Starting phenix.real_space_refine on Wed Mar 4 02:10:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zcu_14633/03_2026/7zcu_14633.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zcu_14633/03_2026/7zcu_14633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zcu_14633/03_2026/7zcu_14633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zcu_14633/03_2026/7zcu_14633.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zcu_14633/03_2026/7zcu_14633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zcu_14633/03_2026/7zcu_14633.map" } resolution = 2.7 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= 0.004 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 7184 2.51 5 N 1383 2.21 5 O 1540 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: 10149 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} 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: "C" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "G" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "I" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "K" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "M" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "O" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Q" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} 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: 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} 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 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: 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: "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: 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: "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: 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.48, per 1000 atoms: 0.24 Number of scatterers: 10149 At special positions: 0 Unit cell: (102.05, 95.55, 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 1540 8.00 N 1383 7.00 C 7184 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: 1.00 Conformation dependent library (CDL) restraints added in 523.4 milliseconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1778 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 73.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 removed outlier: 3.838A pdb=" N TRP A 7 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 38 Proline residue: A 17 - end of helix Processing helix chain 'A' and resid 39 through 47 Processing helix chain 'B' and resid 10 through 43 removed outlier: 3.781A pdb=" N HIS B 20 " --> pdb=" O GLU B 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 9 removed outlier: 3.783A pdb=" N TRP C 7 " --> pdb=" O ALA C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 38 Proline residue: C 17 - end of helix Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'D' and resid 10 through 43 removed outlier: 3.588A pdb=" N HIS D 20 " --> pdb=" O GLU D 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 9 removed outlier: 4.039A pdb=" N TRP E 7 " --> pdb=" O ALA 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 39 through 47 Processing helix chain 'F' and resid 10 through 43 removed outlier: 3.758A pdb=" N HIS F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 9 removed outlier: 4.201A pdb=" N TRP G 7 " --> pdb=" O ALA G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 37 Proline residue: G 17 - end of helix Processing helix chain 'G' and resid 39 through 47 Processing helix chain 'H' and resid 10 through 43 removed outlier: 3.858A pdb=" N HIS H 20 " --> pdb=" O GLU H 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 9 removed outlier: 3.846A pdb=" N TRP I 7 " --> pdb=" O ALA I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 37 Proline residue: I 17 - end of helix Processing helix chain 'I' and resid 39 through 47 Processing helix chain 'J' and resid 10 through 43 removed outlier: 3.877A pdb=" N HIS J 20 " --> pdb=" O GLU J 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 9 removed outlier: 4.055A pdb=" N TRP K 7 " --> pdb=" O ALA K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 37 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 39 through 47 Processing helix chain 'L' and resid 10 through 43 removed outlier: 3.732A pdb=" N HIS L 20 " --> pdb=" O GLU L 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 9 removed outlier: 4.172A pdb=" N TRP M 7 " --> pdb=" O ALA M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 38 Proline residue: M 17 - end of helix Processing helix chain 'M' and resid 39 through 47 Processing helix chain 'N' and resid 10 