Starting phenix.real_space_refine on Fri Feb 14 10:06:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zcu_14633/02_2025/7zcu_14633.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zcu_14633/02_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_14633/02_2025/7zcu_14633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zcu_14633/02_2025/7zcu_14633.map" model { file = "/net/cci-nas-00/data/ceres_data/7zcu_14633/02_2025/7zcu_14633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zcu_14633/02_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-5592/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: 6.95, per 1000 atoms: 0.68 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: 3.55 Conformation dependent library (CDL) restraints added in 887.5 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: 0.78 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: 2.76 Time building geometry restraints manager: 3.84 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: 0.820 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.780 Find NCS groups from input model: 0.570 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: 0.010 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.140 ------------------------------------------------------------------------------- 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 : 0.005 0.046 10612 Z= 0.268 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 *********************** 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 : 0.748 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: 1.4340 time to fit residues: 212.2262 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 : 0.982 ------------------------------------------------------------------------------- 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: 10.0000 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 HIS E 37 HIS L 47 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.125889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.096374 restraints weight = 10666.283| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.43 r_work: 0.2816 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10612 Z= 0.262 Angle : 0.903 15.429 14900 Z= 0.319 Chirality : 0.043 0.124 1516 Planarity : 0.005 0.033 1781 Dihedral : 14.345 109.034 2006 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.52 % Allowed : 8.37 % Favored : 90.11 % 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: 3.08 (0.26), residues: 911 helix: 3.17 (0.18), residues: 585 sheet: None (None), residues: 0 loop : -0.13 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP M 7 HIS 0.010 0.002 HIS M 37 PHE 0.009 0.001 PHE S 56 TYR 0.009 0.001 TYR P 40 ARG 0.002 0.000 ARG P 26 *********************** 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 102 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.969 Fit side-chains REVERT: A 43 LYS cc_start: 0.8091 (tttt) cc_final: 0.7742 (ttpt) REVERT: B 16 GLU cc_start: 0.7845 (tp30) cc_final: 0.7470 (mm-30) REVERT: B 19 LYS cc_start: 0.8366 (mttt) cc_final: 0.8030 (mttm) REVERT: S 93 LEU cc_start: 0.6875 (mt) cc_final: 0.6589 (mm) REVERT: E 5 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7676 (mtt-85) REVERT: E 11 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8322 (mttt) REVERT: G 43 LYS cc_start: 0.8377 (tttt) cc_final: 0.7979 (tmtt) REVERT: H 23 ASP cc_start: 0.8364 (t70) cc_final: 0.8120 (t0) REVERT: I 11 LYS cc_start: 0.8084 (mttt) cc_final: 0.7807 (mppt) REVERT: N 23 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7971 (m-30) outliers start: 12 outliers final: 3 residues processed: 93 average time/residue: 1.5975 time to fit residues: 157.6897 Evaluate side-chains 91 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER 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 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 80 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS S 33 GLN S 65 GLN K 3 GLN P 20 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.123989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.094293 restraints weight = 10830.015| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.45 r_work: 0.2774 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10612 Z= 0.313 Angle : 0.933 17.105 14900 Z= 0.322 Chirality : 0.045 0.129 1516 Planarity : 0.005 0.034 1781 Dihedral : 14.577 111.920 2006 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.52 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 (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: 2.99 (0.26), residues: 911 helix: 2.98 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.09 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 7 HIS 0.008 0.002 HIS M 37 PHE 0.011 0.002 PHE S 56 TYR 0.008 0.001 TYR R 42 ARG 0.002 0.000 ARG G 5 *********************** 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 99 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.969 Fit side-chains REVERT: A 43 LYS cc_start: 0.8099 (tttt) cc_final: 0.7719 (ttpt) REVERT: B 12 GLU