle 0.74062 (14837) hydrogen bonds : bond 0.04427 ( 495) hydrogen bonds : angle 3.43323 ( 1428) Misc. bond : bond 0.14346 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.341 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.1074 time to fit residues: 5.3376 Evaluate side-chains 29 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 75 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 40.0000 chunk 74 optimal weight: 0.0030 chunk 31 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 ASN ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.104798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.090353 restraints weight = 11464.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.090554 restraints weight = 10402.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.090624 restraints weight = 9823.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.090680 restraints weight = 9644.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.090754 restraints weight = 9520.351| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.443 10591 Z= 0.206 Angle : 0.837 10.596 14837 Z= 0.309 Chirality : 0.041 0.130 1480 Planarity : 0.005 0.038 1772 Dihedral : 14.808 99.250 1988 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.38 % Allowed : 6.46 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.26), residues: 893 helix: 2.86 (0.19), residues: 558 sheet: None (None), residues: 0 loop : -0.65 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG Q 5 TYR 0.008 0.001 TYR N 42 PHE 0.016 0.002 PHE K 32 TRP 0.014 0.002 TRP E 40 HIS 0.007 0.002 HIS R 36 Details of bonding type rmsd covalent geometry : bond 0.00538 (10558) covalent geometry : angle 0.83687 (14837) hydrogen bonds : bond 0.04604 ( 495) hydrogen bonds : angle 3.41555 ( 1428) Misc. bond : bond 0.13629 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.289 Fit side-chains REVERT: G 5 ARG cc_start: 0.7715 (mtt180) cc_final: 0.7243 (mtt180) outliers start: 3 outliers final: 3 residues processed: 42 average time/residue: 0.0854 time to fit residues: 5.7592 Evaluate side-chains 38 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain O residue 42 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 75 optimal weight: 0.0050 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 ASN M 37 ASN Q 2 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.111435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.096855 restraints weight = 11143.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.097613 restraints weight = 9232.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.097592 restraints weight = 8405.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.097669 restraints weight = 8407.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.097687 restraints weight = 8328.250| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.322 10591 Z= 0.117 Angle : 0.672 11.300 14837 Z= 0.251 Chirality : 0.036 0.115 1480 Planarity : 0.005 0.040 1772 Dihedral : 14.492 98.374 1988 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.38 % Allowed : 8.37 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.26), residues: 893 helix: 3.33 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.45 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 5 TYR 0.007 0.001 TYR S 21 PHE 0.006 0.001 PHE E 41 TRP 0.012 0.001 TRP K 45 HIS 0.003 0.001 HIS N 20 Details of bonding type rmsd covalent geometry : bond 0.00270 (10558) covalent geometry : angle 0.67184 (14837) hydrogen bonds : bond 0.03685 ( 495) hydrogen bonds : angle 3.05124 ( 1428) Misc. bond : bond 0.09475 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.321 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 46 average time/residue: 0.0861 time to fit residues: 6.4608 Evaluate side-chains 37 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 65 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN Q 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.114008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.098574 restraints weight = 11049.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.100092 restraints weight = 8947.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.101094 restraints weight = 7673.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.101094 restraints weight = 6864.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.101094 restraints weight = 6864.706| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.174 10591 Z= 0.104 Angle : 0.641 11.520 14837 Z= 0.239 Chirality : 0.036 0.113 1480 Planarity : 0.004 0.040 1772 Dihedral : 14.080 100.100 1988 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.51 % Allowed : 9.25 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.40 (0.26), residues: 893 helix: 3.55 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -0.34 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 26 TYR 0.010 0.001 TYR S 21 PHE 0.006 0.001 PHE E 41 TRP 0.010 0.001 TRP O 45 HIS 0.003 0.001 HIS H 20 Details of bonding type rmsd covalent geometry : bond 0.00236 (10558) covalent geometry : angle 0.64068 (14837) hydrogen bonds : bond 0.03436 ( 495) hydrogen bonds : angle 2.90968 ( 1428) Misc. bond : bond 0.06354 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.310 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 0.0738 time to fit residues: 5.9748 Evaluate side-chains 45 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain J residue 47 HIS Chi-restraints excluded: chain N residue 47 HIS Chi-restraints excluded: chain Q residue 46 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 35 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 ASN Q 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.107457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.092244 restraints weight = 11411.