Starting phenix.real_space_refine on Mon Jul 28 10:59:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zdi_14650/07_2025/7zdi_14650.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zdi_14650/07_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_14650/07_2025/7zdi_14650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zdi_14650/07_2025/7zdi_14650.map" model { file = "/net/cci-nas-00/data/ceres_data/7zdi_14650/07_2025/7zdi_14650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zdi_14650/07_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-5711/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: 6.76, per 1000 atoms: 0.66 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: 3.22 Conformation dependent library (CDL) restraints added in 900.7 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: 0.85 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: 2.45 Time building geometry restraints manager: 3.72 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: 1.650 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: 0.070 Set scattering table: 0.090 Process input model: 25.700 Find NCS groups from input model: 0.550 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:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.770 ------------------------------------------------------------------------------- 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 : 3.63 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 Details of bonding type rmsd hydrogen bonds : bond 0.15503 ( 519) hydrogen bonds : angle 6.14862 ( 1476) covalent geometry : bond 0.00466 (10792) covalent geometry : angle 0.93300 (15206) 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 : 0.935 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: 1.4594 time to fit residues: 129.4542 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 : 0.922 ------------------------------------------------------------------------------- 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: 6.9990 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: 0.9990 chunk 73 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3018 r_free = 0.3018 target = 0.103371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.078298 restraints weight = 11381.628| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 1.42 r_work: 0.2433 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2300 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.357 10825 Z= 0.234 Angle : 0.929 10.626 15206 Z= 0.329 Chirality : 0.047 0.132 1507 Planarity : 0.006 0.038 1853 Dihedral : 13.744 122.633 2033 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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 (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: 2.63 (0.25), residues: 929 helix: 2.57 (0.18), residues: 603 sheet: None (None), residues: 0 loop : 0.19 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 45 HIS 0.005 0.001 HIS N 24 PHE 0.009 0.002 PHE B 32 TYR 0.012 0.002 TYR S 69 ARG 0.002 0.000 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.05620 ( 519) hydrogen bonds : angle 4.01412 ( 1476) covalent geometry : bond 0.00619 (10792) covalent geometry : angle 0.92928 (15206) Misc. bond : bond 0.15546 ( 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 58 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.927 Fit side-chains REVERT: C 43 LYS cc_start: 0.8561 (tttm) cc_final: 0.7904 (ttmt) REVERT: P 20 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8494 (mm-30) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 1.7007 time to fit residues: 103.0063 Evaluate side-chains 54 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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: 0.7980 chunk 45 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 33 optimal weight: 0.0370 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 = 0.109148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.084313 restraints weight = 11288.232| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 1.42 r_work: 0.2528 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2398 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.254 10825 Z= 0.121 Angle : 0.732 10.087 15206 Z= 0.257 Chirality : 0.039 0.113 1507 Planarity : 0.005 0.039 1853 Dihedral : 13.361 104.318 2033 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.12 % Allowed : 5.95 % Favored : 93.93 % 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: 3.60 (0.25), residues: 929 helix: 3.39 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.52 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 45 HIS 0.003 0.001 HIS N 24 PHE 0.003 0.001 PHE R 32 TYR 0.006 0.001 TYR S 5 ARG 0.001 0.000 ARG A 5 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 519) hydrogen bonds : angle 3.35113 ( 1476) covalent geometry : bond 0.00276 (10792) covalent geometry : angle 0.73183 (15206) Misc. bond : bond 0.10860 ( 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 57 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.974 Fit side-chains REVERT: C 43 LYS cc_start: 0.8490 (tttm) cc_final: 0.7821 (ttmt) REVERT: P 20 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8395 (mm-30) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 1.5564 time to fit residues: 94.8493 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 : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 68 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3016 r_free = 0.3016 target = 0.103145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.078189 restraints weight = 11327.144| |-----------------------------------------------------------------------------| r_work (start): 0.2628 rms_B_bonded: 1.41 r_work: 0.2445 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2312 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.325 10825 Z= 0.228 Angle : 0.894 11.912 15206 Z= 0.311 Chirality : 0.046 0.134 1507 Planarity : 0.005 0.039 1853 Dihedral : 13.676 107.935 2033 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.12 % Allowed : 6.94 % 