Starting phenix.real_space_refine on Mon Jul 28 11:13:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ze3_14682/07_2025/7ze3_14682.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ze3_14682/07_2025/7ze3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ze3_14682/07_2025/7ze3_14682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ze3_14682/07_2025/7ze3_14682.map" model { file = "/net/cci-nas-00/data/ceres_data/7ze3_14682/07_2025/7ze3_14682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ze3_14682/07_2025/7ze3_14682.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.01, per 1000 atoms: 0.68 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: 3.47 Conformation dependent library (CDL) restraints added in 911.9 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: 0.78 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: 2.40 Time building geometry restraints manager: 3.91 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 48 or resid 101 through 102)) selection = (chain 'C' and (resid 1 through 48 or resid 101 through 102)) selection = (chain 'E' and (resid 1 through 48 or resid 101 through 102)) selection = (chain 'G' and (resid 1 through 48 or resid 101 through 102)) selection = (chain 'I' and (resid 1 through 48 or resid 101 through 102)) selection = (chain 'K' and (resid 1 through 48 or resid 101 through 102)) selection = (chain 'M' and (resid 1 through 48 or resid 101 through 102)) selection = (chain 'O' and (resid 1 through 48 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' 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: 1.670 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: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.110 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.630 ------------------------------------------------------------------------------- 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 : 3.86 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 (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: 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 TRP 0.025 0.003 TRP Q 7 HIS 0.008 0.001 HIS A 37 PHE 0.012 0.001 PHE C 28 TYR 0.017 0.003 TYR S 40 ARG 0.015 0.003 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.13875 ( 522) hydrogen bonds : angle 5.98177 ( 1461) covalent geometry : bond 0.00738 (10738) covalent geometry : angle 1.01306 (15071) 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 : 0.908 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: 1.4269 time to fit residues: 238.2147 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 : 0.911 ------------------------------------------------------------------------------- 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: 0.9990 chunk 61 optimal weight: 10.0000 chunk 34 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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 ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 HIS N 40 HIS Q 37 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.127080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.102024 restraints weight = 9759.066| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.44 r_work: 0.2826 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.267 10771 Z= 0.150 Angle : 0.767 11.134 15071 Z= 0.285 Chirality : 0.041 0.132 1516 Planarity : 0.005 0.028 1826 Dihedral : 14.638 104.792 1997 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.61 % Allowed : 6.86 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 2.78 (0.26), residues: 920 helix: 3.11 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.45 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 40 HIS 0.007 0.001 HIS O 37 PHE 0.015 0.001 PHE C 28 TYR 0.009 0.001 TYR S 53 ARG 0.001 0.000 ARG N 30 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 522) hydrogen bonds : angle 3.64954 ( 1461) covalent geometry : bond 0.00301 (10738) covalent geometry : angle 0.76701 (15071) Misc. bond : bond 0.10458 ( 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: 5 poor density : 126 time to evaluate : 1.030 Fit side-chains REVERT: C 11 LYS cc_start: 0.8678 (mtmt) cc_final: 0.8298 (mttm) REVERT: F 20 GLU cc_start: 0.7968 (tp30) cc_final: 0.7753 (tp30) REVERT: G 11 LYS cc_start: 0.8359 (mtmt) cc_final: 0.8035 (mttt) REVERT: I 43 LYS cc_start: 0.8051 (tttt) cc_final: 0.7736 (mptt) REVERT: J 20 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7749 (mm-30) REVERT: K 48 LYS cc_start: 0.7601 (tttt) cc_final: 0.7126 (mmtm) REVERT: M 5 ARG cc_start: 0.7750 (mtt180) cc_final: 0.7265 (mtp180) REVERT: M 11 LYS cc_start: 0.8458 (mtmt) cc_final: 0.8253 (mtpp) REVERT: O 11 LYS cc_start: 0.8396 (mtmt) cc_final: 0.8159 (mttt) outliers start: 5 outliers final: 1 residues processed: 127 average time/residue: 1.7942 time to fit residues: 241.5535 Evaluate side-chains 117 