Starting phenix.real_space_refine on Fri Feb 14 14:14:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zdi_14650/02_2025/7zdi_14650.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zdi_14650/02_2025/7zdi_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zdi_14650/02_2025/7zdi_14650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zdi_14650/02_2025/7zdi_14650.map" model { file = "/net/cci-nas-00/data/ceres_data/7zdi_14650/02_2025/7zdi_14650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zdi_14650/02_2025/7zdi_14650.cif" } resolution = 2.9 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= 0.013 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 7.40, per 1000 atoms: 0.72 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: 4.31 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.74 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: 2.71 Time building geometry restraints manager: 4.75 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 49 or resid 101 through 102)) selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = (chain 'I' and (resid 1 through 49 or resid 101 through 102)) selection = (chain 'K' and (resid 1 through 49 or resid 101 through 102)) selection = (chain 'M' and (resid 1 through 49 or resid 101 through 102)) selection = (chain 'O' and (resid 1 through 49 or resid 101 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: 1.110 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.280 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: 0.000 Load rotamer database and sin/cos tables:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.780 ------------------------------------------------------------------------------- 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 : 0.005 0.046 10792 Z= 0.264 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 : 3.63 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 (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: 1.10 (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 TRP 0.021 0.002 TRP O 7 HIS 0.003 0.001 HIS N 24 PHE 0.005 0.001 PHE G 41 TYR 0.016 0.004 TYR K 32 ARG 0.016 0.003 ARG R 30 *********************** 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 : 0.972 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: 1.5783 time to fit residues: 139.6556 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 : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3014 r_free = 0.3014 target = 0.103035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.078028 restraints weight = 11405.010| |-----------------------------------------------------------------------------| r_work (start): 0.2608 rms_B_bonded: 1.41 r_work: 0.2424 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2290 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 10792 Z= 0.364 Angle : 0.947 11.398 15206 Z= 0.335 Chirality : 0.047 0.132 1507 Planarity : 0.006 0.038 1853 Dihedral : 13.827 122.615 2033 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.12 % Allowed : 4.96 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.55 (0.25), residues: 929 helix: 2.50 (0.18), residues: 603 sheet: None (None), residues: 0 loop : 0.18 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 45 HIS 0.006 0.001 HIS N 40 PHE 0.009 0.002 PHE B 32 TYR 0.013 0.002 TYR Q 32 ARG 0.002 0.000 ARG J 30 *********************** 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 58 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.891 Fit side-chains REVERT: C 43 LYS cc_start: 0.8567 (tttm) cc_final: 0.7906 (ttmt) REVERT: P 20 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8477 (mm-30) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 1.7554 time to fit residues: 106.2081 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 : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 66 optimal weight: 0.9980 chunk 45 optimal weight: 0.0970 chunk 72 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 58 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3123 r_free = 0.3123 target = 0.110622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.085850 restraints weight = 11233.432| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 1.42 r_work: 0.2552 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2422 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10792 Z= 0.138 Angle : 0.721 10.066 15206 Z= 0.251 Chirality : 0.039 0.112 1507 Planarity : 0.005 0.039 1853 Dihedral : 13.415 103.301 2033 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.12 % Allowed : 6.07 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.69 (0.25), residues: 929 helix: 3.46 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.55 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 45 HIS 0.004 0.001 HIS N 24 PHE 0.003 0.001 PHE L 41 TYR 0.006 0.001 TYR S 5 ARG 0.001 0.000 ARG A 5 *********************** 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 58 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.971 Fit side-chains REVERT: C 43 LYS cc_start: 0.8489 (tttm) cc_final: 0.7819 (ttmt) REVERT: O 43 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8279 (tptp) outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 1.5559 time to fit residues: 96.5317 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 : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 43 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 77 optimal weight: 0.1980 chunk 24 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.3049 r_free = 0.3049 target = 0.105428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.080523 restraints weight = 11233.545| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 1.41 r_work: 0.2469 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2335 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10792 Z= 0.244 Angle : 0.807 9.974 15206 Z= 0.281 Chirality : 0.042 0.117 1507 Planarity : 0.005 0.038 1853 Dihedral : 13.391 102.264 2033 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.25 % Allowed : 7.06 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.41 (0.24), residues: 929 helix: 3.13 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.69 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 40 HIS 0.004 0.001 HIS L 40 PHE 0.007 0.001 PHE R 32 TYR 0.007 0.001 TYR H 46 ARG 0.001 0.000 ARG H 30 *********************** 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 48 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.933 Fit side-chains REVERT: C 43 LYS cc_start: 0.8519 (tttm) cc_final: 0.7853 (ttmt) outliers start: 2 outliers final: 0 residues processed: 47 average time/residue: 1.7567 time to fit residues: 88.1377 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 : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 53 optimal weight: 0.0970 chunk 14 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 = 0.3082 r_free = 0.3082 target = 0.107698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.082875 restraints weight = 11171.076| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 1.41 r_work: 0.2509 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2377 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10792 Z= 0.177 Angle : 0.736 10.061 15206 Z= 0.257 Chirality : 0.040 0.115 1507 Planarity : 0.005 0.038 1853 Dihedral : 13.280 97.359 2033 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.73 (0.25), residues: 929 helix: 3.35 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.88 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 40 HIS 0.003 0.001 HIS N 24 PHE 0.005 0.001 PHE R 32 TYR 0.005 0.001 TYR R 46 ARG 0.001 0.000 ARG L 30 *********************** 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 51 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.943 Fit