Starting phenix.real_space_refine on Wed Mar 4 02:50:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zdi_14650/03_2026/7zdi_14650.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zdi_14650/03_2026/7zdi_14650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zdi_14650/03_2026/7zdi_14650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zdi_14650/03_2026/7zdi_14650.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zdi_14650/03_2026/7zdi_14650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zdi_14650/03_2026/7zdi_14650.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 7274 2.51 5 N 1401 2.21 5 O 1567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10284 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} 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: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "E" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "G" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "I" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "K" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "M" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "O" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "Q" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 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: 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: "G" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 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: "K" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 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: "N" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 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: "P" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.55, per 1000 atoms: 0.25 Number of scatterers: 10284 At special positions: 0 Unit cell: (96.2, 102.7, 80.6, 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 1567 8.00 N 1401 7.00 C 7274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=33, symmetry=0 Number of additional bonds: simple=33, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 468.7 milliseconds 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 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 71.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 removed outlier: 3.944A pdb=" N TRP A 7 " --> pdb=" O GLY 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 14 through 47 removed outlier: 3.951A pdb=" N HIS B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 9 removed outlier: 3.950A pdb=" N TRP C 7 " --> pdb=" O GLY 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 14 through 47 removed outlier: 3.945A pdb=" N HIS D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 9 removed outlier: 3.965A pdb=" N TRP E 7 " --> pdb=" O GLY E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 38 Proline residue: E 17 - end of helix Processing helix chain 'E' and resid 39 through 47 Processing helix chain 'F' and resid 14 through 47 removed outlier: 4.006A pdb=" N HIS F 24 " --> pdb=" O GLU F 20 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL F 25 " --> pdb=" O LEU F 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 9 removed outlier: 3.979A pdb=" N TRP G 7 " --> pdb=" O GLY G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 38 Proline residue: G 17 - end of helix Processing helix chain 'G' and resid 39 through 47 Processing helix chain 'H' and resid 14 through 47 removed outlier: 3.935A pdb=" N HIS H 24 " --> pdb=" O GLU H 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 9 removed outlier: 3.997A pdb=" N TRP I 7 " --> pdb=" O GLY I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 38 Proline residue: I 17 - end of helix Processing helix chain 'I' and resid 39 through 47 Processing helix chain 'J' and resid 14 through 47 removed outlier: 3.965A pdb=" N HIS J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 9 removed outlier: 3.928A pdb=" N TRP K 7 " --> pdb=" O GLY K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 38 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 39 through 47 Processing helix chain 'L' and resid 14 through 47 removed outlier: 3.938A pdb=" N HIS L 24 " --> pdb=" O GLU L 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 9 removed outlier: 3.927A pdb=" N TRP M 7 " --> pdb=" O GLY 