Starting phenix.real_space_refine on Mon Jul 28 05:51:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zcu_14633/07_2025/7zcu_14633.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zcu_14633/07_2025/7zcu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zcu_14633/07_2025/7zcu_14633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zcu_14633/07_2025/7zcu_14633.map" model { file = "/net/cci-nas-00/data/ceres_data/7zcu_14633/07_2025/7zcu_14633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zcu_14633/07_2025/7zcu_14633.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.62, per 1000 atoms: 0.65 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: 3.54 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.82 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: 2.46 Time building geometry restraints manager: 3.70 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: 0.880 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.790 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 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:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.330 ------------------------------------------------------------------------------- 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 : 3.71 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.024 0.003 TRP M 7 HIS 0.008 0.002 HIS I 37 PHE 0.015 0.002 PHE A 32 TYR 0.023 0.004 TYR S 85 ARG 0.020 0.003 ARG R 26 Details of bonding type rmsd hydrogen bonds : bond 0.13414 ( 519) hydrogen bonds : angle 5.72348 ( 1476) covalent geometry : bond 0.00475 (10612) covalent geometry : angle 0.94606 (14900) 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 : 0.933 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: 0.8164 (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: 1.3471 time to fit residues: 200.1006 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 : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 6.9990 chunk 68 optimal weight: 0.0170 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 0.0770 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 HIS M 2 ASN M 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.100365 restraints weight = 10658.829| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.43 r_work: 0.2858 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.248 10645 Z= 0.130 Angle : 0.798 12.297 14900 Z= 0.280 Chirality : 0.038 0.115 1516 Planarity : 0.004 0.029 1781 Dihedral : 13.863 103.121 2006 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.14 % Allowed : 8.24 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.45 (0.26), residues: 911 helix: 3.52 (0.18), residues: 585 sheet: None (None), residues: 0 loop : -0.11 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 45 HIS 0.008 0.001 HIS C 37 PHE 0.005 0.001 PHE O 32 TYR 0.010 0.001 TYR P 40 ARG 0.001 0.000 ARG P 26 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 519) hydrogen bonds : angle 3.48900 ( 1476) covalent geometry : bond 0.00293 (10612) covalent geometry : angle 0.79765 (14900) Misc. bond : bond 0.11395 ( 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 106 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.863 Fit side-chains REVERT: A 43 LYS cc_start: 0.8086 (tttt) cc_final: 0.7718 (ttpt) REVERT: B 16 GLU cc_start: 0.7745 (tp30) cc_final: 0.7351 (mm-30) REVERT: B 19 LYS cc_start: 0.8300 (mttt) cc_final: 0.8062 (mttm) REVERT: S 93 LEU cc_start: 0.6807 (mt) cc_final: 0.6485 (mm) REVERT: D 16 GLU cc_start: 0.7522 (tp30) cc_final: 0.7059 (tp30) REVERT: G 43 LYS cc_start: 0.8307 (tttt) cc_final: 0.7655 (mptm) REVERT: H 13 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7555 (mt-10) REVERT: H 16 GLU cc_start: 0.7970 (mm-30) cc_final: 0.6948 (tm-30) REVERT: H 23 ASP cc_start: 0.8332 (t70) cc_final: 0.8095 (t0) REVERT: I 11 LYS cc_start: 0.8036 (mttt) cc_final: 0.7767 (mttt) REVERT: L 23 ASP cc_start: 0.8264 (t70) cc_final: 0.8049 (t70) REVERT: P 12 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7170 (mm-30) outliers start: 9 outliers final: 0 residues processed: 99 average time/residue: 1.3956 time to fit residues: 147.3684 Evaluate side-chains 87 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 12 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 0.0020 chunk 32 optimal weight: 0.0970 chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 16 optimal weight: 0.0770 chunk 34 optimal weight: 0.9980 overall best weight: 0.