Starting phenix.real_space_refine on Wed Mar 4 02:51:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ze3_14682/03_2026/7ze3_14682.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ze3_14682/03_2026/7ze3_14682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ze3_14682/03_2026/7ze3_14682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ze3_14682/03_2026/7ze3_14682.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ze3_14682/03_2026/7ze3_14682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ze3_14682/03_2026/7ze3_14682.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 27 5.16 5 C 7274 2.51 5 N 1401 2.21 5 O 1550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10285 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, '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: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 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: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, '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: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "E" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, '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: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "G" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, '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: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "I" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, '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: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "K" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, '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: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "M" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, '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: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "O" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, '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: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "Q" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, '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: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 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, 'ZE0': 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, 'ZE0': 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: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'ZE0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'ZE0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'ZE0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'ZE0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'ZE0': 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: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 239 Unusual residues: {'BCL': 3, 'ZE0': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'ZE0': 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} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.24, per 1000 atoms: 0.22 Number of scatterers: 10285 At special positions: 0 Unit cell: (94.25, 103.35, 81.25, 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 27 16.00 Mg 33 11.99 O 1550 8.00 N 1401 7.00 C 7274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=33, symmetry=0 Number of additional bonds: simple=33, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 393.9 milliseconds 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1796 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 74.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 11 through 37 Proline residue: A 17 - end of helix Processing helix chain 'A' and resid 39 through 47 Processing helix chain 'B' and resid 3 through 7 Processing helix chain 'B' and resid 14 through 47 removed outlier: 3.507A pdb=" N HIS B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 11 through 37 Proline residue: C 17 - end of helix Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 14 through 47 removed outlier: 3.700A pdb=" N HIS D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 9 removed outlier: 4.175A pdb=" N TRP E 7 " --> pdb=" O GLY E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 37 Proline residue: E 17 - end of helix Processing helix chain 'E' and resid 39 through 47 Processing helix chain 'F' and resid 3 through 7 Processing helix chain 'F' and resid 14 through 47 removed outlier: 3.600A