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 45 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 0.0670 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 8 optimal weight: 50.0000 chunk 13 optimal weight: 50.0000 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 49 GLN I 2 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.127480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.102491 restraints weight = 9827.158| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.41 r_work: 0.2841 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.269 10771 Z= 0.116 Angle : 0.721 11.831 15071 Z= 0.263 Chirality : 0.039 0.126 1516 Planarity : 0.004 0.028 1826 Dihedral : 14.604 103.194 1997 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.49 % Allowed : 8.21 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 3.14 (0.26), residues: 920 helix: 3.36 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.23 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 40 HIS 0.006 0.001 HIS O 37 PHE 0.012 0.001 PHE G 28 TYR 0.007 0.001 TYR S 53 ARG 0.002 0.000 ARG B 30 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 522) hydrogen bonds : angle 3.39628 ( 1461) covalent geometry : bond 0.00267 (10738) covalent geometry : angle 0.72135 (15071) Misc. bond : bond 0.09910 ( 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 130 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.907 Fit side-chains REVERT: C 11 LYS cc_start: 0.8698 (mtmt) cc_final: 0.8293 (mttm) REVERT: F 20 GLU cc_start: 0.7954 (tp30) cc_final: 0.7718 (tp30) REVERT: I 43 LYS cc_start: 0.8102 (tttt) cc_final: 0.7765 (mptt) REVERT: J 20 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7745 (mm-30) REVERT: K 48 LYS cc_start: 0.7606 (tttt) cc_final: 0.7199 (tppt) REVERT: L 23 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8183 (mtmm) REVERT: M 5 ARG cc_start: 0.7711 (mtt180) cc_final: 0.7248 (mtp180) REVERT: M 11 LYS cc_start: 0.8438 (mtmt) cc_final: 0.8186 (mtpp) REVERT: O 11 LYS cc_start: 0.8372 (mtmt) cc_final: 0.8128 (mttt) outliers start: 4 outliers final: 1 residues processed: 128 average time/residue: 1.5711 time to fit residues: 213.5684 Evaluate side-chains 119 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 68 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.122065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.098232 restraints weight = 9769.710| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.44 r_work: 0.2715 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.378 10771 Z= 0.220 Angle : 0.869 14.118 15071 Z= 0.319 Chirality : 0.046 0.153 1516 Planarity : 0.005 0.030 1826 Dihedral : 14.917 110.659 1997 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.84 % Allowed : 7.97 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 2.50 (0.25), residues: 920 helix: 2.71 (0.19), residues: 585 sheet: None (None), residues: 0 loop : -0.28 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Q 7 HIS 0.007 0.002 HIS O 37 PHE 0.016 0.002 PHE G 28 TYR 0.011 0.001 TYR J 46 ARG 0.006 0.000 ARG K 5 Details of bonding type rmsd hydrogen bonds : bond 0.04784 ( 522) hydrogen bonds : angle 3.75704 ( 1461) covalent geometry : bond 0.00565 (10738) covalent geometry : angle 0.86875 (15071) Misc. bond : bond 0.11724 ( 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 134 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.014 Fit side-chains REVERT: C 11 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8307 (mttm) REVERT: I 43 LYS cc_start: 0.8142 (tttt) cc_final: 0.7825 (mptt) REVERT: J 20 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7887 (mm-30) REVERT: K 48 LYS cc_start: 0.7732 (tttt) cc_final: 0.7280 (tppt) REVERT: L 23 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8335 (mttp) REVERT: M 5 ARG cc_start: 0.7829 (mtt180) cc_final: 0.7323 (mtp180) REVERT: M 11 LYS cc_start: 0.8510 (mtmt) cc_final: 0.8268 (mtpp) REVERT: O 11 LYS cc_start: 0.8378 (mtmt) cc_final: 0.8133 (mttt) outliers start: 15 outliers final: 5 residues processed: 124 average time/residue: 1.4215 time to fit residues: 187.8879 Evaluate side-chains 125 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 J residue 20 GLU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 14 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.124238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.100208 restraints weight = 9800.747| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.46 r_work: 0.2747 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.334 10771 Z= 0.145 Angle : 0.774 14.080 15071 Z= 0.279 Chirality : 0.041 0.129 1516 Planarity : 0.005 0.031 1826 Dihedral : 14.357 105.549 1997 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.59 % Allowed : 8.21 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 2.73 (0.25), residues: 920 helix: 3.04 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.41 