Starting phenix.real_space_refine on Wed Feb 4 19:53:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9muf_48631/02_2026/9muf_48631.cif Found real_map, /net/cci-nas-00/data/ceres_data/9muf_48631/02_2026/9muf_48631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9muf_48631/02_2026/9muf_48631.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9muf_48631/02_2026/9muf_48631.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9muf_48631/02_2026/9muf_48631.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9muf_48631/02_2026/9muf_48631.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.043 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 8262 2.51 5 N 2088 2.21 5 O 2340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12744 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "B" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "D" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "E" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "F" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "I" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "J" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "K" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "L" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "M" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "N" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "O" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "P" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "Q" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "R" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Time building chain proxies: 3.04, per 1000 atoms: 0.24 Number of scatterers: 12744 At special positions: 0 Unit cell: (88.54, 89.705, 139.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2340 8.00 N 2088 7.00 C 8262 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=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 562.4 milliseconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 0 sheets defined 85.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 removed outlier: 3.749A pdb=" N ILE A 8 " --> pdb=" O LYS A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 36 through 43 removed outlier: 3.809A pdb=" N GLU A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 61 through 72 removed outlier: 3.741A pdb=" N ASP A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 Processing helix chain 'B' and resid 5 through 12 Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 36 through 43 removed outlier: 3.900A pdb=" N GLU B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR B 43 " --> pdb=" O MET B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 61 through 72 removed outlier: 3.748A pdb=" N ASP B 71 " --> pdb=" O LYS B 67 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 72 " --> pdb=" O ILE B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 89 Processing helix chain 'C' and resid 5 through 12 Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 36 through 43 removed outlier: 3.739A pdb=" N GLU C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 61 through 72 removed outlier: 3.787A pdb=" N ASP C 71 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 89 Processing helix chain 'D' and resid 5 through 12 Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 36 through 43 removed outlier: 3.596A pdb=" N GLU D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 56 Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.789A pdb=" N ASP D 71 " --> pdb=" O LYS D 67 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE D 72 " --> pdb=" O ILE D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 89 Processing helix chain 'E' and resid 5 through 12 Processing helix chain 'E' and resid 18 through 29 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 43 removed outlier: 3.604A pdb=" N GLU E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 61 through 72 removed outlier: 3.653A pdb=" N ASP E 71 " --> pdb=" O LYS E 67 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE E 72 " --> pdb=" O ILE E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 89 Processing helix chain 'F' and resid 5 through 12 Processing helix chain 'F' and resid 18 through 29 Processing helix chain 'F' and resid 29 through 34 Processing helix chain 'F' and resid 36 through 43 removed outlier: 3.670A pdb=" N GLU F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 61 through 72 removed outlier: 3.737A pdb=" N ASP F 71 " --> pdb=" O LYS F 67 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE F 72 " --> pdb=" O ILE F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 89 Processing helix chain 'G' and resid 5 through 12 Processing helix chain 'G' and resid 18 through 29 Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 36 through 43 removed outlier: 3.732A pdb=" N GLU G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR G 43 " --> pdb=" O MET G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 56 Processing helix