pdb=" N HIS F 24 " --> pdb=" O GLU F 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 9 removed outlier: 4.109A pdb=" N TRP G 7 " --> pdb=" O GLY G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 37 Proline residue: G 17 - end of helix Processing helix chain 'G' and resid 39 through 47 Processing helix chain 'H' and resid 3 through 7 Processing helix chain 'H' and resid 14 through 47 removed outlier: 3.508A pdb=" N HIS H 24 " --> pdb=" O GLU H 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 9 Processing helix chain 'I' and resid 11 through 37 Proline residue: I 17 - end of helix Processing helix chain 'I' and resid 39 through 47 Processing helix chain 'J' and resid 3 through 7 Processing helix chain 'J' and resid 14 through 47 removed outlier: 3.590A pdb=" N HIS J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 9 Processing helix chain 'K' and resid 11 through 37 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 39 through 47 Processing helix chain 'L' and resid 3 through 7 Processing helix chain 'L' and resid 14 through 47 removed outlier: 3.613A pdb=" N HIS L 24 " --> pdb=" O GLU L 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 9 Processing helix chain 'M' and resid 11 through 37 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: 3.602A pdb=" N HIS N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 10 removed outlier: 3.985A pdb=" N VAL O 9 " --> pdb=" O ARG O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 11 through 37 Proline residue: O 17 - end of helix Processing helix chain 'O' and resid 39 through 47 Processing helix chain 'P' and resid 3 through 7 Processing helix chain 'P' and resid 14 through 47 removed outlier: 3.589A pdb=" N HIS P 24 " --> pdb=" O GLU P 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 9 removed outlier: 4.128A pdb=" N TRP Q 7 " --> pdb=" O GLY Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 37 Proline residue: Q 17 - end of helix Processing helix chain 'Q' and resid 39 through 47 Processing helix chain 'R' and resid 3 through 7 Processing helix chain 'R' and resid 14 through 47 removed outlier: 3.578A pdb=" N HIS R 24 " --> pdb=" O GLU R 20 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.36 Time building geometry restraints manager: 1.30 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: 2952 1.37 - 1.57: 7600 1.57 - 1.78: 9 1.78 - 1.98: 45 1.98 - 2.18: 132 Bond restraints: 10738 Sorted by residual: bond pdb=" C35 ZE0 G 103 " pdb=" C36 ZE0 G 103 " ideal model delta sigma weight residual 1.348 1.534 -0.186 2.00e-02 2.50e+03 8.64e+01 bond pdb=" C35 ZE0 O 103 " pdb=" C36 ZE0 O 103 " ideal model delta sigma weight residual 1.348 1.534 -0.186 2.00e-02 2.50e+03 8.63e+01 bond pdb=" C35 ZE0 B 102 " pdb=" C36 ZE0 B 102 " ideal model delta sigma weight residual 1.348 1.534 -0.186 2.00e-02 2.50e+03 8.60e+01 bond pdb=" C35 ZE0 I 103 " pdb=" C36 ZE0 I 103 " ideal model delta sigma weight residual 1.348 1.533 -0.185 2.00e-02 2.50e+03 8.56e+01 bond pdb=" C35 ZE0 E 103 " pdb=" C36 ZE0 E 103 " ideal model delta sigma weight residual 1.348 1.533 -0.185 2.00e-02 2.50e+03 8.56e+01 ... (remaining 10733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 14736 2.84 - 5.67: 282 5.67 - 8.51: 31 8.51 - 11.34: 4 11.34 - 14.18: 18 Bond angle restraints: 15071 Sorted by residual: angle pdb=" C33 ZE0 G 103 " pdb=" C35 ZE0 G 103 " pdb=" C36 ZE0 G 103 " ideal model delta sigma weight residual 127.15 112.97 14.18 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C33 ZE0 B 102 " pdb=" C35 ZE0 B 102 " pdb=" C36 ZE0 B 102 " ideal model delta sigma weight residual 127.15 113.02 14.13 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C33 ZE0 I 103 " pdb=" C35 ZE0 I 103 " pdb=" C36 ZE0 I 103 " ideal model delta sigma weight residual 127.15 113.44 13.71 3.00e+00 1.11e-01 2.09e+01 angle pdb=" C33 ZE0 O 103 " pdb=" C35 ZE0 O 103 " pdb=" C36 ZE0 O 103 " ideal model delta sigma weight residual 127.15 113.45 13.70 3.00e+00 1.11e-01 2.08e+01 angle pdb=" C33 ZE0 A 103 " pdb=" C35 ZE0 A 103 " pdb=" C36 ZE0 A 103 " ideal model delta sigma weight residual 127.15 113.65 13.50 3.00e+00 1.11e-01 2.02e+01 ... (remaining 15066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.86: 5179 21.86 - 43.73: 240 43.73 - 65.59: 27 65.59 - 87.46: 15 87.46 - 109.32: 6 Dihedral angle restraints: 5467 sinusoidal: 2696 harmonic: 2771 Sorted by residual: dihedral pdb=" CA LEU S 61 " pdb=" C LEU S 61 " pdb=" N