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.093416 restraints weight = 9416.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.094515 restraints weight = 8216.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.095028 restraints weight = 7476.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.095536 restraints weight = 7021.088| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.386 10591 Z= 0.168 Angle : 0.753 12.826 14837 Z= 0.275 Chirality : 0.039 0.122 1480 Planarity : 0.005 0.039 1772 Dihedral : 14.277 100.177 1988 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.01 % Allowed : 9.51 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.26), residues: 893 helix: 3.25 (0.19), residues: 558 sheet: None (None), residues: 0 loop : -0.64 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 5 TYR 0.017 0.001 TYR Q 44 PHE 0.010 0.001 PHE K 32 TRP 0.011 0.001 TRP G 7 HIS 0.005 0.001 HIS R 36 Details of bonding type rmsd covalent geometry : bond 0.00435 (10558) covalent geometry : angle 0.75275 (14837) hydrogen bonds : bond 0.03999 ( 495) hydrogen bonds : angle 3.14883 ( 1428) Misc. bond : bond 0.10783 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.310 Fit side-chains REVERT: G 5 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7216 (mtt180) REVERT: P 17 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8077 (tt) outliers start: 8 outliers final: 4 residues processed: 42 average time/residue: 0.0841 time to fit residues: 5.5902 Evaluate side-chains 40 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain N residue 47 HIS Chi-restraints excluded: chain P residue 17 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.108533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.093418 restraints weight = 11263.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.094655 restraints weight = 9311.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.095614 restraints weight = 8079.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.096536 restraints weight = 7274.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.096777 restraints weight = 6729.423| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.350 10591 Z= 0.148 Angle : 0.710 13.289 14837 Z= 0.261 Chirality : 0.037 0.118 1480 Planarity : 0.005 0.040 1772 Dihedral : 14.334 99.475 1988 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.89 % Allowed : 10.14 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.26), residues: 893 helix: 3.28 (0.19), residues: 558 sheet: None (None), residues: 0 loop : -0.67 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 5 TYR 0.011 0.001 TYR S 21 PHE 0.008 0.001 PHE O 41 TRP 0.011 0.001 TRP E 45 HIS 0.004 0.001 HIS R 18 Details of bonding type rmsd covalent geometry : bond 0.00378 (10558) covalent geometry : angle 0.70966 (14837) hydrogen bonds : bond 0.03845 ( 495) hydrogen bonds : angle 3.11473 ( 1428) Misc. bond : bond 0.09323 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.309 Fit side-chains REVERT: G 5 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7202 (mtt180) outliers start: 7 outliers final: 4 residues processed: 41 average time/residue: 0.0877 time to fit residues: 5.6438 Evaluate side-chains 40 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain Q residue 46 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 0.0670 chunk 57 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.110992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.096009 restraints weight = 11110.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.097285 restraints weight = 9058.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.098378 restraints weight = 7815.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.098894 restraints weight = 7073.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.099447 restraints weight = 6639.218| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.239 10591 Z= 0.116 Angle : 0.660 13.229 14837 Z= 0.243 Chirality : 0.036 0.115 1480 Planarity : 0.004 0.040 1772 Dihedral : 14.219 99.689 1988 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.76 % Allowed : 10.39 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.26), residues: 893 helix: 3.51 (0.19), residues: 558 sheet: None (None), residues: 0 loop : -0.65 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 26 TYR 0.009 0.001 TYR S 21 PHE 0.006 0.001 PHE O 41 TRP 0.010 0.001 TRP E 40 HIS 0.003 0.001 HIS N 20 Details of bonding type rmsd covalent geometry : bond 0.00280 (10558) covalent geometry : angle 0.66013 (14837) hydrogen bonds : bond 0.03565 ( 495) hydrogen bonds : angle 2.99437 ( 1428) Misc. bond : bond 0.07314 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.286 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 41 average time/residue: 0.0817 time to fit residues: 5.3610 Evaluate side-chains 41 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain N residue 47 HIS Chi-restraints excluded: chain Q residue 46 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 76 optimal weight: 0.0670 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 0.0870 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 ASN I 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.113809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.100655 restraints weight = 10940.