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 14 through 47 removed outlier: 3.894A pdb=" N HIS N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 9 removed outlier: 3.907A pdb=" N TRP O 7 " --> pdb=" O GLY 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 14 through 47 removed outlier: 3.884A pdb=" N HIS P 24 " --> pdb=" O GLU P 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 9 removed outlier: 3.884A pdb=" N TRP Q 7 " --> pdb=" O GLY 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 14 through 47 removed outlier: 3.904A pdb=" N HIS R 24 " --> pdb=" O GLU R 20 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.55 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.37: 2950 1.37 - 1.57: 7692 1.57 - 1.77: 9 1.77 - 1.98: 9 1.98 - 2.18: 132 Bond restraints: 10792 Sorted by residual: bond pdb=" SD CXM C 1 " pdb=" CE CXM C 1 " ideal model delta sigma weight residual 1.808 1.762 0.046 2.00e-02 2.50e+03 5.27e+00 bond pdb=" SD CXM Q 1 " pdb=" CE CXM Q 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 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 5.05e+00 bond pdb=" SD CXM E 1 " pdb=" CE CXM E 1 " ideal model delta sigma weight residual 1.808 1.763 0.045 2.00e-02 2.50e+03 5.04e+00 bond pdb=" SD CXM O 1 " pdb=" CE CXM O 1 " ideal model delta sigma weight residual 1.808 1.763 0.045 2.00e-02 2.50e+03 5.01e+00 ... (remaining 10787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 15066 4.23 - 8.47: 129 8.47 - 12.70: 8 12.70 - 16.94: 0 16.94 - 21.17: 3 Bond angle restraints: 15206 Sorted by residual: angle pdb=" C1 BCL A 101 " pdb=" C2 BCL A 101 " pdb=" C3 BCL A 101 " ideal model delta sigma weight residual 123.38 144.55 -21.17 4.41e+00 5.14e-02 2.31e+01 angle pdb=" C1 BCL E 101 " pdb=" C2 BCL E 101 " pdb=" C3 BCL E 101 " ideal model delta sigma weight residual 123.38 143.67 -20.30 4.41e+00 5.14e-02 2.12e+01 angle pdb=" C1 BCL C 102 " pdb=" C2 BCL C 102 " pdb=" C3 BCL C 102 " ideal model delta sigma weight residual 123.38 140.54 -17.16 4.41e+00 5.14e-02 1.51e+01 angle pdb=" C1 BCL S1702 " pdb=" O2A BCL S1702 " pdb=" CGA BCL S1702 " ideal model delta sigma weight residual 116.11 124.93 -8.81 4.27e+00 5.48e-02 4.26e+00 angle pdb=" N GLY M 4 " pdb=" CA GLY M 4 " pdb=" C GLY M 4 " ideal model delta sigma weight residual 113.27 115.81 -2.54 1.33e+00 5.65e-01 3.64e+00 ... (remaining 15201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 5215 24.18 - 48.37: 193 48.37 - 72.55: 11 72.55 - 96.73: 0 96.73 - 120.92: 12 Dihedral angle restraints: 5431 sinusoidal: 2651 harmonic: 2780 Sorted by residual: dihedral pdb=" C3 BCL M 102 " pdb=" C5 BCL M 102 " pdb=" C6 BCL M 102 " pdb=" C7 BCL M 102 " ideal model delta sinusoidal sigma weight residual 60.00 116.83 -56.83 3 9.00e+00 1.23e-02 2.62e+01 dihedral pdb=" C3 BCL K 102 " pdb=" C5 BCL K 102 " pdb=" C6 BCL K 102 " pdb=" C7 BCL K 102 " ideal model delta sinusoidal sigma weight residual 60.00 116.57 -56.57 3 9.00e+00 1.23e-02 2.61e+01 dihedral pdb=" C3 BCL Q 102 " pdb=" C5 BCL Q 102 " pdb=" C6 BCL Q 102 " pdb=" C7 BCL Q 102 " ideal model delta sinusoidal sigma weight residual 60.00 114.36 -54.36 3 9.00e+00 1.23e-02 2.58e+01 ... (remaining 5428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 942 0.029 - 0.058: 333 0.058 - 0.086: 108 0.086 - 0.115: 96 0.115 - 0.144: 28 Chirality restraints: 1507 Sorted by residual: chirality pdb=" CA PRO J 10 " pdb=" N PRO J 10 " pdb=" C PRO J 10 " pdb=" CB PRO J 10 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA PRO N 10 " pdb=" N PRO N 10 " pdb=" C PRO N 10 " pdb=" CB PRO N 10 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA PRO L 10 " pdb=" N PRO L 10 " pdb=" C PRO L 10 " pdb=" CB PRO L 10 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1504 not shown) Planarity restraints: 1853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL A 101 " -0.056 1.50e-02 4.44e+03 4.85e-02 5.23e+01 pdb=" C2 BCL A 101 " 0.086 1.50e-02 4.44e+03 pdb=" C3 BCL A 101 " 0.006 1.50e-02 4.44e+03 pdb=" C4 BCL A 101 " -0.000 1.50e-02 4.44e+03 pdb=" C5 BCL A 101 " -0.036 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL E 101 " 0.055 1.50e-02 4.44e+03 4.82e-02 5.16e+01 pdb=" C2 BCL E 101 " -0.084 1.50e-02 4.44e+03 pdb=" C3 BCL E 101 " -0.008 1.50e-02 4.44e+03 pdb=" C4 BCL E 101 " 0.000 1.50e-02 4.44e+03 pdb=" C5 BCL E 101 " 0.037 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL C 102 " 0.053 1.50e-02 4.44e+03 4.60e-02 4.69e+01 pdb=" C2 BCL C 102 " -0.078 1.50e-02 4.44e+03 pdb=" C3 BCL C 102 " -0.014 1.50e-02 4.44e+03 pdb=" C4 BCL C 102 " 0.000 1.50e-02 4.44e+03 pdb=" C5 BCL C 102 " 0.038 1.50e-02 4.44e+03 ... (remaining 1850 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 2932 2.88 - 3.39: 9440 3.39 - 3.89: 18201 3.89 - 4.40: 21695 4.40 - 4.90: 35403 Nonbonded interactions: 87671 Sorted by model distance: nonbonded pdb=" OH TYR S 5 " pdb=" OD2 ASP J 27 " model vdw 2.378 3.040 nonbonded pdb=" ON2 CXM M 1 " pdb=" NE2 HIS N 22 " model vdw 2.385 3.120 nonbonded pdb=" OE1 GLU B 19 " pdb=" ND2 ASN S 96 " model vdw 2.415 3.120 nonbonded pdb=" N LEU S 15 " pdb=" O CXM I 1 " model vdw 2.449 3.120 nonbonded pdb=" OH TYR S 37 " pdb=" OD2 ASP N 27 " model vdw 2.467 3.040 ... (remaining 87666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 102) selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = (chain 'I' and resid 1 through 102) selection = (chain 'K' and resid 1 through 102) selection = (chain 'M' and resid 1 through 102) selection = (chain 'O' and resid 1 through 102) selection = chain 'Q' } ncs_group { reference = (chain 'B' and resid 3 through 51) selection = (chain 'D' and resid 3 through 51) selection = (chain 'F' and resid 3 through 51) selection = (chain 'H' and resid 3 through 51) selection = (chain 'J' and resid 3 through 51) selection = (chain 'L' and resid 3 through 51) selection = (chain 'N' and resid 3 through 51) selection = (chain 'P' and resid 3 through 51) selection = (chain 'R' and resid 3 through 51) } 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: 2.530 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.140 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:10.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 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 0.404 10825 Z= 1.658 Angle : 0.933 21.170 15206 Z= 0.360 Chirality : 0.042 0.144 1507 Planarity : 0.009 0.087 1853 Dihedral : 13.216 120.917 3653 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.24), residues: 929 helix: 1.39 (0.18), residues: 603 sheet: None (None), residues: 0 loop : -0.45 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.003 ARG R 30 TYR 0.016 0.004 TYR K 32 PHE 0.005 0.001 PHE G 41 TRP 0.021 0.002 TRP O 7 HIS 0.003 0.001 HIS N 24 Details of bonding type rmsd covalent geometry : bond 0.00466 (10792) covalent geometry : angle 0.93300 (15206) hydrogen bonds : bond 0.15503 ( 519) hydrogen bonds : angle 6.14862 ( 1476) Misc. bond : bond 0.31330 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.372 Fit side-chains REVERT: J 46 TYR cc_start: 0.8424 (m-80) cc_final: 0.8128 (m-80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.7298 time to fit residues: 64.2552 Evaluate side-chains 57 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3115 r_free = 0.3115 target = 0.110124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.085176 restraints weight = 11153.448| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 1.40 r_work: 0.2547 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2416 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.270 10825 Z= 0.132 Angle : 0.763 9.076 15206 Z= 0.271 Chirality : 0.040 0.118 1507 Planarity : 0.005 0.034 1853 Dihedral : 13.150 113.301 2033 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.12 % Allowed : 4.83 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.46 (0.25), residues: 929 helix: 3.33 (0.18), residues: 603 sheet: None (None), residues: 0 loop : 0.26 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 30 TYR 0.008 0.001 TYR S 5 PHE 0.006 0.001 PHE B 32 TRP 0.016 0.002 TRP K 45 HIS 0.005 0.001 HIS N 24 Details of bonding type rmsd covalent geometry : bond 0.00297 (10792) covalent geometry : angle 0.76279 (15206) hydrogen bonds : bond 0.04509 ( 519) hydrogen bonds : angle 3.59535 ( 1476) Misc. bond : bond 0.11749 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.286 Fit side-chains REVERT: C 43 LYS cc_start: 0.8484 (tttm) cc_final: 0.7824 (ttmt) REVERT: J 46 TYR cc_start: 0.8515 (m-80) cc_final: 0.8216 (m-80) outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.7077 time to fit residues: 43.6534 Evaluate side-chains 47 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 11 