ILE S 62 " pdb=" CA ILE S 62 " ideal model delta harmonic sigma weight residual 180.00 158.25 21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA SER S 55 " pdb=" C SER S 55 " pdb=" N PHE S 56 " pdb=" CA PHE S 56 " ideal model delta harmonic sigma weight residual 180.00 158.68 21.32 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA LEU J 13 " pdb=" C LEU J 13 " pdb=" N THR J 14 " pdb=" CA THR J 14 " ideal model delta harmonic sigma weight residual 180.00 159.39 20.61 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 5464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 876 0.030 - 0.061: 404 0.061 - 0.091: 137 0.091 - 0.121: 84 0.121 - 0.152: 15 Chirality restraints: 1516 Sorted by residual: chirality pdb=" CA MET A 26 " pdb=" N MET A 26 " pdb=" C MET A 26 " pdb=" CB MET A 26 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA MET Q 26 " pdb=" N MET Q 26 " pdb=" C MET Q 26 " pdb=" CB MET Q 26 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA MET I 26 " pdb=" N MET I 26 " pdb=" C MET I 26 " pdb=" CB MET I 26 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 1513 not shown) Planarity restraints: 1826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL S1702 " 0.094 3.00e-02 1.11e+03 8.06e-02 3.61e+01 pdb=" CBA BCL S1702 " 0.083 3.00e-02 1.11e+03 pdb=" CGA BCL S1702 " -0.062 3.00e-02 1.11e+03 pdb=" O1A BCL S1702 " -0.001 3.00e-02 1.11e+03 pdb=" O2A BCL S1702 " -0.114 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C21 ZE0 I 103 " 0.059 2.00e-02 2.50e+03 4.91e-02 3.02e+01 pdb=" C22 ZE0 I 103 " -0.073 2.00e-02 2.50e+03 pdb=" C23 ZE0 I 103 " -0.031 2.00e-02 2.50e+03 pdb=" C24 ZE0 I 103 " -0.004 2.00e-02 2.50e+03 pdb=" C25 ZE0 I 103 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL S1703 " 0.082 3.00e-02 1.11e+03 7.07e-02 2.78e+01 pdb=" CBA BCL S1703 " 0.073 3.00e-02 1.11e+03 pdb=" CGA BCL S1703 " -0.057 3.00e-02 1.11e+03 pdb=" O1A BCL S1703 " -0.001 3.00e-02 1.11e+03 pdb=" O2A BCL S1703 " -0.098 3.00e-02 1.11e+03 ... (remaining 1823 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1357 2.77 - 3.30: 8891 3.30 - 3.83: 18366 3.83 - 4.37: 22210 4.37 - 4.90: 37141 Nonbonded interactions: 87965 Sorted by model distance: nonbonded pdb=" O TRP J 49 " pdb=" O HOH J 201 " model vdw 2.231 3.040 nonbonded pdb=" O TRP P 49 " pdb=" O HOH P 201 " model vdw 2.266 3.040 nonbonded pdb=" O THR I 38 " pdb=" O HOH I 201 " model vdw 2.284 3.040 nonbonded pdb=" O TRP R 49 " pdb=" O HOH R 201 " model vdw 2.304 3.040 nonbonded pdb=" O PHE M 44 " pdb=" O HOH M 201 " model vdw 2.307 3.040 ... (remaining 87960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 102) selection = (chain 'C' and resid 1 through 102) selection = (chain 'E' and resid 1 through 102) selection = (chain 'G' and resid 1 through 102) selection = (chain 'I' and resid 1 through 102) selection = (chain 'K' and resid 1 through 102) selection = (chain 'M' and resid 1 through 102) selection = (chain 'O' and resid 1 through 102) selection = chain 'Q' } ncs_group { reference = (chain 'B' and resid 3 through 51) selection = (chain 'D' and resid 3 through 51) selection = (chain 'F' and resid 3 through 51) selection = (chain 'H' and resid 3 through 51) selection = (chain 'J' and resid 3 through 51) selection = (chain 'L' and resid 3 through 51) selection = chain 'N' 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.720 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.019 0.582 10771 Z= 1.732 Angle : 1.013 14.181 15071 Z= 0.423 Chirality : 0.044 0.152 1516 Planarity : 0.009 0.081 1826 Dihedral : 13.709 109.320 3671 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.24), residues: 920 helix: 1.13 (0.18), residues: 603 sheet: None (None), residues: 0 loop : -0.65 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.003 ARG D 30 TYR 0.017 0.003 TYR S 40 PHE 0.012 0.001 PHE C 28 TRP 0.025 0.003 TRP Q 7 HIS 0.008 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00738 (10738) covalent geometry : angle 1.01306 (15071) hydrogen bonds : bond 0.13875 ( 522) hydrogen bonds : angle 5.98177 ( 1461) Misc. bond : bond 0.31956 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.414 Fit side-chains REVERT: B 19 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7224 (mm-30) REVERT: C 5 ARG cc_start: 0.7960 (mtt180) cc_final: 0.7725 (mtt90) REVERT: C 11 LYS cc_start: 0.8516 (mtmt) cc_final: 0.8141 (mttm) REVERT: G 11 LYS cc_start: 0.8243 (mtmt) cc_final: 0.7982 (mttt) REVERT: I 43 LYS cc_start: 0.8001 (tttt) cc_final: 0.7679 (ttmt) REVERT: K 48 LYS cc_start: 0.7383 (tttt) cc_final: 0.7093 (mmtm) REVERT: M 5 ARG cc_start: 0.7462 (mtt180) cc_final: 0.7082 (mtp180) REVERT: M 11 LYS cc_start: 0.8180 (mtmt) cc_final: 0.7844 (mttp) REVERT: O 11 LYS cc_start: 0.8202 (mtmt) cc_final: 0.7983 (mttt) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.6792 time to fit residues: 113.2270 Evaluate side-chains 126 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 0.0670 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 49 GLN E 37 HIS ** I 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 HIS N 40 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.126438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.101292 restraints weight = 9833.252| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.43 r_work: 0.2815 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.282 10771 Z= 0.170 Angle : 0.781 11.783 15071 Z= 0.289 Chirality : 0.042 0.134 1516 Planarity : 0.005 0.028 1826 Dihedral : 14.771 105.839 1997 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.74 % Allowed : 6.62 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.26), residues: 920 helix: 3.07 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.47 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 30 TYR 0.009 0.001 TYR S 53 PHE 0.015 0.001 PHE C 28 TRP 0.015 0.002 TRP G 40 HIS 0.007 0.001 HIS O 37 Details of bonding type rmsd covalent geometry : bond 0.00323 (10738) covalent geometry : angle 0.78150 (15071) hydrogen bonds : bond 0.04120 ( 522) hydrogen bonds : angle 3.64583 ( 1461) Misc. bond : bond 0.10818 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.368 Fit side-chains REVERT: S 49 GLN cc_start: 0.7589 (tt0) cc_final: 0.7376 (tt0) REVERT: C 11 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8314 (mttm) REVERT: F 20 GLU cc_start: 0.7965 (tp30) cc_final: 0.7746 (tp30) REVERT: G 11 LYS cc_start: 0.8365 (mtmt) cc_final: 0.8034 (mttt) REVERT: I 43 LYS cc_start: 0.8069 (tttt) cc_final: 0.7751 (mptt) REVERT: J 20 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7754 (mm-30) REVERT: K 48 LYS cc_start: 0.7621 (tttt) cc_final: 0.7211 (tppt) REVERT: L 20 GLU cc_start: 0.7975 (tp30) cc_final: 0.7774 (tt0) REVERT: M 5 ARG cc_start: 0.7755 (mtt180) cc_final: 0.7261 (mtp180) REVERT: M 11 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8250 (mtpp) REVERT: O 11 LYS cc_start: 0.8394 (mtmt) cc_final: 0.8152 (mttt) outliers start: 6 outliers final: 2 residues processed: 127 average time/residue: 0.7248 time to fit residues: 97.5962 Evaluate side-chains 116 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain J residue 20 GLU Chi-restraints excluded: chain L residue 29 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 69 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 49 optimal weight: 0.0070 chunk 73 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 11 HIS ** I 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** L 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.127832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.104496 restraints weight = 9783.053| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.44 r_work: 0.2804 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.271 10771 Z= 0.116 Angle : 0.723 11.931 15071 Z= 0.263 Chirality : 0.039 0.126 1516 Planarity : 0.004 0.028 1826 Dihedral : 14.591 103.053 1997 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.49 % Allowed : 8.46 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.26), residues: 920 helix: 3.34 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.25 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 30 TYR 0.006 0.001 TYR S 53 PHE 0.012 0.001 PHE Q 28 TRP 0.012 0.001 TRP E 40 HIS 0.005 0.001 HIS Q 37 Details of bonding type rmsd covalent geometry : bond 0.00267 (10738) covalent geometry : angle 0.72261 (15071) hydrogen bonds : bond 0.03841 ( 522) hydrogen bonds : angle 3.40478 ( 1461) Misc. bond : bond 0.09982 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 0.363 Fit side-chains REVERT: C 11 LYS cc_start: 0.8716 (mtmt) cc_final: 0.8310 (mttm) REVERT: F 20 GLU cc_start: 0.8017 (tp30) cc_final: 0.7776 (tp30) REVERT: I 43 LYS cc_start: 0.8136 (tttt) cc_final: 0.7769 (mptt) REVERT: J 20 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7807 (mm-30) REVERT: K 48 LYS cc_start: 0.7624 (tttt) cc_final: 