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 (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: 2.96 (0.24), residues: 929 helix: 2.76 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.55 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 40 HIS 0.006 0.001 HIS N 40 PHE 0.008 0.002 PHE R 32 TYR 0.010 0.002 TYR H 46 ARG 0.001 0.000 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.05368 ( 519) hydrogen bonds : angle 3.84659 ( 1476) covalent geometry : bond 0.00610 (10792) covalent geometry : angle 0.89393 (15206) Misc. bond : bond 0.13606 ( 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: 1 poor density : 51 time to evaluate : 0.944 Fit side-chains REVERT: C 43 LYS cc_start: 0.8534 (tttm) cc_final: 0.7859 (ttmt) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 1.7169 time to fit residues: 93.1231 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 : 0.870 ------------------------------------------------------------------------------- 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: 1.9990 chunk 14 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.3054 r_free = 0.3054 target = 0.105611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.080709 restraints weight = 11244.071| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 1.42 r_work: 0.2455 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2322 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.276 10825 Z= 0.169 Angle : 0.812 11.078 15206 Z= 0.281 Chirality : 0.042 0.118 1507 Planarity : 0.005 0.040 1853 Dihedral : 13.528 102.921 2033 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % 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: 3.22 (0.24), residues: 929 helix: 2.93 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.71 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 40 HIS 0.004 0.001 HIS N 40 PHE 0.006 0.001 PHE R 32 TYR 0.007 0.001 TYR H 46 ARG 0.001 0.000 ARG N 30 Details of bonding type rmsd hydrogen bonds : bond 0.04728 ( 519) hydrogen bonds : angle 3.61481 ( 1476) covalent geometry : bond 0.00433 (10792) covalent geometry : angle 0.81158 (15206) Misc. bond : bond 0.11905 ( 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 51 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.981 Fit side-chains REVERT: C 43 LYS cc_start: 0.8520 (tttm) cc_final: 0.7835 (ttmt) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 1.8041 time to fit residues: 98.2510 Evaluate side-chains 49 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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: 7.9990 chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 11 optimal weight: 20.0000 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.110637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.085977 restraints weight = 11160.184| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 1.41 r_work: 0.2564 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2433 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.220 10825 Z= 0.109 Angle : 0.701 10.007 15206 Z= 0.242 Chirality : 0.038 0.111 1507 Planarity : 0.005 0.040 1853 Dihedral : 13.268 96.400 2033 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % 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: 3.96 (0.25), residues: 929 helix: 3.51 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 1.03 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 45 HIS 0.004 0.001 HIS P 24 PHE 0.003 0.001 PHE L 41 TYR 0.010 0.001 TYR E 44 ARG 0.001 0.000 ARG P 30 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 519) hydrogen bonds : angle 3.18925 ( 1476) covalent geometry : bond 0.00253 (10792) covalent geometry : angle 0.70061 (15206) Misc. bond : bond 0.08865 ( 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: 0 poor density : 54 time to evaluate : 0.984 Fit side-chains REVERT: C 43 LYS cc_start: 0.8467 (tttm) cc_final: 0.7790 (ttmt) REVERT: P 23 LYS cc_start: 0.8635 (mtpt) cc_final: 0.8416 (mtmt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 1.4828 time to fit residues: 86.6614 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 : 0.961 ------------------------------------------------------------------------------- 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: 0.9980 chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 0.0020 chunk 70 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 33 optimal weight: 0.0270 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 overall best weight: 0.5846 ------------------------------------------------------------------------------- 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 = 0.3114 r_free = 0.3114 target = 0.110011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.085368 restraints weight = 11317.416| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 1.41 r_work: 0.2574 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2445 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.230 10825 Z= 0.113 Angle : 0.695 9.246 15206 Z= 0.241 Chirality : 0.039 0.111 1507 Planarity : 0.004 0.038 1853 Dihedral : 13.004 96.307 2033 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.00 % Allowed : 8.55 % 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: 4.12 (0.24), residues: 929 helix: 3.58 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 1.20 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 40 HIS 0.003 0.001 HIS N 24 PHE 0.004 0.001 PHE R 32 TYR 0.009 0.001 TYR G 44 ARG 0.000 0.000 ARG P 30 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 519) hydrogen bonds : angle 3.14282 ( 1476) covalent geometry : bond 0.00264 (10792) covalent geometry : angle 0.69462 (15206) Misc. bond : bond 0.09110 ( 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 48 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.945 Fit side-chains REVERT: C 43 LYS cc_start: 0.8462 (tttm) cc_final: 0.7770 (ttmt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 1.6277 time to fit residues: 83.6175 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 : 0.830 ------------------------------------------------------------------------------- 