through 43 removed outlier: 3.712A pdb=" N HIS N 20 " --> pdb=" O GLU N 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 9 removed outlier: 3.887A pdb=" N TRP O 7 " --> pdb=" O ALA O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 11 through 38 Proline residue: O 17 - end of helix Processing helix chain 'O' and resid 39 through 47 Processing helix chain 'P' and resid 10 through 43 removed outlier: 3.615A pdb=" N HIS P 20 " --> pdb=" O GLU P 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 9 removed outlier: 3.993A pdb=" N TRP Q 7 " --> pdb=" O ALA Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 38 Proline residue: Q 17 - end of helix Processing helix chain 'Q' and resid 39 through 47 Processing helix chain 'R' and resid 10 through 43 removed outlier: 3.822A pdb=" N HIS R 20 " --> pdb=" O GLU R 16 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1476 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: 1.45 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.36: 2715 1.36 - 1.57: 7747 1.57 - 1.77: 9 1.77 - 1.98: 9 1.98 - 2.18: 132 Bond restraints: 10612 Sorted by residual: bond pdb=" SD CXM G 1 " pdb=" CE CXM G 1 " ideal model delta sigma weight residual 1.808 1.762 0.046 2.00e-02 2.50e+03 5.31e+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 5.23e+00 bond pdb=" SD CXM I 1 " pdb=" CE CXM I 1 " ideal model delta sigma weight residual 1.808 1.763 0.045 2.00e-02 2.50e+03 5.13e+00 bond pdb=" SD CXM C 1 " pdb=" CE CXM C 1 " ideal model delta sigma weight residual 1.808 1.763 0.045 2.00e-02 2.50e+03 5.07e+00 bond pdb=" SD CXM K 1 " pdb=" CE CXM K 1 " ideal model delta sigma weight residual 1.808 1.763 0.045 2.00e-02 2.50e+03 5.07e+00 ... (remaining 10607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.33: 14765 4.33 - 8.66: 130 8.66 - 12.99: 1 12.99 - 17.32: 2 17.32 - 21.65: 2 Bond angle restraints: 14900 Sorted by residual: angle pdb=" C1 BCL S 102 " pdb=" O2A BCL S 102 " pdb=" CGA BCL S 102 " ideal model delta sigma weight residual 116.11 137.77 -21.65 4.27e+00 5.48e-02 2.57e+01 angle pdb=" C1 BCL I 102 " pdb=" C2 BCL I 102 " pdb=" C3 BCL I 102 " ideal model delta sigma weight residual 123.38 143.61 -20.23 4.41e+00 5.14e-02 2.11e+01 angle pdb=" C1 BCL J 101 " pdb=" C2 BCL J 101 " pdb=" C3 BCL J 101 " ideal model delta sigma weight residual 123.38 137.21 -13.84 4.41e+00 5.14e-02 9.85e+00 angle pdb=" C5 IRM G 101 " pdb=" C6 IRM G 101 " pdb=" C7 IRM G 101 " ideal model delta sigma weight residual 126.95 119.33 7.62 3.00e+00 1.11e-01 6.46e+00 angle pdb=" N ALA O 4 " pdb=" CA ALA O 4 " pdb=" C ALA O 4 " ideal model delta sigma weight residual 110.80 116.02 -5.22 2.13e+00 2.20e-01 6.00e+00 ... (remaining 14895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.67: 5245 30.67 - 61.34: 103 61.34 - 92.01: 7 92.01 - 122.68: 12 122.68 - 153.35: 1 Dihedral angle restraints: 5368 sinusoidal: 2615 harmonic: 2753 Sorted by residual: dihedral pdb=" CBD BCL G 102 " pdb=" CGD BCL G 102 " pdb=" O2D BCL G 102 " pdb=" CED BCL G 102 " ideal model delta sinusoidal sigma weight residual -180.00 -26.65 -153.35 1 5.00e+00 4.00e-02 7.27e+02 dihedral pdb=" C1 BCL S 102 " pdb=" CGA BCL S 102 " pdb=" O2A BCL S 102 " pdb=" CBA BCL S 102 " ideal model delta sinusoidal sigma weight residual 180.00 152.12 27.88 1 6.00e+00 2.78e-02 3.10e+01 dihedral pdb=" CA SER S 55 " pdb=" C SER S 55 " pdb=" N PHE S 56 " pdb=" CA PHE S 56 " ideal model delta harmonic sigma weight residual 180.00 153.91 26.09 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 5365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1006 0.035 - 0.070: 366 0.070 - 0.105: 100 0.105 - 0.140: 42 0.140 - 0.176: 2 Chirality restraints: 1516 Sorted by residual: chirality pdb=" C13 BCL M 101 " pdb=" C12 BCL M 101 " pdb=" C14 BCL M 101 " pdb=" C15 BCL M 101 " both_signs ideal model delta sigma weight residual False 2.74 2.57 0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" C8 BCL S 103 " pdb=" C10 BCL S 103 " pdb=" C7 BCL S 103 " pdb=" C9 BCL S 103 " both_signs ideal model delta sigma weight residual False 2.70 2.54 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CA TRP O 7 " pdb=" N TRP O 7 " pdb=" C TRP O 7 " pdb=" CB TRP O 7 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1513 not shown) Planarity restraints: 1781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL I 102 " -0.065 1.50e-02 4.44e+03 5.55e-02 6.85e+01 pdb=" C2 BCL I 102 " 0.095 1.50e-02 4.44e+03 pdb=" C3 BCL I 102 " 0.016 1.50e-02 4.44e+03 pdb=" C4 BCL I 102 " -0.000 1.50e-02 4.44e+03 pdb=" C5 BCL I 102 " -0.045 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL S 102 " 0.116 3.00e-02 1.11e+03 1.03e-01 5.87e+01 pdb=" CBA BCL S 102 " 0.072 3.00e-02 1.11e+03 pdb=" CGA BCL S 102 " -0.002 3.00e-02 1.11e+03 pdb=" O1A BCL S 102 " -0.000 3.00e-02 1.11e+03 pdb=" O2A BCL S 102 " -0.185 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C16 IRM K 101 " -0.078 2.00e-02 2.50e+03 6.55e-02 5.36e+01 pdb=" C17 IRM K 101 " 0.094 2.00e-02 2.50e+03 pdb=" C18 IRM K 101 " 0.047 2.00e-02 2.50e+03 pdb=" C19 IRM K 101 " -0.066 2.00e-02 2.50e+03 pdb=" C36 IRM K 101 " 0.003 2.00e-02 2.50e+03 ... (remaining 1778 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1090 2.75 - 3.29: 9151 3.29 - 3.83: 18085 3.83 - 4.36: 22249 4.36 - 4.90: 36986 Nonbonded interactions: 87561 Sorted by model distance: nonbonded pdb=" OE1 GLU S 18 " pdb=" NH2 ARG Q 5 " model vdw 2.218 3.120 nonbonded pdb=" O THR O 38 " pdb=" O HOH O 201 " model vdw 2.224 3.040 nonbonded pdb=" O THR I 38 " pdb=" O HOH I 201 " model vdw 2.239 3.040 nonbonded pdb=" O THR A 38 " pdb=" O HOH A 201 " model vdw 2.252 3.040 nonbonded pdb=" O THR C 38 " pdb=" O HOH C 201 " model vdw 2.260 3.040 ... (remaining 87556 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 50 or resid 102)) selection = (chain 'C' and (resid 1 through 50 or resid 102)) selection = (chain 'E' and (resid 1 through 50 or resid 102)) selection = (chain 'G' and (resid 1 through 50 or resid 102)) selection = (chain 'I' and (resid 1 through 50 or resid 102)) selection = (chain 'K' and (resid 1 through 50 or resid 102)) selection = (chain 'M' and (resid 1 through 50 or resid 102)) selection = (chain 'O' and (resid 1 through 50 or resid 102)) selection = (chain 'Q' and (resid 1 through 50 or resid 102)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.410 Find NCS groups from input model: 0.250 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:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 : 0.018 0.405 10645 Z= 1.671 Angle : 0.946 21.650 14900 Z= 0.374 Chirality : 0.042 0.176 1516 Planarity : 0.010 0.103 1781 Dihedral : 14.366 153.350 3590 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.25), residues: 911 helix: 1.69 (0.19), residues: 612 sheet: None (None), residues: 0 loop : -0.45 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.003 ARG R 26 TYR 0.023 0.004 TYR S 85 PHE 0.015 0.002 PHE A 32 TRP 0.024 0.003 TRP M 7 HIS 0.008 0.002 HIS I 37 Details of bonding type rmsd covalent geometry : bond 0.00475 (10612) covalent geometry : angle 0.94606 (14900) hydrogen bonds : bond 0.13414 ( 519) hydrogen bonds : angle 5.72348 ( 1476) Misc. bond : bond 0.31854 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.318 Fit side-chains REVERT: A 43 LYS cc_start: 0.7859 (tttt) cc_final: 0.7585 (ttpt) REVERT: B 19 LYS cc_start: 0.8207 (mttt) cc_final: 0.8002 (mttm) REVERT: D 16 GLU cc_start: 0.7407 (tp30) cc_final: 0.7081 (tp30) REVERT: G 43 LYS cc_start: 0.8163 (tttt) cc_final: 0.7838 (tmtt) REVERT: I 11 LYS cc_start: 0.8010 (mttt) cc_final: 0.7739 (mtmt) REVERT: J 15 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7608 (mt-10) REVERT: L 23 ASP cc_start: 0.7278 (t70) cc_final: 0.7076 (t70) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.6444 time to fit residues: 95.2303 Evaluate side-chains 94 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.0570 chunk 74 optimal weight: 6.9990 overall best weight: 1.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 HIS K 3 GLN L 47 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.127536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.098108 restraints weight = 10733.695| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.43 r_work: 0.2820 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.290 10645 Z= 0.153 Angle : 0.839 12.492 14900 Z= 0.295 Chirality : 0.040 0.119 1516 Planarity : 0.005 0.030 1781 Dihedral : 14.076 105.574 2006 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.52 % Allowed : 7.73 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 3.33 (0.26), residues: 911 helix: 3.39 (0.18), residues: 585 sheet: None (None), residues: 0 loop : -0.10 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG O 5 TYR 0.010 0.001 TYR P 40 PHE 0.006 0.001 PHE S 56 TRP 0.017 0.002 TRP M 45 HIS 0.009 0.002 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00363 (10612) covalent geometry : angle 0.83945 (14900) hydrogen bonds : bond 0.04322 ( 519) hydrogen bonds : angle 3.54045 ( 1476) Misc. bond : bond 0.12481 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.252 Fit side-chains REVERT: A 43 LYS cc_start: 0.8090 (tttt) cc_final: 0.7712 (ttpt) REVERT: B 16 GLU cc_start: 0.7793 (tp30) cc_final: 0.7405 (mm-30) REVERT: B 19 LYS cc_start: 0.8339 (mttt) cc_final: 0.8078 (mttm) REVERT: S 93 LEU cc_start: 0.6847 (mt) cc_final: 0.6566 (mm) REVERT: G 43 LYS cc_start: 0.8330 (tttt) cc_final: 0.7670 (mptm) REVERT: H 13 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7573 (mt-10) REVERT: H 23 ASP cc_start: 0.8351 (t70) cc_final: 0.8112 (t0) REVERT: I 11 LYS cc_start: 0.8056 (mttt) cc_final: 0.7781 (mppt) outliers start: 12 outliers final: 3 residues processed: 96 average time/residue: 0.6939 time to fit residues: 70.7279 Evaluate side-chains 88 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain N residue 23 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 3 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 65 GLN D 47 HIS P 20 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.124241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.094292 restraints weight = 10800.953| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.46 r_work: 0.2775 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.339 10645 Z= 0.212 Angle : 0.924 17.610 14900 Z= 0.318 Chirality : 0.044 0.120 1516 Planarity : 0.005 0.032 1781 Dihedral : 14.488 111.823 2006 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.77 % Allowed : 8.75 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 911 helix: 3.10 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.09 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 5 TYR 0.008 0.001 TYR P 40 PHE 0.010 0.002 PHE S 56 TRP 0.014 0.002 TRP M 7 HIS 0.008 0.002 HIS M 37 Details of bonding type rmsd covalent geometry : bond 0.00538 (10612) covalent geometry : angle 0.92428 (14900) hydrogen bonds : bond 0.04817 ( 519) hydrogen bonds : angle 3.68147 ( 1476) Misc. bond : bond 0.12497 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.259 Fit side-chains REVERT: A 43 LYS cc_start: 0.8084 (tttt) cc_final: 0.7703 (ttpt) REVERT: B 12 GLU cc_start: 0.7109 (mp0) cc_final: 0.6894 (mp0) REVERT: B 16 GLU cc_start: 0.7930 (tp30) cc_final: 0.7518 (mm-30) REVERT: B 19 LYS cc_start: 0.8414 (mttt) cc_final: 0.8081 (mttm) REVERT: E 5 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7701 (mtt-85) REVERT: E 11 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8317 (mttt) REVERT: G 43 LYS cc_start: 0.8345 (tttt) cc_final: 0.7941 (tmtt) REVERT: H 23 ASP cc_start: 0.8403 (t70) cc_final: 0.8153 (t0) REVERT: I 11 LYS cc_start: 0.8086 (mttt) cc_final: 0.7829 (mttt) REVERT: N 23 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7926 (m-30) outliers start: 14 outliers final: 5 residues processed: 88 average time/residue: 0.7823 time to fit residues: 72.5520 Evaluate side-chains 88 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain N residue 23 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 57 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.126029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.096136 restraints weight = 10784.114| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.45 r_work: 0.2805 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.308 10645 Z= 0.148 Angle : 0.814 12.024 14900 Z= 0.277 Chirality : 0.039 0.111 1516 Planarity : 0.004 0.030 1781 Dihedral : 13.974 105.366 2006 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.52 % Allowed : 9.76 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 3.37 (0.26), residues: 911 helix: 3.29 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.22 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 5 TYR 0.007 0.001 TYR P 40 PHE 0.006 0.001 PHE J 28 TRP 0.011 0.002 TRP C 40 HIS 0.006 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00361 (10612) covalent geometry : angle 0.81411 (14900) hydrogen bonds : bond 0.04238 ( 519) hydrogen bonds : angle 3.42667 ( 1476) Misc. bond : bond 0.11212 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.325 Fit side-chains REVERT: A 43 LYS cc_start: 0.8086 (tttt) cc_final: 0.7679 (ttpt) REVERT: B 16 GLU cc_start: 0.7895 (tp30) cc_final: 0.7486 (mm-30) REVERT: B 19 LYS cc_start: 0.8381 (mttt) cc_final: 0.8101 (mttm) REVERT: E 11 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8272 (mttt) REVERT: G 43 LYS cc_start: 0.8345 (tttt) cc_final: 0.7941 (tmtt) REVERT: N 23 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7898 (m-30) outliers start: 12 outliers final: 4 residues processed: 86 average time/residue: 0.7355 time to fit residues: 66.7581 Evaluate side-chains 84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain Q residue 43 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 28 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.0870 chunk 54 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 77 optimal weight: 0.0170 chunk 20 optimal weight: 0.