cc_start: 0.7130 (mp0) cc_final: 0.6894 (mp0) REVERT: B 19 LYS cc_start: 0.8415 (mttt) cc_final: 0.8163 (mttm) REVERT: D 16 GLU cc_start: 0.7699 (tp30) cc_final: 0.7221 (tp30) REVERT: E 5 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7735 (mtt-85) REVERT: E 11 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8325 (mttt) REVERT: G 43 LYS cc_start: 0.8366 (tttt) cc_final: 0.7962 (tmtt) REVERT: H 23 ASP cc_start: 0.8408 (t70) cc_final: 0.8152 (t0) REVERT: I 11 LYS cc_start: 0.8095 (mttt) cc_final: 0.7869 (mttt) outliers start: 14 outliers final: 6 residues processed: 89 average time/residue: 1.6254 time to fit residues: 153.4381 Evaluate side-chains 89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 M residue 42 SER Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain P residue 11 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 88 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.124831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.095424 restraints weight = 10727.619| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.42 r_work: 0.2788 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10612 Z= 0.246 Angle : 0.855 13.711 14900 Z= 0.293 Chirality : 0.041 0.112 1516 Planarity : 0.005 0.034 1781 Dihedral : 14.216 106.472 2006 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.77 % Allowed : 9.38 % Favored : 88.85 % 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: 3.17 (0.26), residues: 911 helix: 3.12 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.18 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 40 HIS 0.006 0.001 HIS C 37 PHE 0.008 0.001 PHE J 28 TYR 0.008 0.001 TYR P 40 ARG 0.002 0.000 ARG I 5 *********************** 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 97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 1.133 Fit side-chains REVERT: A 43 LYS cc_start: 0.8144 (tttt) cc_final: 0.7731 (ttpt) REVERT: B 16 GLU cc_start: 0.7906 (tp30) cc_final: 0.7500 (mm-30) REVERT: B 19 LYS cc_start: 0.8403 (mttt) cc_final: 0.8075 (mttm) REVERT: D 16 GLU cc_start: 0.7713 (tp30) cc_final: 0.7227 (tp30) REVERT: E 5 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7751 (mtt-85) REVERT: E 11 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8304 (mttt) REVERT: G 43 LYS cc_start: 0.8362 (tttt) cc_final: 0.7965 (tmtt) REVERT: I 11 LYS cc_start: 0.8143 (mttt) cc_final: 0.7854 (mttt) outliers start: 14 outliers final: 7 residues processed: 87 average time/residue: 1.6062 time to fit residues: 148.5617 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 : 0.946 ------------------------------------------------------------------------------- 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 P residue 9 LEU 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 63 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.125518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.095880 restraints weight = 10704.193| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.44 r_work: 0.2798 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10612 Z= 0.217 Angle : 0.827 12.920 14900 Z= 0.280 Chirality : 0.040 0.111 1516 Planarity : 0.004 0.032 1781 Dihedral : 13.903 104.417 2006 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.90 % Allowed : 10.14 % Favored : 87.96 % 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: 3.28 (0.26), residues: 911 helix: 3.21 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.21 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 40 HIS 0.006 0.001 HIS C 37 PHE 0.007 0.001 PHE J 28 TYR 0.009 0.001 TYR P 40 ARG 0.002 0.000 ARG I 5 *********************** 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 97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.897 Fit side-chains REVERT: A 43 LYS cc_start: 0.8122 (tttt) cc_final: 0.7701 (ttpt) REVERT: B 16 GLU cc_start: 0.7958 (tp30) cc_final: 0.7539 (mm-30) REVERT: B 19 LYS cc_start: 0.8365 (mttt) cc_final: 0.8112 (mttm) REVERT: D 16 GLU cc_start: 0.7661 (tp30) cc_final: 0.7172 (tp30) REVERT: E 5 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7743 (mtt-85) REVERT: E 11 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8302 (mttt) REVERT: G 43 LYS cc_start: 0.8368 (tttt) cc_final: 0.7959 (tmtt) REVERT: L 46 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8609 (mp) REVERT: N 23 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8012 (m-30) outliers start: 15 outliers final: 5 residues processed: 86 average time/residue: 1.6330 time to fit residues: 149.1617 Evaluate side-chains 89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 P residue 9 LEU 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: 0.9990 chunk 30 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 HIS ** L 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.093341 restraints weight = 10810.320| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.44 r_work: 0.2758 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 10612 Z= 0.385 Angle : 0.996 19.624 14900 Z= 0.337 Chirality : 0.047 0.138 1516 Planarity : 0.005 0.037 1781 Dihedral : 14.500 111.713 2006 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.41 % Allowed : 10.52 % 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 (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: 2.82 (0.26), residues: 911 helix: 2.79 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.16 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 7 HIS 0.007 0.002 HIS J 36 PHE 0.012 0.002 PHE S 56 TYR 0.010 0.002 TYR P 40 ARG 0.003 0.001 ARG I 5 *********************** 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 99 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.925 Fit side-chains REVERT: A 43 LYS cc_start: 0.8139 (tttt) cc_final: 0.7738 (ttpt) REVERT: B 19 LYS cc_start: 0.8459 (mttt) cc_final: 0.8184 (mttm) REVERT: D 16 GLU cc_start: 0.7702 (tp30) cc_final: 0.7208 (tp30) REVERT: E 5 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7751 (mtt-85) REVERT: E 11 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8387 (mttt) REVERT: G 43 LYS cc_start: 0.8414 (tttt) cc_final: 0.8000 (tmtt) REVERT: L 46 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8638 (mp) outliers start: 19 outliers final: 9 residues processed: 89 average time/residue: 1.5695 time to fit residues: 148.5812 Evaluate side-chains 91 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 K residue 25 VAL 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 P residue 9 LEU Chi-restraints excluded: chain P residue 11 VAL 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: 0.9990 chunk 69 optimal weight: 5.9990 chunk 59 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.128194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.098580 restraints weight = 10859.471| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.45 r_work: 0.2868 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10612 Z= 0.145 Angle : 0.746 12.088 14900 Z= 0.253 Chirality : 0.036 0.111 1516 Planarity : 0.004 0.030 1781 Dihedral : 13.501 99.528 2006 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.27 % Allowed : 12.29 % 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 (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: 3.51 (0.26), residues: 911 helix: 3.42 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.25 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 40 HIS 0.006 0.001 HIS C 37 PHE 0.004 0.001 PHE B 28 TYR 0.007 0.001 TYR P 40 ARG 0.002 0.000 ARG K 5 *********************** 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 95 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.870 Fit side-chains REVERT: A 43 LYS cc_start: 0.8113 (tttt) cc_final: 0.7694 (ttpt) REVERT: B 16 GLU cc_start: 0.7930 (tp30) cc_final: 0.7535 (mm-30) REVERT: B 19 LYS cc_start: 0.8402 (mttt) cc_final: 0.8100 (mttm) REVERT: S 31 LEU cc_start: 0.6120 (mt) cc_final: 0.5766 (mt) REVERT: E 5 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7661 (mtt-85) REVERT: G 43 LYS cc_start: 0.8300 (tttt) cc_final: 0.7624 (mptm) REVERT: M 43 LYS cc_start: 0.8424 (ttpt) cc_final: 0.7704 (mttt) REVERT: N 23 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7989 (m-30) outliers start: 10 outliers final: 4 residues processed: 88 average time/residue: 1.6211 time to fit residues: 151.5869 Evaluate side-chains 87 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 P residue 9 LEU 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: 5.9990 chunk 22 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.125769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.096057 restraints weight = 10802.561| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.45 r_work: 0.2798 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10612 Z= 0.218 Angle : 0.816 13.609 14900 Z= 0.277 Chirality : 0.039 0.111 1516 Planarity : 0.004 0.030 1781 Dihedral : 13.542 102.387 2006 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: 3.37 (0.26), residues: 911 helix: 3.28 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.26 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 40 HIS 0.006 0.001 HIS C 37 PHE 0.007 0.001 PHE J 28 TYR 0.007 0.001 TYR P 40 ARG 0.001 0.000 ARG G 5 *********************** 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 90 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.880 Fit side-chains REVERT: A 43 LYS cc_start: 0.8114 (tttt) cc_final: 0.7710 (ttpt) REVERT: B 16 GLU cc_start: 0.7972 (tp30) cc_final: 0.7561 (mm-30) REVERT: B 19 LYS cc_start: 0.8429 (mttt) cc_final: 0.8126 (mttm) REVERT: E 5 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7691 (mtt-85) REVERT: F 15 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7787 (mt-10) REVERT: G 43 LYS cc_start: 0.8330 (tttt) cc_final: 0.7938 (tmtt) REVERT: L 46 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8542 (mp) outliers start: 9 outliers final: 6 residues processed: 84 average time/residue: 1.5311 time to fit residues: 136.5694 Evaluate side-chains 89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 L residue 46 LEU Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain P residue 9 LEU 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: 0.8980 chunk 32 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.127521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.098003 restraints weight = 10867.372| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.45 r_work: 0.2832 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10612 Z= 0.167 Angle : 0.756 12.448 14900 Z= 0.257 Chirality : 0.037 0.110 1516 Planarity : 0.004 0.030 1781 Dihedral : 13.224 99.534 2006 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.01 % Allowed : 13.05 % Favored : 85.93 % 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: 3.54 (0.26), residues: 911 helix: 3.44 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.27 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 40 HIS 0.005 0.001 HIS C 37 PHE 0.005 0.001 PHE B 28 TYR 0.008 0.001 TYR P 40 ARG 0.001 0.000 ARG K 5 *********************** 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 89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.988 Fit side-chains REVERT: A 43 LYS cc_start: 0.8121 (tttt) cc_final: 0.7703 (ttpt) REVERT: B 16 GLU cc_start: 0.7944 (tp30) cc_final: 0.7542 (mm-30) REVERT: B 19 LYS cc_start: 0.8409 (mttt) cc_final: 0.8108 (mttm) REVERT: E 5 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7665 (mtt-85) REVERT: F 15 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7750 (mt-10) REVERT: G 43 LYS cc_start: 0.8290 (tttt) cc_final: 0.7642 (mptm) REVERT: M 43 LYS cc_start: 0.8444 (ttpt) cc_final: 0.7713 (mttt) outliers start: 8 outliers final: 4 residues processed: 84 average time/residue: 1.6387 time to fit residues: 146.1585 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 : 0.966 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 39 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 77 optimal weight: 0.1980 chunk 79 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 overall best weight: 2.0388 ------------------------------------------------------------------------------- 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 = 0.125507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.095973 restraints weight = 10798.913| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.44 r_work: 0.2806 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10612 Z= 0.237 Angle : 0.834 13.988 14900 Z= 0.283 Chirality : 0.040 0.111 1516 Planarity : 0.004 0.030 1781 Dihedral : 13.460 103.090 2006 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.01 % Allowed : 13.31 % 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 (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: 3.33 (0.26), residues: 911 helix: 3.24 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.25 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 7 HIS 0.006 0.001 HIS C 37 PHE 0.008 0.001 PHE J 28 TYR 0.009 0.001 TYR P 40 ARG 0.001 0.000 ARG G 5 ********************** 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 90 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.905 Fit side-chains REVERT: A 43 LYS cc_start: 0.8111 (tttt) cc_final: 0.7710 (ttpt) REVERT: B 16 GLU cc_start: 0.7984 (tp30) cc_final: 0.7576 (mm-30) REVERT: B 19 LYS cc_start: 0.8425 (mttt) cc_final: 0.8118 (mttm) REVERT: E 5 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7720 (mtt-85) REVERT: F 15 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7823 (mt-10) REVERT: G 43 LYS cc_start: 0.8347 (tttt) cc_final: 0.7955 (tmtt) REVERT: L 46 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8530 (mp) outliers start: 8 outliers final: 5 residues processed: 85 average time/residue: 1.6188 time to fit residues: 146.0703 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 : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain E residue 5 ARG 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 P residue 9 LEU 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: 2.9990 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 47 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.0040 chunk 11 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.8594 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.128141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.098670 restraints weight = 10823.244| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.44 r_work: 0.2841 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10612 Z= 0.148 Angle : 0.738 12.383 14900 Z= 0.251 Chirality : 0.036 0.111 1516 Planarity : 0.004 0.029 1781 Dihedral : 13.107 98.156 2006 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.01 % Allowed : 13.56 % Favored : 85.42 % 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: 3.50 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.27 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 40 HIS 0.005 0.001 HIS C 37 PHE 0.005 0.001 PHE H 28 TYR 0.007 0.001 TYR S 37 ARG 0.001 0.000 ARG K 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6249.80 seconds wall clock time: 111 minutes 16.56 seconds (6676.56 seconds total)