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN I 3 GLN M 2 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.132146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.103537 restraints weight = 10934.035| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.44 r_work: 0.2910 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.217 10645 Z= 0.102 Angle : 0.727 11.549 14900 Z= 0.245 Chirality : 0.036 0.113 1516 Planarity : 0.004 0.028 1781 Dihedral : 13.524 95.859 2006 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.14 % Allowed : 9.51 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.26), residues: 911 helix: 3.75 (0.17), residues: 585 sheet: None (None), residues: 0 loop : 0.25 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 45 HIS 0.007 0.001 HIS C 37 PHE 0.007 0.001 PHE I 32 TYR 0.007 0.001 TYR S 5 ARG 0.001 0.000 ARG C 5 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 519) hydrogen bonds : angle 3.11953 ( 1476) covalent geometry : bond 0.00223 (10612) covalent geometry : angle 0.72657 (14900) Misc. bond : bond 0.09346 ( 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 103 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 1.036 Fit side-chains REVERT: A 43 LYS cc_start: 0.7999 (tttt) cc_final: 0.7611 (ttpt) REVERT: B 16 GLU cc_start: 0.7759 (tp30) cc_final: 0.7352 (mm-30) REVERT: B 19 LYS cc_start: 0.8287 (mttt) cc_final: 0.8086 (mttm) REVERT: B 23 ASP cc_start: 0.8014 (m-30) cc_final: 0.7551 (t0) REVERT: S 31 LEU cc_start: 0.6012 (mt) cc_final: 0.5608 (mt) REVERT: D 16 GLU cc_start: 0.7530 (tp30) cc_final: 0.7086 (tp30) REVERT: G 43 LYS cc_start: 0.8193 (tttt) cc_final: 0.7554 (mptm) REVERT: H 13 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7498 (mt-10) REVERT: H 23 ASP cc_start: 0.8294 (t70) cc_final: 0.8055 (t0) REVERT: I 11 LYS cc_start: 0.8052 (mttt) cc_final: 0.7819 (mppt) REVERT: L 23 ASP cc_start: 0.8263 (t70) cc_final: 0.8040 (t70) REVERT: M 43 LYS cc_start: 0.8370 (ttpt) cc_final: 0.7695 (mttp) outliers start: 9 outliers final: 1 residues processed: 97 average time/residue: 1.4708 time to fit residues: 152.1445 Evaluate side-chains 83 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 43 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 88 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 16 optimal weight: 0.0270 chunk 33 optimal weight: 5.9990 chunk 11 optimal weight: 40.0000 chunk 20 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.128763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.099699 restraints weight = 10786.611| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.42 r_work: 0.2886 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.254 10645 Z= 0.122 Angle : 0.757 12.189 14900 Z= 0.255 Chirality : 0.037 0.111 1516 Planarity : 0.004 0.025 1781 Dihedral : 13.487 98.034 2006 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.89 % Allowed : 10.14 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.26), residues: 911 helix: 3.63 (0.17), residues: 585 sheet: None (None), residues: 0 loop : 0.33 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 7 HIS 0.006 0.001 HIS C 37 PHE 0.007 0.001 PHE H 28 TYR 0.007 0.001 TYR S 37 ARG 0.002 0.000 ARG I 5 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 519) hydrogen bonds : angle 3.19343 ( 1476) covalent geometry : bond 0.00286 (10612) covalent geometry : angle 0.75731 (14900) Misc. bond : bond 0.09931 ( 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 92 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.940 Fit side-chains REVERT: A 43 LYS cc_start: 0.8037 (tttt) cc_final: 0.7677 (ttpt) REVERT: B 16 GLU cc_start: 0.7854 (tp30) cc_final: 0.7438 (mm-30) REVERT: B 19 LYS cc_start: 0.8338 (mttt) cc_final: 0.8078 (mttm) REVERT: D 16 GLU cc_start: 0.7567 (tp30) cc_final: 0.7112 (tp30) REVERT: G 43 LYS cc_start: 0.8271 (tttt) cc_final: 0.7653 (mptm) REVERT: H 13 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7597 (mt-10) REVERT: H 23 ASP cc_start: 0.8339 (t70) cc_final: 0.8107 (t0) REVERT: I 11 LYS cc_start: 0.8058 (mttt) cc_final: 0.7840 (mppt) REVERT: M 43 LYS cc_start: 0.8455 (ttpt) cc_final: 0.7750 (mttt) outliers start: 7 outliers final: 1 residues processed: 86 average time/residue: 1.5470 time to fit residues: 141.4090 Evaluate side-chains 83 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 23 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 11 optimal weight: 30.