Starting phenix.real_space_refine on Fri Feb 14 14:28:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ze3_14682/02_2025/7ze3_14682.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ze3_14682/02_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_14682/02_2025/7ze3_14682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ze3_14682/02_2025/7ze3_14682.map" model { file = "/net/cci-nas-00/data/ceres_data/7ze3_14682/02_2025/7ze3_14682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ze3_14682/02_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-5592/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: 7.07, per 1000 atoms: 0.69 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: 3.55 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.83 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: 2.72 Time building geometry restraints manager: 3.84 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.970 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.940 ------------------------------------------------------------------------------- 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 : 0.007 0.186 10738 Z= 0.345 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 *********************** 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 : 0.946 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: 1.4839 time to fit residues: 248.1433 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 : 0.939 ------------------------------------------------------------------------------- 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: 10.0000 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.102630 restraints weight = 9759.812| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.43 r_work: 0.2836 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10738 Z= 0.165 Angle : 0.762 11.162 15071 Z= 0.280 Chirality : 0.041 0.132 1516 Planarity : 0.005 0.029 1826 Dihedral : 14.770 104.837 1997 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.74 % Allowed : 6.74 % 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: 2.86 (0.26), residues: 920 helix: 3.17 (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 0.002 TRP G 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 *********************** 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 133 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 1.019 Fit side-chains REVERT: S 49 GLN cc_start: 0.7573 (tt0) cc_final: 0.7362 (tt0) REVERT: C 11 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8293 (mttm) REVERT: F 20 GLU cc_start: 0.7947 (tp30) cc_final: 0.7717 (tp30) REVERT: G 11 LYS cc_start: 0.8359 (mtmt) cc_final: 0.8022 (mttt) REVERT: I 43 LYS cc_start: 0.8069 (tttt) cc_final: 0.7742 (mptt) REVERT: J 20 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7719 (mm-30) REVERT: K 48 LYS cc_start: 0.7628 (tttt) cc_final: 0.7156 (mmtm) REVERT: L 20 GLU cc_start: 0.7968 (tp30) cc_final: 0.7720 (tt0) REVERT: M 5 ARG cc_start: 0.7746 (mtt180) cc_final: 0.7265 (mtp180) REVERT: M 11 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8242 (mtpp) REVERT: O 11 LYS cc_start: 0.8394 (mtmt) cc_final: 0.8150 (mttt) outliers start: 6 outliers final: 2 residues processed: 128 average time/residue: 1.5362 time to fit residues: 208.9354 Evaluate side-chains 119 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 116 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 GLU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain R residue 8 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3357 r_free = 0.3357 target = 0.123849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100194 restraints weight = 9847.044| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.45 r_work: 0.2742 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10738 Z= 0.238 Angle : 0.815 13.729 15071 Z= 0.300 Chirality : 0.043 0.141 1516 Planarity : 0.005 0.028 1826 Dihedral : 14.957 108.516 1997 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.59 % Allowed : 7.23 % Favored : 91.18 % 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: 2.72 (0.26), residues: 920 helix: 3.03 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.40 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 40 HIS 0.006 0.002 HIS O 37 PHE 0.015 0.002 PHE Q 28 TYR 0.008 0.001 TYR J 46 ARG 