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 40 HIS 0.005 0.001 HIS O 37 PHE 0.012 0.001 PHE Q 28 TYR 0.007 0.001 TYR R 46 ARG 0.002 0.000 ARG K 5 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 522) hydrogen bonds : angle 3.54718 ( 1461) covalent geometry : bond 0.00358 (10738) covalent geometry : angle 0.77379 (15071) Misc. bond : bond 0.11069 ( 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 138 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.924 Fit side-chains REVERT: S 52 GLU cc_start: 0.6198 (pp20) cc_final: 0.5435 (pp20) REVERT: C 5 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7776 (mtt90) REVERT: C 11 LYS cc_start: 0.8744 (mtmt) cc_final: 0.8328 (mttm) REVERT: I 43 LYS cc_start: 0.8139 (tttt) cc_final: 0.7805 (mptt) REVERT: I 46 ASN cc_start: 0.8844 (t0) cc_final: 0.8496 (m-40) REVERT: J 20 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7792 (mm-30) REVERT: K 48 LYS cc_start: 0.7679 (tttt) cc_final: 0.7223 (tppt) REVERT: L 23 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8271 (mttm) REVERT: M 5 ARG cc_start: 0.7780 (mtt180) cc_final: 0.7294 (mtp180) REVERT: M 11 LYS cc_start: 0.8469 (mtmt) cc_final: 0.8225 (mtpp) REVERT: O 11 LYS cc_start: 0.8393 (mtmt) cc_final: 0.8139 (mttt) outliers start: 13 outliers final: 4 residues processed: 132 average time/residue: 1.3706 time to fit residues: 192.8923 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 : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 29 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.125106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.100823 restraints weight = 9758.758| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.48 r_work: 0.2754 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.297 10771 Z= 0.131 Angle : 0.746 13.937 15071 Z= 0.268 Chirality : 0.040 0.125 1516 Planarity : 0.004 0.032 1826 Dihedral : 14.043 104.238 1997 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.35 % Allowed : 9.56 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 2.89 (0.26), residues: 920 helix: 3.16 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.34 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 40 HIS 0.005 0.001 HIS O 37 PHE 0.012 0.001 PHE Q 28 TYR 0.006 0.001 TYR B 46 ARG 0.001 0.000 ARG B 30 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 522) hydrogen bonds : angle 3.45078 ( 1461) covalent geometry : bond 0.00319 (10738) covalent geometry : angle 0.74588 (15071) Misc. bond : bond 0.10268 ( 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 133 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 1.198 Fit side-chains REVERT: S 30 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7554 (pp) REVERT: C 5 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7758 (mtt90) REVERT: C 11 LYS cc_start: 0.8732 (mtmt) cc_final: 0.8305 (mttm) REVERT: I 43 LYS cc_start: 0.8172 (tttt) cc_final: 0.7779 (mptt) REVERT: I 46 ASN cc_start: 0.8823 (t0) cc_final: 0.8456 (m-40) REVERT: J 20 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7798 (mm-30) REVERT: K 48 LYS cc_start: 0.7627 (tttt) cc_final: 0.7166 (tppt) REVERT: L 23 LYS cc_start: 0.8688 (ttmm) cc_final: 0.8281 (mttp) REVERT: M 5 ARG cc_start: 0.7810 (mtt180) cc_final: 0.7298 (mtp180) REVERT: M 11 LYS cc_start: 0.8446 (mtmt) cc_final: 0.8180 (mtpp) REVERT: O 11 LYS cc_start: 0.8371 (mtmt) cc_final: 0.8108 (mttt) outliers start: 11 outliers final: 5 residues processed: 127 average time/residue: 1.7477 time to fit residues: 238.0783 Evaluate side-chains 129 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 ILE 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 29 SER Chi-restraints excluded: chain M residue 14 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.126602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.102432 restraints weight = 9791.011| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.48 r_work: 0.2776 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.273 10771 Z= 0.118 Angle : 0.717 13.646 15071 Z= 0.258 Chirality : 0.039 0.123 1516 Planarity : 0.004 0.029 1826 Dihedral : 13.861 102.631 1997 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.47 % Allowed : 9.80 % 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 (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: 3.04 (0.25), residues: 920 helix: 3.28 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -0.27 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 40 HIS 0.004 0.001 HIS C 37 PHE 0.012 0.001 PHE K 28 TYR 0.006 0.001 TYR B 46 ARG 0.001 0.000 ARG B 30 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 522) hydrogen bonds : angle 3.36235 ( 1461) covalent geometry : bond 0.00279 (10738) covalent geometry : angle 0.71723 (15071) Misc. bond : bond 0.09639 ( 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 137 