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 K 3 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.126669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.096777 restraints weight = 10643.723| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.45 r_work: 0.2811 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.302 10645 Z= 0.151 Angle : 0.813 12.783 14900 Z= 0.275 Chirality : 0.039 0.111 1516 Planarity : 0.004 0.027 1781 Dihedral : 13.603 104.063 2006 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.27 % Allowed : 10.65 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.56 (0.26), residues: 911 helix: 3.42 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.33 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 7 HIS 0.006 0.001 HIS C 37 PHE 0.007 0.001 PHE Q 32 TYR 0.007 0.001 TYR J 42 ARG 0.001 0.000 ARG O 5 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 519) hydrogen bonds : angle 3.35764 ( 1476) covalent geometry : bond 0.00371 (10612) covalent geometry : angle 0.81269 (14900) Misc. bond : bond 0.10848 ( 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: 10 poor density : 84 time to evaluate : 0.855 Fit side-chains REVERT: A 43 LYS cc_start: 0.8075 (tttt) cc_final: 0.7664 (ttpt) REVERT: B 16 GLU cc_start: 0.7881 (tp30) cc_final: 0.7466 (mm-30) REVERT: B 19 LYS cc_start: 0.8412 (mttt) cc_final: 0.8099 (mttm) REVERT: E 5 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7665 (mtt-85) REVERT: F 15 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7770 (mt-10) REVERT: G 43 LYS cc_start: 0.8321 (tttt) cc_final: 0.7650 (mptm) REVERT: H 13 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7618 (mt-10) REVERT: H 23 ASP cc_start: 0.8367 (t70) cc_final: 0.8121 (t0) REVERT: I 11 LYS cc_start: 0.8065 (mttt) cc_final: 0.7790 (mttt) outliers start: 10 outliers final: 6 residues processed: 89 average time/residue: 1.5753 time to fit residues: 148.7288 Evaluate side-chains 89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 G 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 56 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 10 optimal weight: 0.0970 chunk 12 optimal weight: 30.0000 chunk 59 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.128209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.099348 restraints weight = 10748.503| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.41 r_work: 0.2828 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.290 10645 Z= 0.137 Angle : 0.785 12.576 14900 Z= 0.264 Chirality : 0.038 0.111 1516 Planarity : 0.004 0.027 1781 Dihedral : 13.505 101.872 2006 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.52 % Allowed : 11.15 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.58 (0.26), residues: 911 helix: 3.44 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.34 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 7 HIS 0.006 0.001 HIS C 37 PHE 0.006 0.001 PHE H 28 TYR 0.006 0.001 TYR S 5 ARG 0.001 0.000 ARG K 5 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 519) hydrogen bonds : angle 3.28465 ( 1476) covalent geometry : bond 0.00332 (10612) covalent geometry : angle 0.78464 (14900) Misc. bond : bond 0.10339 ( 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 96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.949 Fit side-chains REVERT: A 43 LYS cc_start: 0.8046 (tttt) cc_final: 0.7637 (ttpt) REVERT: B 16 GLU cc_start: 0.7868 (tp30) cc_final: 0.7515 (mm-30) REVERT: B 19 LYS cc_start: 0.8366 (mttt) cc_final: 0.8100 (mttm) REVERT: E 5 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7622 (mtt-85) REVERT: E 11 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8251 (mttt) REVERT: G 43 LYS cc_start: 0.8289 (tttt) cc_final: 0.7625 (mptm) REVERT: H 13 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7589 (mt-10) REVERT: H 23 ASP cc_start: 0.8354 (t70) cc_final: 0.8113 (t0) REVERT: L 46 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8606 (mp) outliers start: 12 outliers final: 5 residues processed: 88 average time/residue: 1.9452 time to fit residues: 182.2761 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 : 0.955 ------------------------------------------------------------------------------- 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 G residue 42 SER Chi-restraints excluded: chain L residue 46 LEU 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 40 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.127784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.098870 restraints weight = 10880.900| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.42 r_work: 0.2847 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.275 10645 Z= 0.131 Angle : 0.774 12.557 14900 Z= 0.260 Chirality : 0.038 0.111 1516 Planarity : 0.004 0.027 1781 Dihedral : 13.401 99.985 2006 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.52 % Allowed : 11.53 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.26), residues: 911 helix: 3.46 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.36 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 7 HIS 0.005 0.001 HIS C 37 