0.002 0.000 ARG B 30 *********************** 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: 13 poor density : 119 time to evaluate : 1.007 Fit side-chains REVERT: C 5 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7800 (mtt90) REVERT: C 11 LYS cc_start: 0.8739 (mtmt) cc_final: 0.8324 (mttm) REVERT: E 43 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8210 (mtpt) REVERT: F 20 GLU cc_start: 0.8083 (tp30) cc_final: 0.7835 (tp30) REVERT: I 43 LYS cc_start: 0.8097 (tttt) cc_final: 0.7785 (mptt) REVERT: J 20 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7872 (mm-30) REVERT: K 48 LYS cc_start: 0.7717 (tttt) cc_final: 0.7273 (tppt) REVERT: L 20 GLU cc_start: 0.8153 (tp30) cc_final: 0.7870 (tt0) REVERT: L 23 LYS cc_start: 0.8724 (ttmm) cc_final: 0.8244 (mtmm) REVERT: M 5 ARG cc_start: 0.7790 (mtt180) cc_final: 0.7299 (mtp180) REVERT: M 11 LYS cc_start: 0.8517 (mtmt) cc_final: 0.8274 (mtpp) REVERT: O 11 LYS cc_start: 0.8385 (mtmt) cc_final: 0.8145 (mttt) outliers start: 13 outliers final: 4 residues processed: 125 average time/residue: 1.4903 time to fit residues: 198.2501 Evaluate side-chains 122 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 E residue 43 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3353 r_free = 0.3353 target = 0.123494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.099959 restraints weight = 9749.569| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.43 r_work: 0.2740 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10738 Z= 0.231 Angle : 0.800 14.139 15071 Z= 0.290 Chirality : 0.042 0.133 1516 Planarity : 0.005 0.030 1826 Dihedral : 14.520 107.126 1997 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.72 % Allowed : 7.60 % Favored : 90.69 % 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: 2.66 (0.25), residues: 920 helix: 2.98 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.42 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 40 HIS 0.006 0.001 HIS O 37 PHE 0.013 0.002 PHE Q 28 TYR 0.008 0.001 TYR R 44 ARG 0.002 0.000 ARG K 5 *********************** 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 136 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.977 Fit side-chains REVERT: C 11 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8312 (mttm) REVERT: I 43 LYS cc_start: 0.8120 (tttt) cc_final: 0.7785 (mptt) REVERT: I 46 ASN cc_start: 0.8851 (t0) cc_final: 0.8519 (m-40) REVERT: J 20 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7789 (mm-30) REVERT: K 48 LYS cc_start: 0.7680 (tttt) cc_final: 0.7146 (tptp) REVERT: L 20 GLU cc_start: 0.8163 (tp30) cc_final: 0.7875 (tt0) REVERT: L 23 LYS cc_start: 0.8689 (ttmm) cc_final: 0.8267 (mttp) REVERT: M 5 ARG cc_start: 0.7794 (mtt180) cc_final: 0.7286 (mtp180) REVERT: M 11 LYS cc_start: 0.8481 (mtmt) cc_final: 0.8219 (mtpp) REVERT: O 11 LYS cc_start: 0.8399 (mtmt) cc_final: 0.8152 (mttt) outliers start: 14 outliers final: 5 residues processed: 127 average time/residue: 1.4404 time to fit residues: 194.9457 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 : 0.955 ------------------------------------------------------------------------------- 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 29 SER Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain Q residue 11 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 12 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 = 0.3326 r_free = 0.3326 target = 0.121364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.097358 restraints weight = 9865.108| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.46 r_work: 0.2705 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10738 Z= 0.316 Angle : 0.884 15.201 15071 Z= 0.321 Chirality : 0.046 0.144 1516 Planarity : 0.005 0.032 1826 Dihedral : 14.908 110.656 1997 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.21 % Allowed : 7.97 % 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 (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: 2.32 (0.26), residues: 920 helix: 2.56 (0.19), residues: 585 sheet: None (None), residues: 0 loop : -0.35 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 40 HIS 0.007 0.002 HIS O 37 PHE 0.018 0.002 PHE Q 28 TYR 0.010 0.001 TYR J 46 ARG 0.002 0.000 ARG K 5 *********************** 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 136 