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.100669 restraints weight = 10500.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.100684 restraints weight = 10138.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.100719 restraints weight = 9717.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.100788 restraints weight = 9590.394| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 10591 Z= 0.103 Angle : 0.630 12.919 14837 Z= 0.234 Chirality : 0.035 0.113 1480 Planarity : 0.004 0.039 1772 Dihedral : 13.984 99.138 1988 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.51 % Allowed : 10.77 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.53 (0.26), residues: 893 helix: 3.57 (0.18), residues: 585 sheet: None (None), residues: 0 loop : -0.23 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 26 TYR 0.013 0.001 TYR S 21 PHE 0.005 0.001 PHE B 28 TRP 0.014 0.001 TRP E 45 HIS 0.003 0.001 HIS N 20 Details of bonding type rmsd covalent geometry : bond 0.00243 (10558) covalent geometry : angle 0.62989 (14837) hydrogen bonds : bond 0.03342 ( 495) hydrogen bonds : angle 2.89470 ( 1428) Misc. bond : bond 0.05766 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.184 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 46 average time/residue: 0.0752 time to fit residues: 5.3810 Evaluate side-chains 43 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain N residue 47 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 73 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.111350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.096490 restraints weight = 11030.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.097758 restraints weight = 9157.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.098808 restraints weight = 7882.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.099391 restraints weight = 7129.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.099996 restraints weight = 6642.873| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.256 10591 Z= 0.120 Angle : 0.660 12.969 14837 Z= 0.243 Chirality : 0.036 0.116 1480 Planarity : 0.004 0.039 1772 Dihedral : 14.010 98.263 1988 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.38 % Allowed : 11.41 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.45 (0.26), residues: 893 helix: 3.61 (0.18), residues: 567 sheet: None (None), residues: 0 loop : -0.21 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 26 TYR 0.021 0.001 TYR E 44 PHE 0.006 0.001 PHE E 41 TRP 0.014 0.001 TRP E 45 HIS 0.003 0.001 HIS R 18 Details of bonding type rmsd covalent geometry : bond 0.00298 (10558) covalent geometry : angle 0.66048 (14837) hydrogen bonds : bond 0.03517 ( 495) hydrogen bonds : angle 2.95260 ( 1428) Misc. bond : bond 0.07616 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.308 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 40 average time/residue: 0.0838 time to fit residues: 5.3126 Evaluate side-chains 42 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain N residue 47 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 3 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 74 optimal weight: 0.1980 chunk 73 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.113336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.099283 restraints weight = 11140.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.100477 restraints weight = 9082.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.101493 restraints weight = 7828.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.102415 restraints weight = 6978.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.102415 restraints weight = 6478.306| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 10591 Z= 0.104 Angle : 0.629 12.647 14837 Z= 0.233 Chirality : 0.035 0.113 1480 Planarity : 0.004 0.039 1772 Dihedral : 13.847 96.761 1988 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.63 % Allowed : 11.15 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.61 (0.26), residues: 893 helix: 3.64 (0.18), residues: 585 sheet: None (None), residues: 0 loop : -0.20 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 26 TYR 0.022 0.001 TYR E 44 PHE 0.005 0.001 PHE B 28 TRP 0.013 0.001 TRP E 45 HIS 0.003 0.001 HIS N 20 Details of bonding type rmsd covalent geometry : bond 0.00246 (10558) covalent geometry : angle 0.62939 (14837) hydrogen bonds : bond 0.03345 ( 495) hydrogen bonds : angle 2.89055 ( 1428) Misc. bond : bond 0.05939 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1225.93 seconds wall clock time: 22 minutes 6.59 seconds (1326.59 seconds total)