0.7182 (tppt) REVERT: L 20 GLU cc_start: 0.8074 (tp30) cc_final: 0.7810 (tt0) REVERT: L 23 LYS cc_start: 0.8700 (ttmm) cc_final: 0.8190 (mtmm) REVERT: M 5 ARG cc_start: 0.7771 (mtt180) cc_final: 0.7301 (mtp180) REVERT: M 11 LYS cc_start: 0.8487 (mtmt) cc_final: 0.8229 (mtpp) REVERT: O 11 LYS cc_start: 0.8393 (mtmt) cc_final: 0.8138 (mttt) outliers start: 4 outliers final: 2 residues processed: 130 average time/residue: 0.7011 time to fit residues: 96.9672 Evaluate side-chains 121 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 118 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain J residue 20 GLU Chi-restraints excluded: chain L residue 29 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 46 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 33 optimal weight: 0.0870 chunk 14 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 2 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.127877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.104221 restraints weight = 9793.650| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.45 r_work: 0.2800 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.271 10771 Z= 0.114 Angle : 0.709 12.159 15071 Z= 0.257 Chirality : 0.039 0.123 1516 Planarity : 0.004 0.027 1826 Dihedral : 14.198 102.636 1997 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.59 % Allowed : 8.58 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.25), residues: 920 helix: 3.43 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -0.20 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 5 TYR 0.006 0.001 TYR B 46 PHE 0.013 0.001 PHE Q 28 TRP 0.011 0.001 TRP E 40 HIS 0.005 0.001 HIS Q 37 Details of bonding type rmsd covalent geometry : bond 0.00263 (10738) covalent geometry : angle 0.70860 (15071) hydrogen bonds : bond 0.03691 ( 522) hydrogen bonds : angle 3.31370 ( 1461) Misc. bond : bond 0.09628 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.320 Fit side-chains REVERT: S 52 GLU cc_start: 0.6338 (pp20) cc_final: 0.5763 (pp20) REVERT: F 20 GLU cc_start: 0.8034 (tp30) cc_final: 0.7785 (tp30) REVERT: I 43 LYS cc_start: 0.8164 (tttt) cc_final: 0.7796 (mptt) REVERT: I 46 ASN cc_start: 0.8797 (t0) cc_final: 0.8507 (m-40) REVERT: J 20 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7806 (mm-30) REVERT: K 48 LYS cc_start: 0.7549 (tttt) cc_final: 0.7143 (tppt) REVERT: L 20 GLU cc_start: 0.8096 (tp30) cc_final: 0.7855 (tt0) REVERT: L 23 LYS cc_start: 0.8677 (ttmm) cc_final: 0.8195 (mtmm) REVERT: M 5 ARG cc_start: 0.7794 (mtt180) cc_final: 0.7329 (mtp180) REVERT: M 11 LYS cc_start: 0.8483 (mtmt) cc_final: 0.8224 (mtpp) REVERT: N 20 GLU cc_start: 0.8178 (tp30) cc_final: 0.7914 (mm-30) REVERT: O 11 LYS cc_start: 0.8366 (mtmt) cc_final: 0.8114 (mttt) outliers start: 13 outliers final: 4 residues processed: 134 average time/residue: 0.6829 time to fit residues: 97.4171 Evaluate side-chains 127 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain J residue 20 GLU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 29 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 28 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 74 optimal weight: 0.0670 chunk 68 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 50.0000 chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.129171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.102552 restraints weight = 10073.339| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.32 r_work: 0.2905 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.251 10771 Z= 0.111 Angle : 0.695 12.388 15071 Z= 0.251 Chirality : 0.039 0.122 1516 Planarity : 0.004 0.027 1826 Dihedral : 13.810 101.992 1997 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.23 % Allowed : 10.05 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.28 (0.25), residues: 920 helix: 3.45 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -0.12 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 5 TYR 0.006 0.001 TYR B 46 PHE 0.013 0.001 PHE Q 28 TRP 0.011 0.001 TRP E 40 HIS 0.005 0.001 HIS Q 37 Details of bonding type rmsd covalent geometry : bond 0.00258 (10738) covalent geometry : angle 0.69512 (15071) hydrogen bonds : bond 0.03637 ( 522) hydrogen bonds : angle 3.26878 ( 1461) Misc. bond : bond 0.09008 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.345 Fit side-chains REVERT: F 20 GLU cc_start: 0.7924 (tp30) cc_final: 0.7612 (tp30) REVERT: I 43 LYS cc_start: 0.8115 (tttt) cc_final: 0.7692 (mptt) REVERT: I 46 ASN cc_start: 0.8757 (t0) cc_final: 0.8396 (m-40) REVERT: J 20 GLU cc_start: 0.7819 (tp30) cc_final: 0.7561 (mm-30) REVERT: K 48 LYS cc_start: 0.7440 (tttt) cc_final: 0.7055 (tppt) REVERT: L 20 GLU cc_start: 0.7830 (tp30) cc_final: 0.7622 (tt0) REVERT: L 23 LYS cc_start: 0.8498 (ttmm) cc_final: 0.7953 (mttp) REVERT: M 5 ARG cc_start: 0.7616 (mtt180) cc_final: 0.7077 (mtp180) REVERT: M 11 LYS cc_start: 0.8311 (mtmt) cc_final: 0.8039 (mtpp) REVERT: N 20 GLU cc_start: 0.7899 (tp30) cc_final: 0.7603 (mm-30) REVERT: O 11 LYS cc_start: 0.8290 (mtmt) cc_final: 0.7982 (mttt) outliers start: 10 outliers final: 6 residues processed: 130 average time/residue: 0.6901 time to fit residues: 95.5107 Evaluate side-chains 128 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain Q residue 11 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 3 optimal weight: 10.0000 chunk 17 optimal weight: 0.0870 chunk 49 optimal weight: 0.0970 chunk 58 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 20 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 0 optimal weight: 0.1980 chunk 35 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.133269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.107549 restraints weight = 10258.560| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.28 r_work: 0.2959 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.185 10771 Z= 0.092 Angle : 0.649 11.257 15071 Z= 0.232 Chirality : 0.037 0.116 1516 Planarity : 0.004 0.026 1826 Dihedral : 13.369 98.677 1997 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.49 % Allowed : 11.27 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.62 (0.26), residues: 920 helix: 3.70 (0.18), residues: 576 sheet: None (None), residues: 0 loop : 0.04 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 30 TYR 0.008 0.001 TYR S 53 PHE 0.010 0.001 PHE K 28 TRP 0.012 0.001 TRP J 9 HIS 0.004 0.001 HIS K 37 Details of bonding type rmsd covalent geometry : bond 0.00204 (10738) covalent geometry : angle 0.64867 (15071) hydrogen bonds : bond 0.03229 ( 522) hydrogen bonds : angle 3.07124 ( 1461) Misc. bond : bond 0.07318 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 0.387 Fit side-chains REVERT: S 30 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7477 (pp) REVERT: C 5 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7279 (mtp85) REVERT: I 43 LYS cc_start: 0.8102 (tttt) cc_final: 0.7761 (mptt) REVERT: I 46 ASN cc_start: 0.8679 (t0) cc_final: 0.8368 (m-40) REVERT: J 20 GLU cc_start: 0.7835 (tp30) cc_final: 0.7634 (mm-30) REVERT: K 48 LYS cc_start: 0.7381 (tttt) cc_final: 0.7019 (tppt) REVERT: L 23 LYS cc_start: 0.8543 (ttmm) cc_final: 0.8071 (mttp) REVERT: M 5 ARG cc_start: 0.7648 (mtt180) cc_final: 0.7141 (mtp180) REVERT: M 11 LYS cc_start: 0.8305 (mtmt) cc_final: 0.8026 (mtpp) REVERT: N 20 GLU cc_start: 0.7928 (tp30) cc_final: 0.7628 (mm-30) REVERT: O 11 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7943 (mttt) outliers start: 4 outliers final: 1 residues processed: 132 average time/residue: 0.7109 time to fit residues: 99.7019 Evaluate side-chains 125 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain H residue 8 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 3 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.124393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.098017 restraints weight = 10110.463| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.30 r_work: 0.2835 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.356 10771 Z= 0.219 Angle : 0.843 13.798 15071 Z= 0.313 Chirality : 0.046 0.140 1516 Planarity : 0.005 0.029 1826 Dihedral : 14.608 108.984 1997 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.35 % Allowed : 11.03 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.25), residues: 920 helix: 3.05 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.25 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 5 TYR 0.012 0.002 TYR J 46 PHE 0.015 0.002 PHE K 28 TRP 0.011 0.002 TRP Q 7 HIS 0.007 0.002 HIS O 37 Details of bonding type rmsd covalent geometry : bond 0.00555 (10738) covalent geometry : angle 0.84324 (15071) hydrogen bonds : bond 0.04609 ( 522) hydrogen bonds : angle 3.67469 ( 1461) Misc. bond : bond 0.11090 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.471 Fit side-chains REVERT: C 5 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7686 (mtt90) REVERT: C 11 