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: 9.9990 chunk 44 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 41 optimal weight: 0.0070 chunk 53 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- 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 = 0.3130 r_free = 0.3130 target = 0.111139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.086616 restraints weight = 11278.465| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 1.41 r_work: 0.2597 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.216 10825 Z= 0.110 Angle : 0.682 9.211 15206 Z= 0.239 Chirality : 0.039 0.111 1507 Planarity : 0.004 0.036 1853 Dihedral : 12.936 96.297 2033 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 4.25 (0.24), residues: 929 helix: 3.65 (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 M 40 HIS 0.002 0.001 HIS N 24 PHE 0.003 0.001 PHE R 32 TYR 0.005 0.001 TYR E 44 ARG 0.000 0.000 ARG A 5 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 519) hydrogen bonds : angle 3.09192 ( 1476) covalent geometry : bond 0.00257 (10792) covalent geometry : angle 0.68228 (15206) Misc. bond : bond 0.08466 ( 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 46 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.895 Fit side-chains REVERT: C 43 LYS cc_start: 0.8500 (tttm) cc_final: 0.7808 (ttmt) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 1.5561 time to fit residues: 76.6979 Evaluate side-chains 42 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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: 0.9990 chunk 61 optimal weight: 0.3980 chunk 8 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3111 r_free = 0.3111 target = 0.109761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.085098 restraints weight = 11358.375| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 1.42 r_work: 0.2551 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2420 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2232 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= 0.118 Angle : 0.696 9.046 15206 Z= 0.244 Chirality : 0.039 0.112 1507 Planarity : 0.004 0.036 1853 Dihedral : 12.849 96.107 2033 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.00 % Allowed : 9.17 % 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 (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: 4.21 (0.24), residues: 929 helix: 3.60 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 1.34 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 40 HIS 0.002 0.001 HIS P 22 PHE 0.004 0.001 PHE R 32 TYR 0.004 0.001 TYR D 46 ARG 0.000 0.000 ARG A 5 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 519) hydrogen bonds : angle 3.12976 ( 1476) covalent geometry : bond 0.00279 (10792) covalent geometry : angle 0.69554 (15206) Misc. bond : bond 0.09004 ( 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 45 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.876 Fit side-chains REVERT: C 43 LYS cc_start: 0.8503 (tttm) cc_final: 0.7818 (ttmt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 1.7135 time to fit residues: 83.1991 Evaluate side-chains 44 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3133 r_free = 0.3133 target = 0.111264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.086887 restraints weight = 11158.149| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 1.39 r_work: 0.2593 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2463 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.216 10825 Z= 0.111 Angle : 0.677 8.932 15206 Z= 0.238 Chirality : 0.039 0.111 1507 Planarity : 0.004 0.036 1853 Dihedral : 12.753 95.962 2033 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.62 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: 4.32 (0.24), residues: 929 helix: 3.68 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 1.41 (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 N 24 PHE 0.003 0.001 PHE R 32 TYR 0.004 0.001 TYR D 46 ARG 0.001 0.000 ARG A 5 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 519) hydrogen bonds : angle 3.06512 ( 1476) covalent geometry : bond 0.00259 (10792) covalent geometry : angle 0.67739 (15206) Misc. bond : bond 0.08373 ( 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 46 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.329 Fit side-chains REVERT: C 43 LYS cc_start: 0.8504 (tttm) cc_final: 0.7805 (ttmt) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 2.1555 time to fit residues: 105.9124 Evaluate side-chains 44 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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: 0.9990 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 34 optimal weight: 0.0570 chunk 45 optimal weight: 0.0670 chunk 47 optimal weight: 0.8980 overall best weight: 0.5636 ------------------------------------------------------------------------------- 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 = 0.3139 r_free = 0.3139 target = 0.111713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.087262 restraints weight = 11203.323| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 1.41 r_work: 0.2598 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.217 10825 Z= 0.108 Angle : 0.671 8.618 15206 Z= 0.236 Chirality : 0.039 0.111 1507 Planarity : 0.004 0.035 1853 Dihedral : 12.745 95.674 2033 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.00 % Allowed : 9.17 % 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 (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: 4.38 (0.24), residues: 929 helix: 3.71 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 1.47 (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 N 24 PHE 0.003 0.001 PHE R 32 TYR 0.006 0.001 TYR G 44 ARG 0.000 0.000 ARG E 5 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 519) hydrogen bonds : angle 3.03275 ( 1476) covalent geometry : bond 0.00252 (10792) covalent geometry : angle 0.67131 (15206) Misc. bond : bond 0.08302 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5809.06 seconds wall clock time: 102 minutes 41.40 seconds (6161.40 seconds total)