PHE 0.006 0.001 PHE H 28 TYR 0.005 0.001 TYR S 5 ARG 0.001 0.000 ARG K 5 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 519) hydrogen bonds : angle 3.24068 ( 1476) covalent geometry : bond 0.00317 (10612) covalent geometry : angle 0.77401 (14900) Misc. bond : bond 0.10077 ( 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 96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.832 Fit side-chains REVERT: A 43 LYS cc_start: 0.8088 (tttt) cc_final: 0.7665 (ttpt) REVERT: B 16 GLU cc_start: 0.7874 (tp30) cc_final: 0.7527 (mm-30) REVERT: B 19 LYS cc_start: 0.8376 (mttt) cc_final: 0.8107 (mttm) REVERT: E 5 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7612 (mtt-85) REVERT: E 11 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8237 (mttt) REVERT: F 15 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7757 (mt-10) REVERT: G 43 LYS cc_start: 0.8288 (tttt) cc_final: 0.7648 (mptm) REVERT: H 13 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7561 (mt-10) REVERT: L 46 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8589 (mp) outliers start: 12 outliers final: 6 residues processed: 89 average time/residue: 1.6433 time to fit residues: 155.1425 Evaluate side-chains 90 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 G residue 42 SER Chi-restraints excluded: chain L residue 46 LEU 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 62 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 59 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 47 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.126218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.097157 restraints weight = 10855.531| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.42 r_work: 0.2822 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.302 10645 Z= 0.152 Angle : 0.813 13.142 14900 Z= 0.273 Chirality : 0.039 0.111 1516 Planarity : 0.004 0.027 1781 Dihedral : 13.533 102.748 2006 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.27 % Allowed : 12.04 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.50 (0.26), residues: 911 helix: 3.36 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.34 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 7 HIS 0.005 0.001 HIS C 37 PHE 0.007 0.001 PHE H 28 TYR 0.006 0.001 TYR H 42 ARG 0.001 0.000 ARG K 5 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 519) hydrogen bonds : angle 3.33160 ( 1476) covalent geometry : bond 0.00375 (10612) covalent geometry : angle 0.81305 (14900) Misc. bond : bond 0.10827 ( 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: 10 poor density : 83 time to evaluate : 1.277 Fit side-chains REVERT: A 43 LYS cc_start: 0.8108 (tttt) cc_final: 0.7680 (ttpt) REVERT: B 16 GLU cc_start: 0.7907 (tp30) cc_final: 0.7561 (mm-30) REVERT: B 19 LYS cc_start: 0.8391 (mttt) cc_final: 0.8118 (mttm) REVERT: E 5 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7640 (mtt-85) REVERT: E 11 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8288 (mttt) REVERT: F 15 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7788 (mt-10) REVERT: G 43 LYS cc_start: 0.8314 (tttt) cc_final: 0.7637 (mptm) REVERT: H 13 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7604 (mt-10) REVERT: L 46 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8571 (mp) outliers start: 10 outliers final: 6 residues processed: 88 average time/residue: 1.7500 time to fit residues: 163.5016 Evaluate side-chains 88 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 G residue 42 SER Chi-restraints excluded: chain L residue 46 LEU 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 44 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 55 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.129420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.100584 restraints weight = 10851.615| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.43 r_work: 0.2875 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.212 10645 Z= 0.109 Angle : 0.736 12.411 14900 Z= 0.246 Chirality : 0.036 0.110 1516 Planarity : 0.004 0.026 1781 Dihedral : 13.229 96.798 2006 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.14 % Allowed : 12.55 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.26), residues: 911 helix: 3.59 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.36 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 40 HIS 0.005 0.001 HIS C 37 PHE 0.006 0.001 PHE H 28 TYR 0.005 0.001 TYR S 5 ARG 0.002 0.000 ARG K 5 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 519) hydrogen bonds : angle 3.12150 ( 1476) covalent geometry : bond 0.00252 (10612) covalent geometry : angle 0.73588 (14900) Misc. bond : bond 0.08646 ( 