side-chains REVERT: C 43 LYS cc_start: 0.8490 (tttm) cc_final: 0.7815 (ttmt) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 1.5799 time to fit residues: 86.3080 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 : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 0.0970 chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 18 optimal weight: 0.0870 chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 0.0000 overall best weight: 0.3360 ------------------------------------------------------------------------------- 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 = 0.3159 r_free = 0.3159 target = 0.113354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.088904 restraints weight = 11116.163| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 1.41 r_work: 0.2612 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10792 Z= 0.129 Angle : 0.664 9.443 15206 Z= 0.232 Chirality : 0.038 0.112 1507 Planarity : 0.004 0.037 1853 Dihedral : 13.170 96.495 2033 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 4.27 (0.25), residues: 929 helix: 3.72 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 1.23 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 45 HIS 0.003 0.000 HIS N 24 PHE 0.003 0.000 PHE B 32 TYR 0.010 0.001 TYR E 44 ARG 0.000 0.000 ARG G 5 *********************** 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 56 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.952 Fit side-chains REVERT: C 43 LYS cc_start: 0.8439 (tttm) cc_final: 0.7781 (ttmt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 1.4023 time to fit residues: 84.5874 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 : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 79 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3085 r_free = 0.3085 target = 0.107868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.083037 restraints weight = 11370.228| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 1.42 r_work: 0.2511 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2379 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10792 Z= 0.189 Angle : 0.729 9.405 15206 Z= 0.256 Chirality : 0.040 0.115 1507 Planarity : 0.004 0.035 1853 Dihedral : 13.073 96.292 2033 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.12 % Allowed : 8.18 % 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 (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: 4.01 (0.24), residues: 929 helix: 3.47 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 1.22 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 40 HIS 0.003 0.001 HIS L 40 PHE 0.006 0.001 PHE R 32 TYR 0.010 0.001 TYR G 44 ARG 0.000 0.000 ARG A 5 *********************** 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 48 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.965 Fit side-chains REVERT: C 43 LYS cc_start: 0.8472 (tttm) cc_final: 0.7790 (ttmt) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 1.7072 time to fit residues: 85.6743 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 : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 0.0980 chunk 44 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3053 r_free = 0.3053 target = 0.105618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.080702 restraints weight = 11428.091| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 1.42 r_work: 0.2475 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2343 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10792 Z= 0.234 Angle : 0.780 9.922 15206 Z= 0.274 Chirality : 0.042 0.118 1507 Planarity : 0.005 0.036 1853 Dihedral : 13.210 97.564 2033 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.12 % Allowed : 8.43 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.73 (0.24), residues: 929 helix: 3.23 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 1.15 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 40 HIS 0.004 0.001 HIS L 40 PHE 0.006 0.001 PHE R 32 TYR 0.008 0.001 TYR G 44 ARG 0.001 0.000 ARG L 30 *********************** 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 48 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.895 Fit side-chains REVERT: C 43 LYS cc_start: 0.8495 (tttm) cc_final: 0.7788 (ttmt) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 1.7130 time to fit residues: 86.0139 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 : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 0.0050 chunk 67 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.3109 r_free = 0.3109 target = 0.109654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.085078 restraints weight = 11363.674| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 1.40 r_work: 0.2547 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2417 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10792 Z= 0.153 Angle : 0.694 9.701 15206 Z= 0.244 Chirality : 0.039 0.112 1507 Planarity : 0.004 0.037 1853 Dihedral : 12.995 96.187 2033 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.12 % Allowed : 8.80 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 4.17 (0.24), residues: 929 helix: 3.58 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 1.30 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 40 HIS 0.002 0.001 HIS J 22 PHE 0.004 0.001 PHE R 32 TYR 0.008 0.001 TYR G 44 ARG 0.001 0.000 ARG Q 5 *********************** 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 : 0.912 Fit side-chains REVERT: C 43 LYS cc_start: 0.8504 (tttm) cc_final: 0.7816 (ttmt) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 1.6491 time to fit residues: 83.2646 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 : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 3 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.108444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.083812 restraints weight = 11223.584| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 1.41 r_work: 0.2529 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2396 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10792 Z= 0.164 Angle : 0.706 9.322 15206 Z= 0.248 Chirality : 0.039 0.114 1507 Planarity : 0.004 0.036 1853 Dihedral : 12.868 95.750 2033 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 4.13 (0.24), residues: 929 helix: 3.54 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 1.32 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 40 HIS 0.002 0.001 HIS H 22 PHE 0.004 0.001 PHE R 32 TYR 0.007 0.001 TYR G 44 ARG 0.000 0.000 ARG L 30 ********************** 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 48 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.888 Fit side-chains REVERT: C 43 LYS cc_start: 0.8513 (tttm) cc_final: 0.7819 (ttmt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 1.6563 time to fit residues: 84.9183 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 : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3101 r_free = 0.3101 target = 0.109040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.084478 restraints weight = 11254.753| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 1.40 r_work: 0.2537 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2405 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10792 Z= 0.162 Angle : 0.700 9.319 15206 Z= 0.246 Chirality : 0.039 0.114 1507 Planarity : 0.004 0.036 1853 Dihedral : 12.840 95.805 2033 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.18 (0.24), residues: 929 helix: 3.56 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 1.37 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 40 HIS 0.002 0.001 HIS J 22 PHE 0.004 0.001 PHE R 32 TYR 0.007 0.001 TYR G 44 ARG 0.000 0.000 ARG N 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5303.11 seconds wall clock time: 94 minutes 43.58 seconds (5683.58 seconds total)