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 1.053 Fit side-chains REVERT: S 30 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7600 (pp) REVERT: S 52 GLU cc_start: 0.6198 (pp20) cc_final: 0.5431 (pp20) REVERT: C 5 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7763 (mtt90) REVERT: I 43 LYS cc_start: 0.8199 (tttt) cc_final: 0.7789 (mptt) REVERT: I 46 ASN cc_start: 0.8792 (t0) cc_final: 0.8461 (m-40) REVERT: J 13 LEU cc_start: 0.7834 (mt) cc_final: 0.7580 (mt) REVERT: J 20 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7820 (mm-30) REVERT: K 48 LYS cc_start: 0.7551 (tttt) cc_final: 0.7117 (tppt) REVERT: L 23 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8298 (mttp) REVERT: M 5 ARG cc_start: 0.7805 (mtt180) cc_final: 0.7306 (mtp180) REVERT: M 11 LYS cc_start: 0.8437 (mtmt) cc_final: 0.8194 (mtpp) REVERT: O 11 LYS cc_start: 0.8354 (mtmt) cc_final: 0.8081 (mttt) outliers start: 12 outliers final: 6 residues processed: 129 average time/residue: 1.4468 time to fit residues: 199.2696 Evaluate side-chains 131 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 ILE 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 14 VAL Chi-restraints excluded: chain J residue 20 GLU 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 41 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.128954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.102863 restraints weight = 10171.266| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.30 r_work: 0.2898 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.264 10771 Z= 0.116 Angle : 0.710 13.451 15071 Z= 0.256 Chirality : 0.039 0.122 1516 Planarity : 0.004 0.029 1826 Dihedral : 13.809 102.415 1997 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.35 % Allowed : 10.78 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 3.11 (0.25), residues: 920 helix: 3.32 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -0.22 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 40 HIS 0.004 0.001 HIS G 37 PHE 0.012 0.001 PHE K 28 TYR 0.006 0.001 TYR S 53 ARG 0.001 0.000 ARG I 5 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 522) hydrogen bonds : angle 3.37753 ( 1461) covalent geometry : bond 0.00274 (10738) covalent geometry : angle 0.71037 (15071) Misc. bond : bond 0.09292 ( 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 134 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.798 Fit side-chains REVERT: S 30 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7499 (pp) REVERT: S 52 GLU cc_start: 0.6156 (pp20) cc_final: 0.5390 (pp20) REVERT: C 5 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7653 (mtt90) REVERT: I 43 LYS cc_start: 0.8125 (tttt) cc_final: 0.7724 (mptt) REVERT: I 46 ASN cc_start: 0.8733 (t0) cc_final: 0.8342 (m-40) REVERT: J 13 LEU cc_start: 0.7756 (mt) cc_final: 0.7525 (mt) REVERT: J 20 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7540 (mm-30) REVERT: K 48 LYS cc_start: 0.7455 (tttt) cc_final: 0.7034 (tppt) REVERT: L 23 LYS cc_start: 0.8547 (ttmm) cc_final: 0.8040 (mttp) REVERT: M 5 ARG cc_start: 0.7663 (mtt180) cc_final: 0.7108 (mtp180) REVERT: M 11 LYS cc_start: 0.8307 (mtmt) cc_final: 0.8040 (mtpp) REVERT: O 11 LYS cc_start: 0.8310 (mtmt) cc_final: 0.7993 (mttt) outliers start: 11 outliers final: 7 residues processed: 126 average time/residue: 2.1268 time to fit residues: 285.2528 Evaluate side-chains 132 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 ILE 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 14 VAL Chi-restraints excluded: chain J residue 20 GLU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain Q residue 11 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.0770 chunk 67 optimal weight: 0.7980 chunk 70 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.129987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.104058 restraints weight = 10143.307| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.30 r_work: 0.2927 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.243 10771 Z= 0.108 Angle : 0.691 13.181 15071 Z= 0.248 Chirality : 0.038 0.120 1516 Planarity : 0.004 0.029 1826 Dihedral : 13.628 101.300 1997 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.10 % Allowed : 10.78 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 3.24 (0.25), residues: 920 helix: 3.41 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -0.15 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 40 HIS 0.004 0.001 HIS C 37 PHE 0.011 0.001 PHE K 28 TYR 0.006 0.001 TYR S 53 ARG 0.001 0.000 ARG G 5 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 522) hydrogen bonds : angle 3.29530 ( 1461) covalent geometry : bond 0.00252 (10738) covalent geometry : angle 0.69136 (15071) Misc. bond : bond 0.08680 ( 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 133 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.956 Fit