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.128406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.099598 restraints weight = 10783.614| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.41 r_work: 0.2849 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.238 10645 Z= 0.113 Angle : 0.747 11.934 14900 Z= 0.251 Chirality : 0.037 0.111 1516 Planarity : 0.004 0.027 1781 Dihedral : 13.471 98.711 2006 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.14 % Allowed : 11.15 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 3.67 (0.26), residues: 911 helix: 3.55 (0.17), residues: 585 sheet: None (None), residues: 0 loop : 0.28 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 5 TYR 0.006 0.001 TYR S 5 PHE 0.006 0.001 PHE H 28 TRP 0.010 0.001 TRP K 40 HIS 0.006 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00261 (10612) covalent geometry : angle 0.74734 (14900) hydrogen bonds : bond 0.03784 ( 519) hydrogen bonds : angle 3.19284 ( 1476) Misc. bond : bond 0.09274 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.229 Fit side-chains REVERT: A 43 LYS cc_start: 0.8033 (tttt) cc_final: 0.7623 (ttpt) REVERT: B 16 GLU cc_start: 0.7854 (tp30) cc_final: 0.7449 (mm-30) REVERT: B 19 LYS cc_start: 0.8362 (mttt) cc_final: 0.8099 (mttm) REVERT: E 5 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7664 (mtt-85) REVERT: F 15 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7763 (mt-10) REVERT: G 43 LYS cc_start: 0.8279 (tttt) cc_final: 0.7602 (mptm) REVERT: H 13 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7570 (mt-10) REVERT: M 42 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8336 (m) REVERT: M 43 LYS cc_start: 0.8466 (ttpt) cc_final: 0.7746 (mttt) REVERT: N 23 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7878 (m-30) outliers start: 9 outliers final: 2 residues processed: 88 average time/residue: 0.7314 time to fit residues: 68.2287 Evaluate side-chains 85 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain Q residue 43 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 13 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.127789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.098966 restraints weight = 10872.078| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.42 r_work: 0.2840 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.242 10645 Z= 0.121 Angle : 0.764 12.349 14900 Z= 0.255 Chirality : 0.037 0.111 1516 Planarity : 0.004 0.026 1781 Dihedral : 13.275 98.368 2006 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.39 % Allowed : 11.41 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 3.70 (0.26), residues: 911 helix: 3.55 (0.17), residues: 585 sheet: None (None), residues: 0 loop : 0.36 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 5 TYR 0.006 0.001 TYR S 5 PHE 0.006 0.001 PHE H 28 TRP 0.010 0.001 TRP C 40 HIS 0.005 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00288 (10612) covalent geometry : angle 0.76351 (14900) hydrogen bonds : bond 0.03885 ( 519) hydrogen bonds : angle 3.18589 ( 1476) Misc. bond : bond 0.09648 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.246 Fit side-chains REVERT: A 43 LYS cc_start: 0.8045 (tttt) cc_final: 0.7659 (ttpt) REVERT: B 16 GLU cc_start: 0.7903 (tp30) cc_final: 0.7486 (mm-30) REVERT: B 19 LYS cc_start: 0.8379 (mttt) cc_final: 0.8110 (mttm) REVERT: E 5 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7657 (mtt-85) REVERT: E 11 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8249 (mttt) REVERT: G 43 LYS cc_start: 0.8274 (tttt) cc_final: 0.7596 (mptm) REVERT: H 13 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7571 (mt-10) REVERT: L 46 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8571 (mp) REVERT: M 42 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.8347 (m) REVERT: M 43 LYS cc_start: 0.8446 (ttpt) cc_final: 0.7726 (mttt) REVERT: N 23 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7840 (m-30) outliers start: 11 outliers final: 3 residues processed: 84 average time/residue: 0.7492 time to fit residues: 66.5969 Evaluate side-chains 88 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain Q residue 43 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 HIS F 20 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.123709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.094269 restraints weight = 