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 16 optimal weight: 30.0000 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3013 r_free = 0.3013 target = 0.103003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.077993 restraints weight = 11356.918| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 1.42 r_work: 0.2423 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2290 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.343 10825 Z= 0.248 Angle : 0.938 12.329 15206 Z= 0.327 Chirality : 0.048 0.146 1507 Planarity : 0.005 0.039 1853 Dihedral : 13.789 115.726 2033 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.24), residues: 929 helix: 2.69 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.40 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 30 TYR 0.012 0.002 TYR O 32 PHE 0.009 0.002 PHE R 32 TRP 0.010 0.002 TRP K 7 HIS 0.007 0.001 HIS N 40 Details of bonding type rmsd covalent geometry : bond 0.00661 (10792) covalent geometry : angle 0.93807 (15206) hydrogen bonds : bond 0.05670 ( 519) hydrogen bonds : angle 3.96338 ( 1476) Misc. bond : bond 0.14983 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.243 Fit side-chains REVERT: C 43 LYS cc_start: 0.8550 (tttm) cc_final: 0.7883 (ttmt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.8370 time to fit residues: 45.9011 Evaluate side-chains 51 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 69 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 14 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.108858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.083883 restraints weight = 11273.853| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 1.43 r_work: 0.2521 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2390 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.249 10825 Z= 0.119 Angle : 0.733 10.331 15206 Z= 0.255 Chirality : 0.039 0.113 1507 Planarity : 0.005 0.038 1853 Dihedral : 13.407 102.756 2033 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.68 (0.25), residues: 929 helix: 3.38 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.70 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG O 5 TYR 0.006 0.001 TYR S 5 PHE 0.004 0.001 PHE B 32 TRP 0.010 0.001 TRP C 40 HIS 0.003 0.001 HIS N 24 Details of bonding type rmsd covalent geometry : bond 0.00273 (10792) covalent geometry : angle 0.73299 (15206) hydrogen bonds : bond 0.04056 ( 519) hydrogen bonds : angle 3.34547 ( 1476) Misc. bond : bond 0.10562 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.202 Fit side-chains REVERT: C 43 LYS cc_start: 0.8485 (tttm) cc_final: 0.7811 (ttmt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.7355 time to fit residues: 40.6192 Evaluate side-chains 46 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 42 optimal weight: 0.0270 chunk 64 optimal weight: 6.9990 chunk 33 optimal weight: 0.0170 chunk 28 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 overall best weight: 2.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.103736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.078765 restraints weight = 11447.540| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 1.42 r_work: 0.2451 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2318 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.310 10825 Z= 0.219 Angle : 0.879 12.350 15206 Z= 0.305 Chirality : 0.045 0.130 1507 Planarity : 0.005 0.039 1853 Dihedral : 13.591 105.430 2033 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.24), residues: 929 helix: 2.82 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.68 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 30 TYR 0.009 0.001 TYR E 44 PHE 0.008 0.002 PHE R 32 TRP 0.009 0.001 TRP M 40 HIS 0.006 0.001 HIS N 40 Details of bonding type rmsd covalent geometry : bond 0.00580 (10792) covalent geometry : angle 0.87915 (15206) hydrogen bonds : bond 0.05245 ( 519) hydrogen bonds : angle 3.78241 ( 1476) Misc. bond : bond 0.13057 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.316 Fit side-chains REVERT: C 43 LYS cc_start: 0.8543 (tttm) cc_final: 0.7865 (ttmt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.8029 time to fit residues: 40.7982 Evaluate side-chains 48 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 50 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 0 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3086 