side-chains REVERT: S 30 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7495 (pp) REVERT: S 52 GLU cc_start: 0.6143 (pp20) cc_final: 0.5410 (pp20) REVERT: C 5 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7643 (mtt90) REVERT: E 43 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7832 (ttmt) REVERT: I 43 LYS cc_start: 0.8147 (tttt) cc_final: 0.7741 (mptt) REVERT: I 46 ASN cc_start: 0.8712 (t0) cc_final: 0.8331 (m-40) REVERT: J 13 LEU cc_start: 0.7660 (mt) cc_final: 0.7454 (mt) REVERT: J 20 GLU cc_start: 0.7792 (tp30) cc_final: 0.7506 (mm-30) REVERT: K 48 LYS cc_start: 0.7430 (tttt) cc_final: 0.7011 (tppt) REVERT: L 23 LYS cc_start: 0.8558 (ttmm) cc_final: 0.8069 (mttp) REVERT: M 5 ARG cc_start: 0.7650 (mtt180) cc_final: 0.7103 (mtp180) REVERT: M 11 LYS cc_start: 0.8293 (mtmt) cc_final: 0.8024 (mtpp) REVERT: N 20 GLU cc_start: 0.7947 (tp30) cc_final: 0.7645 (mm-30) REVERT: O 11 LYS cc_start: 0.8294 (mtmt) cc_final: 0.7966 (mttt) outliers start: 9 outliers final: 6 residues processed: 127 average time/residue: 1.4073 time to fit residues: 190.5756 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 : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain Q residue 11 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 4 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 0.0020 chunk 49 optimal weight: 0.0770 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.0152 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.128728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.102643 restraints weight = 10128.835| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.30 r_work: 0.2890 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.277 10771 Z= 0.124 Angle : 0.716 13.278 15071 Z= 0.259 Chirality : 0.039 0.122 1516 Planarity : 0.004 0.029 1826 Dihedral : 13.814 103.025 1997 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.35 % Allowed : 10.66 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 3.14 (0.25), residues: 920 helix: 3.32 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -0.16 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 40 HIS 0.004 0.001 HIS C 37 PHE 0.012 0.001 PHE K 28 TYR 0.007 0.001 TYR B 46 ARG 0.001 0.000 ARG K 5 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 522) hydrogen bonds : angle 3.38236 ( 1461) covalent geometry : bond 0.00298 (10738) covalent geometry : angle 0.71649 (15071) Misc. bond : bond 0.09314 ( 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 133 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 1.005 Fit side-chains REVERT: S 30 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7476 (pp) REVERT: C 5 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7635 (mtt90) REVERT: I 43 LYS cc_start: 0.8112 (tttt) cc_final: 0.7694 (mptt) REVERT: I 46 ASN cc_start: 0.8723 (t0) cc_final: 0.8315 (m-40) REVERT: J 13 LEU cc_start: 0.7661 (mt) cc_final: 0.7455 (mt) REVERT: J 20 GLU cc_start: 0.7820 (tp30) cc_final: 0.7521 (mm-30) REVERT: K 48 LYS cc_start: 0.7436 (tttt) cc_final: 0.7027 (tppt) REVERT: L 23 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8129 (mttp) REVERT: M 5 ARG cc_start: 0.7674 (mtt180) cc_final: 0.7090 (mtp180) REVERT: M 11 LYS cc_start: 0.8299 (mtmt) cc_final: 0.8027 (mtpp) REVERT: N 20 GLU cc_start: 0.7941 (tp30) cc_final: 0.7630 (mm-30) REVERT: O 11 LYS cc_start: 0.8305 (mtmt) cc_final: 0.7980 (mttt) outliers start: 11 outliers final: 7 residues processed: 127 average time/residue: 1.4015 time to fit residues: 190.0786 Evaluate side-chains 131 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 ILE 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 H residue 47 SER Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 14 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.129175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.103178 restraints weight = 10079.690| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.29 r_work: 0.2905 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.264 10771 Z= 0.115 Angle : 0.704 13.331 15071 Z= 0.254 Chirality : 0.039 0.121 1516 Planarity : 0.004 0.029 1826 Dihedral : 13.759 102.291 1997 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.47 % Allowed : 10.66 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 3.19 (0.25), residues: 920 helix: 3.36 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -0.12 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 40 HIS 0.004 0.001 HIS C 37 PHE 0.011 0.001 PHE K 28 TYR 0.007 0.001 TYR S 53 ARG 0.001 0.000 ARG G 5 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 522) hydrogen bonds : angle 3.33121 ( 1461) covalent geometry : bond 0.00272 (10738) covalent geometry : angle 0.70418 (15071) Misc. bond : bond 0.09015 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8047.20 seconds wall clock time: 142 minutes 32.78 seconds (8552.78 seconds total)