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.923 Fit side-chains REVERT: C 5 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7806 (mtt90) REVERT: C 11 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8328 (mttm) REVERT: I 43 LYS cc_start: 0.8156 (tttt) cc_final: 0.7817 (mptt) REVERT: J 20 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7846 (mm-30) REVERT: K 48 LYS cc_start: 0.7726 (tttt) cc_final: 0.7260 (tppt) REVERT: L 20 GLU cc_start: 0.8240 (tp30) cc_final: 0.7953 (tt0) REVERT: L 23 LYS cc_start: 0.8697 (ttmm) cc_final: 0.8392 (mttp) REVERT: M 5 ARG cc_start: 0.7825 (mtt180) cc_final: 0.7315 (mtp180) REVERT: M 11 LYS cc_start: 0.8463 (mtmt) cc_final: 0.8233 (mtpp) REVERT: O 11 LYS cc_start: 0.8399 (mtmt) cc_final: 0.8154 (mttt) outliers start: 18 outliers final: 6 residues processed: 125 average time/residue: 1.5268 time to fit residues: 202.7317 Evaluate side-chains 124 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 11 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.128421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.102489 restraints weight = 10115.689| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.29 r_work: 0.2900 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10738 Z= 0.157 Angle : 0.731 14.259 15071 Z= 0.260 Chirality : 0.039 0.124 1516 Planarity : 0.004 0.030 1826 Dihedral : 14.172 102.098 1997 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.23 % Allowed : 9.19 % Favored : 89.58 % 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: 2.88 (0.26), residues: 920 helix: 3.19 (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 0.010 0.001 PHE K 28 TYR 0.005 0.001 TYR R 46 ARG 0.001 0.000 ARG B 30 *********************** 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 139 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 1.049 Fit side-chains REVERT: S 30 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7536 (pp) REVERT: C 5 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7622 (mtt90) REVERT: I 43 LYS cc_start: 0.8117 (tttt) cc_final: 0.7704 (mptt) REVERT: I 46 ASN cc_start: 0.8716 (t0) cc_final: 0.8343 (m-40) REVERT: J 20 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7493 (mm-30) REVERT: K 48 LYS cc_start: 0.7534 (tttt) cc_final: 0.7111 (tppt) REVERT: L 20 GLU cc_start: 0.7869 (tp30) cc_final: 0.7654 (tt0) REVERT: L 23 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8093 (mttp) REVERT: M 5 ARG cc_start: 0.7653 (mtt180) cc_final: 0.7091 (mtp180) REVERT: M 11 LYS cc_start: 0.8318 (mtmt) cc_final: 0.8047 (mtpp) REVERT: N 20 GLU cc_start: 0.7954 (tp30) cc_final: 0.7628 (mm-30) REVERT: O 11 LYS cc_start: 0.8312 (mtmt) cc_final: 0.8006 (mttt) outliers start: 10 outliers final: 4 residues processed: 133 average time/residue: 1.4325 time to fit residues: 203.4256 Evaluate side-chains 130 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.124849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.100585 restraints weight = 9832.495| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.48 r_work: 0.2755 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10738 Z= 0.186 Angle : 0.749 13.874 15071 Z= 0.269 Chirality : 0.040 0.124 1516 Planarity : 0.004 0.030 1826 Dihedral : 14.242 104.055 1997 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.23 % Allowed : 10.42 % Favored : 88.36 % 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 (0.25), residues: 920 helix: 3.19 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.38 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 40 HIS 0.005 0.001 HIS Q 37 PHE 0.012 0.001 PHE K 28 TYR 0.006 0.001 TYR R 44 ARG 0.001 0.000 ARG B 30 *********************** 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 131 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.942 Fit side-chains REVERT: S 30 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7630 (pp) REVERT: S 52 GLU cc_start: 0.6117 (pp20) cc_final: 0.5331 (pp20) REVERT: C 5 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7748 (mtt90) REVERT: C 11 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8461 (mttm) REVERT: I 43 LYS cc_start: 0.8149 (tttt) cc_final: 0.7776 (mptt) REVERT: I 46 ASN cc_start: 0.8831 (t0) cc_final: 0.8464 (m-40) REVERT: J 20 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7779 (mm-30) REVERT: K 48 LYS cc_start: 0.7585 (tttt) cc_final: 0.7154 (tppt) REVERT: L 20 GLU cc_start: 0.8168 (tp30) cc_final: 0.7872 (tt0) REVERT: L 23 LYS cc_start: 0.8680 (ttmm) cc_final: 0.8280 (mttp) REVERT: M 5 ARG cc_start: 0.7758 (mtt180) cc_final: 0.7252 (mtp180) REVERT: M 11 LYS cc_start: 0.8427 (mtmt) cc_final: 0.8162 (mtpp) REVERT: N 20 GLU cc_start: 0.8247 (tp30) cc_final: 0.7949 (mm-30) REVERT: O 11 LYS cc_start: 0.8348 (mtmt) cc_final: 0.8080 (mttt) outliers start: 10 outliers final: 5 residues processed: 126 average time/residue: 1.4437 time to fit residues: 193.8160 Evaluate side-chains 127 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 H residue 8 VAL Chi-restraints excluded: chain J residue 20 GLU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 11 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 41 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 0.0370 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 overall best weight: 0.9660 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.127606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.101680 restraints weight = 10205.324| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.29 r_work: 0.2890 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10738 Z= 0.167 Angle : 0.726 13.817 15071 Z= 0.260 Chirality : 0.039 0.123 1516 Planarity : 0.004 0.030 1826 Dihedral : 14.114 103.078 1997 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: 3.00 (0.25), residues: 920 helix: 3.26 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -0.33 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 40 HIS 0.005 0.001 HIS Q 37 PHE 0.012 0.001 PHE K 28 TYR 0.006 0.001 TYR R 44 ARG 0.001 0.000 ARG B 30 *********************** 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 135 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.904 Fit side-chains REVERT: S 30 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7527 (pp) REVERT: S 52 GLU cc_start: 0.6129 (pp20) cc_final: 0.5335 (pp20) REVERT: C 5 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7607 (mtt90) REVERT: I 43 LYS cc_start: 0.8102 (tttt) cc_final: 0.7683 (mptt) REVERT: I 46 ASN cc_start: 0.8732 (t0) cc_final: 0.8324 (m-40) REVERT: J 20 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7501 (mm-30) REVERT: K 48 LYS cc_start: 0.7495 (tttt) cc_final: 0.7080 (tppt) REVERT: L 20 GLU cc_start: 0.7868 (tp30) cc_final: 0.7648 (tt0) REVERT: L 23 LYS cc_start: 0.8545 (ttmm) cc_final: 0.8120 (mttp) REVERT: M 5 ARG cc_start: 0.7654 (mtt180) cc_final: 0.7088 (mtp180) REVERT: M 11 LYS cc_start: 0.8295 (mtmt) cc_final: 0.8010 (mtpp) REVERT: N 20 GLU cc_start: 0.7959 (tp30) cc_final: 0.7646 (mm-30) REVERT: O 11 LYS cc_start: 0.8318 (mtmt) cc_final: 0.8003 (mttt) outliers start: 12 outliers final: 7 residues processed: 126 average time/residue: 1.4613 time to fit residues: 195.9256 Evaluate side-chains 133 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 27 ASP Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain P residue 29 SER 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: 1.9990 chunk 34 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 12 optimal weight: 0.0770 chunk 21 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.128242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.102292 restraints weight = 10187.446| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.29 r_work: 0.2894 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10738 Z= 0.162 Angle : 0.717 13.535 15071 Z= 0.257 Chirality : 0.039 0.123 1516 Planarity : 0.004 0.030 1826 Dihedral : 13.979 102.728 1997 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.35 % Allowed : 10.91 % Favored : 87.75 % 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: 3.30 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -0.31 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 40 HIS 0.005 0.001 HIS Q 37 PHE 0.012 0.001 PHE K 28 TYR 0.006 0.001 TYR R 44 ARG 0.001 0.000 ARG K 5 *********************** 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 134 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.796 Fit side-chains REVERT: S 30 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7580 (pp) REVERT: S 52 GLU cc_start: 0.6129 (pp20) cc_final: 0.5351 (pp20) REVERT: C 5 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7621 (mtt90) REVERT: I 43 LYS cc_start: 0.8121 (tttt) cc_final: 0.7723 (mptt) REVERT: I 46 ASN cc_start: 0.8719 (t0) cc_final: 0.8324 (m-40) REVERT: J 20 GLU cc_start: 0.7810 (tp30) cc_final: 0.7538 (mm-30) REVERT: K 48 LYS cc_start: 0.7435 (tttt) cc_final: 0.7054 (tppt) REVERT: L 23 LYS cc_start: 0.8544 (ttmm) cc_final: 0.8136 (mttp) REVERT: M 5 ARG cc_start: 0.7670 (mtt180) cc_final: 0.7110 (mtp180) REVERT: M 11 LYS cc_start: 0.8293 (mtmt) cc_final: 0.8008 (mtpp) REVERT: N 20 GLU cc_start: 0.7968 (tp30) cc_final: 0.7654 (mm-30) REVERT: O 11 LYS cc_start: 0.8303 (mtmt) cc_final: 0.7989 (mttt) outliers start: 11 outliers final: 9 residues processed: 127 average time/residue: 1.4417 time to fit residues: 195.4791 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 : 0.925 ------------------------------------------------------------------------------- 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 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 27 ASP Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain P residue 29 SER 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: 0.0670 chunk 29 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.127603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.101711 restraints weight = 10159.492| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.28 r_work: 0.2888 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10738 Z= 0.168 Angle : 0.720 13.533 15071 Z= 0.259 Chirality : 0.039 0.123 1516 Planarity : 0.004 0.030 1826 Dihedral : 13.985 103.037 1997 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.47 % Allowed : 10.78 % Favored : 87.75 % 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: 3.01 (0.25), residues: 920 helix: 3.27 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -0.31 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 40 HIS 0.005 0.001 HIS Q 37 PHE 0.012 0.001 PHE K 28 TYR 0.006 0.001 TYR R 44 ARG 0.001 0.000 ARG K 5 ********************** 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 134 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.955 Fit side-chains REVERT: S 30 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7569 (pp) REVERT: S 52 GLU cc_start: 0.6082 (pp20) cc_final: 0.5341 (pp20) REVERT: C 5 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7640 (mtt90) REVERT: I 43 LYS cc_start: 0.8126 (tttt) cc_final: 0.7718 (mptt) REVERT: I 46 ASN cc_start: 0.8719 (t0) cc_final: 0.8331 (m-40) REVERT: J 20 GLU cc_start: 0.7832 (tp30) cc_final: 0.7549 (mm-30) REVERT: K 48 LYS cc_start: 0.7446 (tttt) cc_final: 0.7065 (tppt) REVERT: L 23 LYS cc_start: 0.8565 (ttmm) cc_final: 0.8154 (mttp) REVERT: M 5 ARG cc_start: 0.7681 (mtt180) cc_final: 0.7115 (mtp180) REVERT: M 11 LYS cc_start: 0.8289 (mtmt) cc_final: 0.8009 (mtpp) REVERT: N 20 GLU cc_start: 0.7937 (tp30) cc_final: 0.7627 (mm-30) REVERT: O 11 LYS cc_start: 0.8304 (mtmt) cc_final: 0.7986 (mttt) outliers start: 12 outliers final: 10 residues processed: 127 average time/residue: 1.5017 time to fit residues: 202.9927 Evaluate side-chains 134 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 27 ASP Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain P residue 29 SER 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 45 optimal weight: 0.0010 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 61 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.130117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.104050 restraints weight = 10049.593| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.30 r_work: 0.2914 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10738 Z= 0.142 Angle : 0.689 13.211 15071 Z= 0.246 Chirality : 0.038 0.122 1516 Planarity : 0.004 0.030 1826 Dihedral : 13.663 101.017 1997 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.35 % Allowed : 11.27 % 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 (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: 3.20 (0.26), residues: 920 helix: 3.42 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -0.23 (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 Q 37 PHE 0.011 0.001 PHE K 28 TYR 0.006 0.001 TYR S 53 ARG 0.001 0.000 ARG N 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7176.39 seconds wall clock time: 127 minutes 30.75 seconds (7650.75 seconds total)