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8244 (mttt) REVERT: I 43 LYS cc_start: 0.8088 (tttt) cc_final: 0.7728 (mptt) REVERT: I 46 ASN cc_start: 0.8795 (t0) cc_final: 0.8424 (m-40) REVERT: J 20 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7682 (mm-30) REVERT: K 48 LYS cc_start: 0.7647 (tttt) cc_final: 0.7214 (tppt) REVERT: L 23 LYS cc_start: 0.8569 (ttmm) cc_final: 0.8170 (mttp) REVERT: M 5 ARG cc_start: 0.7659 (mtt180) cc_final: 0.7099 (mtp180) REVERT: M 11 LYS cc_start: 0.8338 (mtmt) cc_final: 0.8078 (mtpp) REVERT: O 11 LYS cc_start: 0.8307 (mtmt) cc_final: 0.8009 (mttt) outliers start: 11 outliers final: 7 residues processed: 132 average time/residue: 0.7027 time to fit residues: 98.6351 Evaluate side-chains 132 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain J residue 20 GLU Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 14 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 74 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 15 optimal weight: 0.0270 chunk 54 optimal weight: 6.9990 chunk 16 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 0.0770 chunk 9 optimal weight: 3.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 HIS ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.130126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.104132 restraints weight = 10217.755| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.31 r_work: 0.2942 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.207 10771 Z= 0.102 Angle : 0.686 13.404 15071 Z= 0.246 Chirality : 0.038 0.120 1516 Planarity : 0.004 0.029 1826 Dihedral : 13.733 100.370 1997 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.61 % Allowed : 12.01 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.29 (0.26), residues: 920 helix: 3.44 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -0.09 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 30 TYR 0.009 0.001 TYR S 53 PHE 0.010 0.001 PHE K 28 TRP 0.011 0.001 TRP E 40 HIS 0.004 0.001 HIS Q 37 Details of bonding type rmsd covalent geometry : bond 0.00230 (10738) covalent geometry : angle 0.68633 (15071) hydrogen bonds : bond 0.03490 ( 522) hydrogen bonds : angle 3.25943 ( 1461) Misc. bond : bond 0.08536 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.339 Fit side-chains REVERT: C 5 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7208 (mtp85) REVERT: I 5 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8030 (mtm180) REVERT: I 43 LYS cc_start: 0.8125 (tttt) cc_final: 0.7697 (mptt) REVERT: I 46 ASN cc_start: 0.8703 (t0) cc_final: 0.8345 (m-40) REVERT: J 20 GLU cc_start: 0.7793 (tp30) cc_final: 0.7521 (mm-30) REVERT: J 23 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8229 (mttt) REVERT: K 48 LYS cc_start: 0.7480 (tttt) cc_final: 0.7082 (tppt) REVERT: L 23 LYS cc_start: 0.8508 (ttmm) cc_final: 0.8036 (mttp) REVERT: M 5 ARG cc_start: 0.7605 (mtt180) cc_final: 0.7059 (mtp180) REVERT: M 11 LYS cc_start: 0.8289 (mtmt) cc_final: 0.7999 (mtpp) REVERT: N 20 GLU cc_start: 0.7901 (tp30) cc_final: 0.7580 (mm-30) REVERT: O 11 LYS cc_start: 0.8287 (mtmt) cc_final: 0.7976 (mttt) outliers start: 5 outliers final: 3 residues processed: 127 average time/residue: 0.7259 time to fit residues: 97.8376 Evaluate side-chains 128 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain L residue 11 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 18 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 57 optimal weight: 0.0970 chunk 25 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 37 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.130865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.104985 restraints weight = 10086.372| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.29 r_work: 0.2943 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.214 10771 Z= 0.106 Angle : 0.684 12.691 15071 Z= 0.247 Chirality : 0.038 0.118 1516 Planarity : 0.004 0.031 1826 Dihedral : 13.463 101.088 1997 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.49 % Allowed : 12.13 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.39 (0.26), residues: 920 helix: 3.51 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -0.02 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 30 TYR 0.009 0.001 TYR S 53 PHE 0.011 0.001 PHE K 28 TRP 0.012 0.001 TRP J 9 HIS 0.004 0.001 HIS Q 37 Details of bonding type rmsd covalent geometry : bond 0.00242 (10738) covalent geometry : angle 