10820.501| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.42 r_work: 0.2767 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.343 10645 Z= 0.253 Angle : 0.962 19.462 14900 Z= 0.326 Chirality : 0.046 0.139 1516 Planarity : 0.005 0.032 1781 Dihedral : 14.254 110.617 2006 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.65 % Allowed : 11.28 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 911 helix: 3.02 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.29 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 5 TYR 0.008 0.002 TYR F 40 PHE 0.011 0.002 PHE J 28 TRP 0.014 0.002 TRP M 7 HIS 0.008 0.002 HIS J 36 Details of bonding type rmsd covalent geometry : bond 0.00655 (10612) covalent geometry : angle 0.96240 (14900) hydrogen bonds : bond 0.04862 ( 519) hydrogen bonds : angle 3.64163 ( 1476) Misc. bond : bond 0.11998 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.275 Fit side-chains REVERT: A 43 LYS cc_start: 0.8127 (tttt) cc_final: 0.7721 (ttpt) REVERT: B 16 GLU cc_start: 0.8000 (tp30) cc_final: 0.7641 (mm-30) REVERT: B 19 LYS cc_start: 0.8423 (mttt) cc_final: 0.8156 (mttm) REVERT: E 5 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7721 (mtt-85) REVERT: E 11 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8335 (mttt) REVERT: F 15 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7854 (mt-10) REVERT: G 43 LYS cc_start: 0.8380 (tttt) cc_final: 0.7719 (tptm) REVERT: L 46 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8579 (mp) outliers start: 13 outliers final: 7 residues processed: 86 average time/residue: 0.7587 time to fit residues: 69.0162 Evaluate side-chains 89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain Q residue 43 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 30.0000 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.0570 chunk 52 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.128750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.099872 restraints weight = 10794.700| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.44 r_work: 0.2851 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.205 10645 Z= 0.109 Angle : 0.749 12.181 14900 Z= 0.250 Chirality : 0.036 0.113 1516 Planarity : 0.004 0.027 1781 Dihedral : 13.453 99.062 2006 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 1.39 % Allowed : 12.17 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 911 helix: 3.49 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.29 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 5 TYR 0.005 0.001 TYR A 44 PHE 0.006 0.001 PHE H 28 TRP 0.009 0.001 TRP K 40 HIS 0.005 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00251 (10612) covalent geometry : angle 0.74860 (14900) hydrogen bonds : bond 0.03737 ( 519) hydrogen bonds : angle 3.18108 ( 1476) Misc. bond : bond 0.08858 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.472 Fit side-chains REVERT: A 43 LYS cc_start: 0.8068 (tttt) cc_final: 0.7651 (ttpt) REVERT: B 16 GLU cc_start: 0.7916 (tp30) cc_final: 0.7505 (mm-30) REVERT: B 19 LYS cc_start: 0.8397 (mttt) cc_final: 0.8100 (mttm) REVERT: E 5 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7610 (mtt-85) REVERT: E 11 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8261 (mttt) REVERT: F 15 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7732 (mt-10) REVERT: G 43 LYS cc_start: 0.8238 (tttt) cc_final: 0.7554 (mptm) REVERT: H 13 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7505 (mt-10) REVERT: M 43 LYS cc_start: 0.8418 (ttpt) cc_final: 0.7682 (mttt) REVERT: N 23 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7852 (m-30) outliers start: 11 outliers final: 4 residues processed: 85 average time/residue: 0.7442 time to fit residues: 67.4002 Evaluate side-chains 88 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain Q residue 43 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 81 optimal weight: 0.0670 chunk 83 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 30.0000 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.126597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.098064 restraints weight = 10844.215| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.40 r_work: 0.2827 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.250 10645 Z= 0.139 Angle : 0.792 12.615 14900 Z= 0.266 Chirality : 0.038 0.113 1516 Planarity : 0.004 0.027 1781 Dihedral : 13.416 100.764 2006 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.27 % Allowed : 12.93 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 3.55 (0.26), residues: 911 helix: 3.44 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.28 