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 92 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 1.085 Fit side-chains REVERT: A 43 LYS cc_start: 0.8072 (tttt) cc_final: 0.7618 (ttpt) REVERT: B 16 GLU cc_start: 0.7851 (tp30) cc_final: 0.7505 (mm-30) REVERT: B 19 LYS cc_start: 0.8362 (mttt) cc_final: 0.8089 (mttm) REVERT: E 5 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7614 (mtt-85) REVERT: E 11 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8236 (mttt) REVERT: F 15 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7719 (mt-10) REVERT: G 43 LYS cc_start: 0.8277 (tttt) cc_final: 0.7635 (mptm) REVERT: H 13 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7539 (mt-10) REVERT: M 43 LYS cc_start: 0.8403 (ttpt) cc_final: 0.7701 (mttt) outliers start: 9 outliers final: 5 residues processed: 86 average time/residue: 1.8469 time to fit residues: 167.9996 Evaluate side-chains 87 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 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 39 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 77 optimal weight: 0.0470 chunk 79 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.0086 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.127964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.099240 restraints weight = 10804.317| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.40 r_work: 0.2852 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.217 10645 Z= 0.121 Angle : 0.754 12.584 14900 Z= 0.253 Chirality : 0.037 0.111 1516 Planarity : 0.004 0.027 1781 Dihedral : 13.237 97.233 2006 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.39 % Allowed : 12.55 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.26), residues: 911 helix: 3.54 (0.17), residues: 585 sheet: None (None), residues: 0 loop : 0.38 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 40 HIS 0.005 0.001 HIS C 37 PHE 0.006 0.001 PHE H 28 TYR 0.006 0.001 TYR S 5 ARG 0.001 0.000 ARG K 5 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 519) hydrogen bonds : angle 3.14985 ( 1476) covalent geometry : bond 0.00289 (10612) covalent geometry : angle 0.75414 (14900) Misc. bond : bond 0.09323 ( 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 92 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.846 Fit side-chains REVERT: A 43 LYS cc_start: 0.8078 (tttt) cc_final: 0.7643 (ttpt) REVERT: B 16 GLU cc_start: 0.7874 (tp30) cc_final: 0.7527 (mm-30) REVERT: B 19 LYS cc_start: 0.8387 (mttt) cc_final: 0.8125 (mttm) REVERT: E 5 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7630 (mtt-85) REVERT: E 11 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8246 (mttt) REVERT: F 15 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7769 (mt-10) REVERT: G 43 LYS cc_start: 0.8251 (tttt) cc_final: 0.7625 (mptm) REVERT: H 13 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7565 (mt-10) REVERT: M 43 LYS cc_start: 0.8440 (ttpt) cc_final: 0.7729 (mttt) outliers start: 11 outliers final: 5 residues processed: 85 average time/residue: 1.8243 time to fit residues: 164.0796 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 : 1.049 ------------------------------------------------------------------------------- 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 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 60 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 50.0000 chunk 12 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 HIS S 33 GLN F 20 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.124311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.094518 restraints weight = 10852.567| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.46 r_work: 0.2776 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2381 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= 0.243 Angle : 0.949 19.427 14900 Z= 0.323 Chirality : 0.046 0.134 1516 Planarity : 0.005 0.030 1781 Dihedral : 14.070 109.155 2006 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.14 % Allowed : 12.55 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.26), residues: 911 helix: 3.04 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.30 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 45 HIS 0.009 0.002 HIS B 36 PHE 0.012 0.002 PHE Q 32 TYR 0.010 0.002 TYR H 42 ARG 0.002 0.000 ARG P 26 Details of bonding type rmsd hydrogen bonds : bond 0.04794 ( 519) hydrogen bonds : angle 3.58236 ( 1476) covalent geometry : bond 0.00626 (10612) covalent geometry : angle 0.94917 (14900) Misc. bond : bond 0.11853 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6919.72 seconds wall clock time: 121 minutes 11.11 seconds (7271.11 seconds total)