0.68372 (15071) hydrogen bonds : bond 0.03509 ( 522) hydrogen bonds : angle 3.21761 ( 1461) Misc. bond : bond 0.08357 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 0.327 Fit side-chains REVERT: C 5 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7654 (mtt90) REVERT: I 43 LYS cc_start: 0.8107 (tttt) cc_final: 0.7696 (mptt) REVERT: I 46 ASN cc_start: 0.8717 (t0) cc_final: 0.8336 (m-40) REVERT: J 20 GLU cc_start: 0.7807 (tp30) cc_final: 0.7535 (mm-30) REVERT: K 48 LYS cc_start: 0.7408 (tttt) cc_final: 0.7028 (tppt) REVERT: L 23 LYS cc_start: 0.8519 (ttmm) cc_final: 0.8056 (mttp) REVERT: M 5 ARG cc_start: 0.7600 (mtt180) cc_final: 0.7062 (mtp180) REVERT: M 11 LYS cc_start: 0.8302 (mtmt) cc_final: 0.7996 (mtpp) REVERT: N 20 GLU cc_start: 0.7899 (tp30) cc_final: 0.7573 (mm-30) REVERT: O 11 LYS cc_start: 0.8276 (mtmt) cc_final: 0.7955 (mttt) outliers start: 4 outliers final: 3 residues processed: 129 average time/residue: 0.6949 time to fit residues: 95.3555 Evaluate side-chains 125 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 29 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 70 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 42 optimal weight: 0.3980 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.124555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.098128 restraints weight = 9955.116| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.29 r_work: 0.2821 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.354 10771 Z= 0.210 Angle : 0.842 13.885 15071 Z= 0.310 Chirality : 0.045 0.134 1516 Planarity : 0.004 0.031 1826 Dihedral : 14.553 108.916 1997 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.61 % Allowed : 12.62 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.25), residues: 920 helix: 2.95 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.25 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 30 TYR 0.010 0.001 TYR S 37 PHE 0.014 0.002 PHE K 28 TRP 0.010 0.002 TRP B 49 HIS 0.007 0.002 HIS B 24 Details of bonding type rmsd covalent geometry : bond 0.00533 (10738) covalent geometry : angle 0.84160 (15071) hydrogen bonds : bond 0.04557 ( 522) hydrogen bonds : angle 3.65178 ( 1461) Misc. bond : bond 0.11112 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 0.295 Fit side-chains REVERT: C 5 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7682 (mtt90) REVERT: C 11 LYS cc_start: 0.8767 (mtmt) cc_final: 0.8271 (mttt) REVERT: I 43 LYS cc_start: 0.8114 (tttt) cc_final: 0.7725 (mptt) REVERT: I 46 ASN cc_start: 0.8780 (t0) cc_final: 0.8409 (m-40) REVERT: J 20 GLU cc_start: 0.7917 (tp30) cc_final: 0.7599 (mm-30) REVERT: K 48 LYS cc_start: 0.7622 (tttt) cc_final: 0.7218 (tppt) REVERT: L 23 LYS cc_start: 0.8542 (ttmm) cc_final: 0.8172 (mttp) REVERT: M 5 ARG cc_start: 0.7702 (mtt180) cc_final: 0.7110 (mtp180) REVERT: M 11 LYS cc_start: 0.8322 (mtmt) cc_final: 0.8056 (mtpp) REVERT: N 20 GLU cc_start: 0.7978 (tp30) cc_final: 0.7642 (mm-30) REVERT: O 11 LYS cc_start: 0.8311 (mtmt) cc_final: 0.8019 (mttt) outliers start: 5 outliers final: 4 residues processed: 126 average time/residue: 0.6790 time to fit residues: 90.9870 Evaluate side-chains 124 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 29 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 0 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.127975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.102032 restraints weight = 10166.203| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.30 r_work: 0.2899 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.259 10771 Z= 0.119 Angle : 0.724 14.021 15071 Z= 0.261 Chirality : 0.039 0.123 1516 Planarity : 0.004 0.030 1826 Dihedral : 13.890 103.247 1997 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.61 % Allowed : 12.50 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.05 (0.26), residues: 920 helix: 3.23 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -0.16 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 30 TYR 0.009 0.001 TYR S 53 PHE 0.012 0.001 PHE K 28 TRP 0.010 0.001 TRP E 40 HIS 0.004 0.001 HIS Q 37 Details of bonding type rmsd covalent geometry : bond 0.00279 (10738) covalent geometry : angle 0.72406 (15071) hydrogen bonds : bond 0.03787 ( 522) hydrogen bonds : angle 3.36412 ( 1461) Misc. bond : bond 0.09392 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3629.01 seconds wall clock time: 62 minutes 34.52 seconds (3754.52 seconds total)