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 5 TYR 0.005 0.001 TYR S 5 PHE 0.006 0.001 PHE H 28 TRP 0.011 0.001 TRP C 40 HIS 0.005 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00341 (10612) covalent geometry : angle 0.79231 (14900) hydrogen bonds : bond 0.04025 ( 519) hydrogen bonds : angle 3.26757 ( 1476) Misc. bond : bond 0.10037 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.348 Fit side-chains REVERT: A 43 LYS cc_start: 0.8089 (tttt) cc_final: 0.7697 (ttpt) REVERT: B 16 GLU cc_start: 0.7965 (tp30) cc_final: 0.7557 (mm-30) REVERT: B 19 LYS cc_start: 0.8408 (mttt) cc_final: 0.8124 (mttm) REVERT: E 5 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7614 (mtt-85) REVERT: E 11 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8265 (mttt) REVERT: F 15 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7760 (mt-10) REVERT: G 43 LYS cc_start: 0.8291 (tttt) cc_final: 0.7628 (mptm) REVERT: L 46 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8524 (mp) REVERT: M 43 LYS cc_start: 0.8486 (ttpt) cc_final: 0.7740 (mttt) outliers start: 10 outliers final: 4 residues processed: 84 average time/residue: 0.7701 time to fit residues: 68.2945 Evaluate side-chains 88 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain Q residue 43 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 15 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.125501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.096856 restraints weight = 10810.662| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.41 r_work: 0.2814 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.272 10645 Z= 0.155 Angle : 0.823 13.403 14900 Z= 0.276 Chirality : 0.039 0.113 1516 Planarity : 0.004 0.028 1781 Dihedral : 13.464 102.911 2006 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.14 % Allowed : 13.18 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 911 helix: 3.34 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.27 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 5 TYR 0.005 0.001 TYR F 40 PHE 0.007 0.001 PHE J 28 TRP 0.011 0.001 TRP M 7 HIS 0.006 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00385 (10612) covalent geometry : angle 0.82340 (14900) hydrogen bonds : bond 0.04191 ( 519) hydrogen bonds : angle 3.34529 ( 1476) Misc. bond : bond 0.10525 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.268 Fit side-chains REVERT: A 43 LYS cc_start: 0.8074 (tttt) cc_final: 0.7702 (ttpt) REVERT: B 16 GLU cc_start: 0.7969 (tp30) cc_final: 0.7622 (mm-30) REVERT: B 19 LYS cc_start: 0.8423 (mttt) cc_final: 0.8129 (mttm) REVERT: E 5 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7636 (mtt-85) REVERT: E 11 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8297 (mttt) REVERT: F 15 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7789 (mt-10) REVERT: G 43 LYS cc_start: 0.8307 (tttt) cc_final: 0.7921 (tmtt) REVERT: L 46 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8521 (mp) REVERT: N 23 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7968 (m-30) outliers start: 9 outliers final: 4 residues processed: 85 average time/residue: 0.7765 time to fit residues: 69.7218 Evaluate side-chains 90 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain Q residue 43 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 72 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 14 optimal weight: 30.0000 chunk 52 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3372 r_free = 0.3372 target = 0.124632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.095162 restraints weight = 10871.070| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.43 r_work: 0.2788 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.321 10645 Z= 0.201 Angle : 0.900 17.299 14900 Z= 0.303 Chirality : 0.042 0.118 1516 Planarity : 0.005 0.029 1781 Dihedral : 13.797 106.249 2006 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.39 % Allowed : 12.93 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 3.20 (0.26), residues: 911 helix: 3.12 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.22 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 5 TYR 0.007 0.001 TYR F 40 PHE 0.009 0.002 PHE J 28 TRP 0.012 0.002 TRP M 7 HIS 0.006 0.002 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00514 (10612) covalent geometry : angle 0.90047 (14900) hydrogen bonds : bond 0.04541 ( 519) hydrogen bonds : angle 3.50613 ( 1476) Misc. bond : bond 0.11455 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3164.14 seconds wall clock time: 54 minutes 41.94 seconds (3281.94 seconds total)