r_free = 0.3086 target = 0.107981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.083059 restraints weight = 11399.403| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 1.42 r_work: 0.2516 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2383 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.229 10825 Z= 0.123 Angle : 0.736 10.210 15206 Z= 0.255 Chirality : 0.039 0.113 1507 Planarity : 0.005 0.039 1853 Dihedral : 13.349 97.683 2033 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.12 % Allowed : 7.93 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.73 (0.25), residues: 929 helix: 3.33 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.93 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 5 TYR 0.005 0.001 TYR A 44 PHE 0.004 0.001 PHE R 32 TRP 0.009 0.001 TRP E 40 HIS 0.003 0.001 HIS N 24 Details of bonding type rmsd covalent geometry : bond 0.00289 (10792) covalent geometry : angle 0.73555 (15206) hydrogen bonds : bond 0.04110 ( 519) hydrogen bonds : angle 3.34444 ( 1476) Misc. bond : bond 0.10153 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.373 Fit side-chains REVERT: C 43 LYS cc_start: 0.8502 (tttm) cc_final: 0.7810 (ttmt) outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 0.7020 time to fit residues: 39.6405 Evaluate side-chains 48 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 67 optimal weight: 5.9990 chunk 16 optimal weight: 30.0000 chunk 78 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3061 r_free = 0.3061 target = 0.106131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.081302 restraints weight = 11265.923| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 1.41 r_work: 0.2483 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2350 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.261 10825 Z= 0.157 Angle : 0.784 12.013 15206 Z= 0.272 Chirality : 0.041 0.117 1507 Planarity : 0.005 0.038 1853 Dihedral : 13.275 97.452 2033 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.59 (0.24), residues: 929 helix: 3.17 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.98 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 30 TYR 0.010 0.001 TYR E 44 PHE 0.006 0.001 PHE R 32 TRP 0.009 0.001 TRP E 40 HIS 0.003 0.001 HIS L 40 Details of bonding type rmsd covalent geometry : bond 0.00397 (10792) covalent geometry : angle 0.78377 (15206) hydrogen bonds : bond 0.04529 ( 519) hydrogen bonds : angle 3.47252 ( 1476) Misc. bond : bond 0.11202 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.324 Fit side-chains REVERT: C 43 LYS cc_start: 0.8520 (tttm) cc_final: 0.7837 (ttmt) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.7626 time to fit residues: 38.1299 Evaluate side-chains 45 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 57 optimal weight: 0.0060 chunk 38 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 15 optimal weight: 0.0470 chunk 16 optimal weight: 0.0770 chunk 42 optimal weight: 0.0870 chunk 0 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 overall best weight: 0.1630 ------------------------------------------------------------------------------- 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 = 0.3175 r_free = 0.3175 target = 0.114519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.090195 restraints weight = 11147.301| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 1.40 r_work: 0.2627 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.194 10825 Z= 0.097 Angle : 0.660 9.632 15206 Z= 0.231 Chirality : 0.038 0.112 1507 Planarity : 0.004 0.039 1853 Dihedral : 13.223 97.164 2033 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.33 (0.25), residues: 929 helix: 3.69 (0.17), residues: 603 sheet: None (None), residues: 0 loop : 1.33 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 30 TYR 0.012 0.001 TYR E 44 PHE 0.003 0.001 PHE N 32 TRP 0.015 0.002 TRP E 45 HIS 0.003 0.001 HIS N 24 Details of bonding type rmsd covalent geometry : bond 0.00216 (10792) covalent geometry : angle 0.66042 (15206) hydrogen bonds : bond 0.03466 ( 519) hydrogen bonds : angle 3.03166 ( 1476) Misc. bond : bond 0.06912 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.335 Fit side-chains REVERT: C 43 LYS cc_start: 0.8428 (tttm) cc_final: 0.7758 (ttmt) REVERT: H 46 TYR cc_start: 0.8618 (m-80) cc_final: 0.7865 (m-80) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.7250 time to fit residues: 44.1233 Evaluate side-chains 46 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 57 optimal weight: 0.0370 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.111330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.086779 restraints weight = 11186.526| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 1.41 r_work: 0.2575 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2444 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.228 10825 Z= 0.115 Angle : 0.688 8.973 15206 Z= 0.241 Chirality : 0.039 0.113 1507 Planarity : 0.004 0.036 1853 Dihedral : 12.932 95.835 2033 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.12 % Allowed : 8.67 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.28 (0.24), residues: 929 helix: 3.68 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 1.33 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 5 TYR 0.008 0.001 TYR E 44 PHE 0.004 0.001 PHE B 32 TRP 0.010 0.001 TRP C 40 HIS 0.002 0.001 HIS N 24 Details of bonding type rmsd covalent geometry : bond 0.00271 (10792) covalent geometry : angle 0.68822 (15206) hydrogen bonds : bond 0.03825 ( 519) hydrogen bonds : angle 3.11466 ( 1476) Misc. bond : bond 0.08946 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.214 Fit side-chains REVERT: C 43 LYS cc_start: 0.8456 (tttm) cc_final: 0.7751 (ttmt) REVERT: H 46 TYR cc_start: 0.8626 (m-80) cc_final: 0.7899 (m-80) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.8009 time to fit residues: 40.0251 Evaluate side-chains 43 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 51 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.103456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.078694 restraints weight = 11385.781| |-----------------------------------------------------------------------------| r_work (start): 0.2608 rms_B_bonded: 1.41 r_work: 0.2424 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2292 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.299 10825 Z= 0.296 Angle : 0.971 15.370 15206 Z= 0.341 Chirality : 0.051 0.169 1507 Planarity : 0.005 0.040 1853 Dihedral : 13.602 99.226 2033 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.12 % Allowed : 9.05 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.24), residues: 929 helix: 2.58 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.91 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 5 TYR 0.015 0.002 TYR C 44 PHE 0.011 0.002 PHE M 41 TRP 0.018 0.002 TRP C 45 HIS 0.009 0.002 HIS N 40 Details of bonding type rmsd covalent geometry : bond 0.00805 (10792) covalent geometry : angle 0.97140 (15206) hydrogen bonds : bond 0.05835 ( 519) hydrogen bonds : angle 3.93006 ( 1476) Misc. bond : bond 0.13491 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.352 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 0.8105 time to fit residues: 45.5482 Evaluate side-chains 50 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 25 optimal weight: 0.1980 chunk 70 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.0870 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 0.1980 chunk 41 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3112 r_free = 0.3112 target = 0.110046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.085426 restraints weight = 11273.425| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 1.41 r_work: 0.2556 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2427 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.218 10825 Z= 0.109 Angle : 0.708 10.162 15206 Z= 0.246 Chirality : 0.038 0.111 1507 Planarity : 0.004 0.039 1853 Dihedral : 13.243 97.176 2033 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.99 (0.25), residues: 929 helix: 3.47 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 1.17 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 5 TYR 0.010 0.001 TYR E 44 PHE 0.004 0.001 PHE D 41 TRP 0.010 0.001 TRP G 45 HIS 0.003 0.001 HIS J 24 Details of bonding type rmsd covalent geometry : bond 0.00250 (10792) covalent geometry : angle 0.70750 (15206) hydrogen bonds : bond 0.03783 ( 519) hydrogen bonds : angle 3.20513 ( 1476) Misc. bond : bond 0.08945 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2630.96 seconds wall clock time: 45 minutes 36.74 seconds (2736.74 seconds total)