chain 'G' and resid 61 through 72 removed outlier: 3.699A pdb=" N ASP G 71 " --> pdb=" O LYS G 67 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE G 72 " --> pdb=" O ILE G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 89 Processing helix chain 'H' and resid 5 through 12 Processing helix chain 'H' and resid 18 through 29 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 36 through 43 removed outlier: 3.715A pdb=" N GLU H 41 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR H 43 " --> pdb=" O MET H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 56 Processing helix chain 'H' and resid 61 through 72 removed outlier: 3.682A pdb=" N ASP H 71 " --> pdb=" O LYS H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 89 Processing helix chain 'I' and resid 5 through 12 Processing helix chain 'I' and resid 18 through 29 Processing helix chain 'I' and resid 29 through 34 Processing helix chain 'I' and resid 36 through 43 removed outlier: 3.725A pdb=" N GLU I 41 " --> pdb=" O LEU I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 56 Processing helix chain 'I' and resid 61 through 72 removed outlier: 3.752A pdb=" N ASP I 71 " --> pdb=" O LYS I 67 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE I 72 " --> pdb=" O ILE I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 89 Processing helix chain 'J' and resid 5 through 12 Processing helix chain 'J' and resid 18 through 29 Processing helix chain 'J' and resid 29 through 34 Processing helix chain 'J' and resid 36 through 43 removed outlier: 3.677A pdb=" N GLU J 41 " --> pdb=" O LEU J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 56 Processing helix chain 'J' and resid 61 through 72 removed outlier: 3.704A pdb=" N ASP J 71 " --> pdb=" O LYS J 67 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE J 72 " --> pdb=" O ILE J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 89 Processing helix chain 'K' and resid 5 through 12 removed outlier: 3.939A pdb=" N LEU K 11 " --> pdb=" O ASN K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 29 Processing helix chain 'K' and resid 29 through 34 Processing helix chain 'K' and resid 36 through 43 removed outlier: 4.055A pdb=" N GLU K 41 " --> pdb=" O LEU K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 56 Processing helix chain 'K' and resid 61 through 71 removed outlier: 3.790A pdb=" N ASP K 71 " --> pdb=" O LYS K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 74 No H-bonds generated for 'chain 'K' and resid 72 through 74' Processing helix chain 'K' and resid 75 through 89 Processing helix chain 'L' and resid 5 through 12 Processing helix chain 'L' and resid 18 through 29 Processing helix chain 'L' and resid 29 through 34 Processing helix chain 'L' and resid 36 through 43 removed outlier: 4.038A pdb=" N GLU L 41 " --> pdb=" O LEU L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 56 Processing helix chain 'L' and resid 61 through 72 removed outlier: 3.727A pdb=" N ASP L 71 " --> pdb=" O LYS L 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE L 72 " --> pdb=" O ILE L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 89 Processing helix chain 'M' and resid 5 through 11 Processing helix chain 'M' and resid 18 through 29 Processing helix chain 'M' and resid 29 through 34 Processing helix chain 'M' and resid 36 through 43 removed outlier: 3.614A pdb=" N GLU M 41 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 56 Processing helix chain 'M' and resid 61 through 72 removed outlier: 3.747A pdb=" N ASP M 71 " --> pdb=" O LYS M 67 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE M 72 " --> pdb=" O ILE M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 89 Processing helix chain 'N' and resid 5 through 11 Processing helix chain 'N' and resid 18 through 29 Processing helix chain 'N' and resid 29 through 34 Processing helix chain 'N' and resid 36 through 42 removed outlier: 3.881A pdb=" N GLU N 41 " --> pdb=" O LEU N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 56 Processing helix chain 'N' and resid 61 through 71 removed outlier: 3.759A pdb=" N ASP N 71 " --> pdb=" O LYS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 89 Processing helix chain 'O' and resid 5 through 12 Processing helix chain 'O' and resid 18 through 29 Processing helix chain 'O' and resid 29 through 34 Processing helix chain 'O' and resid 36 through 42 removed outlier: 3.933A pdb=" N GLU O 41 " --> pdb=" O LEU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 56 Processing helix chain 'O' and resid 61 through 72 removed outlier: 3.645A pdb=" N ASP O 71 " --> pdb=" O LYS O 67 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE O 72 " --> pdb=" O ILE O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 89 Processing helix chain 'P' and resid 5 through 12 Processing helix chain 'P' and resid 18 through 29 Processing helix chain 'P' and resid 29 through 34 Processing helix chain 'P' and resid 36 through 43 removed outlier: 3.541A pdb=" N GLU P 41 " --> pdb=" O LEU P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 56 Processing helix chain 'P' and resid 61 through 72 removed outlier: 3.807A pdb=" N ASP P 71 " --> pdb=" O LYS P 67 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE P 72 " --> pdb=" O ILE P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 89 Processing helix chain 'Q' and resid 5 through 11 Processing helix chain 'Q' and resid 18 through 29 Processing helix chain 'Q' and resid 29 through 34 Processing helix chain 'Q' and resid 36 through 43 removed outlier: 3.824A pdb=" N GLU Q 41 " --> pdb=" O LEU Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 56 Processing helix chain 'Q' and resid 61 through 72 removed outlier: 3.710A pdb=" N ASP Q 71 " --> pdb=" O LYS Q 67 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE Q 72 " --> pdb=" O ILE Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 89 Processing helix chain 'R' and resid 5 through 12 Processing helix chain 'R' and resid 18 through 29 Processing helix chain 'R' and resid 29 through 34 Processing helix chain 'R' and resid 36 through 43 removed outlier: 3.646A pdb=" N GLU R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 56 Processing helix chain 'R' and resid 61 through 72 removed outlier: 3.619A pdb=" N ASP R 71 " --> pdb=" O LYS R 67 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE R 72 " --> pdb=" O ILE R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 89 766 hydrogen bonds defined for protein. 2298 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3671 1.34 - 1.45: 1265 1.45 - 1.57: 7826 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 12870 Sorted by residual: bond pdb=" CA ILE B 8 " pdb=" C ILE B 8 " ideal model delta sigma weight residual 1.524 1.500 0.025 1.23e-02 6.61e+03 4.00e+00 bond pdb=" C ILE B 8 " pdb=" O ILE B 8 " ideal model delta sigma weight residual 1.237 1.217 0.020 1.12e-02 7.97e+03 3.11e+00 bond pdb=" C ASN B 7 " pdb=" O ASN B 7 " ideal model delta sigma weight residual 1.237 1.217 0.020 1.17e-02 7.31e+03 2.83e+00 bond pdb=" C ILE B 8 " pdb=" N VAL B 9 " ideal model delta sigma weight residual 1.335 1.317 0.018 1.10e-02 8.26e+03 2.73e+00 bond pdb=" CA VAL H 16 " pdb=" C VAL H 16 " ideal model delta sigma weight residual 1.527 1.508 0.019 1.37e-02 5.33e+03 1.90e+00 ... (remaining 12865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 16586 1.16 - 2.33: 417 2.33 - 3.49: 106 3.49 - 4.66: 20 4.66 - 5.82: 7 Bond angle restraints: 17136 Sorted by residual: angle pdb=" N VAL H 16 " pdb=" CA VAL H 16 " pdb=" C VAL H 16 " ideal model delta sigma weight residual 112.35 107.44 4.91 1.41e+00 5.03e-01 1.21e+01 angle pdb=" C ILE B 8 " pdb=" CA ILE B 8 " pdb=" CB ILE B 8 " ideal model delta sigma weight residual 112.02 107.65 4.37 1.31e+00 5.83e-01 1.11e+01 angle pdb=" C ILE K 68 " pdb=" CA ILE K 68 " pdb=" CB ILE K 68 " ideal model delta sigma weight residual 112.02 107.71 4.31 1.31e+00 5.83e-01 1.08e+01 angle pdb=" N VAL B 16 " pdb=" CA VAL B 16 " pdb=" C VAL B 16 " ideal model delta sigma weight residual 112.35 107.78 4.57 1.41e+00 5.03e-01 1.05e+01 angle pdb=" N ASN N 7 " pdb=" CA ASN N 7 " pdb=" C ASN N 7 " ideal model delta sigma weight residual 112.89 109.02 3.87 1.24e+00 6.50e-01 9.76e+00 ... (remaining 17131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7089 18.00 - 36.00: 916 36.00 - 54.00: 125 54.00 - 72.00: 14 72.00 - 90.00: 10 Dihedral angle restraints: 8154 sinusoidal: 3618 harmonic: 4536 Sorted by residual: dihedral pdb=" CB GLU G 42 " pdb=" CG GLU G 42 " pdb=" CD GLU G 42 " pdb=" OE1 GLU G 42 " ideal model delta sinusoidal sigma weight residual 0.00 90.00 -90.00 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU H 42 " pdb=" CG GLU H 42 " pdb=" CD GLU H 42 " pdb=" OE1 GLU H 42 " ideal model delta sinusoidal sigma weight residual 0.00 89.76 -89.76 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU N 42 " pdb=" CG GLU N 42 " pdb=" CD GLU N 42 " pdb=" OE1 GLU N 42 " ideal model delta sinusoidal sigma weight residual 0.00 -89.40 89.40 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 8151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1188 0.030 - 0.059: 568 0.059 - 0.089: 172 0.089 - 0.119: 34 0.119 - 0.148: 18 Chirality restraints: 1980 Sorted by residual: chirality pdb=" CA VAL H 16 " pdb=" N VAL H 16 " pdb=" C VAL H 16 " pdb=" CB VAL H 16 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ILE D 72 " pdb=" N ILE D 72 " pdb=" C ILE D 72 " pdb=" CB ILE D 72 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA VAL B 16 " pdb=" N VAL B 16 " pdb=" C VAL B 16 " pdb=" CB VAL B 16 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 1977 not shown) Planarity restraints: 2106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE N 72 " -0.034 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO N 73 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO N 73 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO N 73 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS K 67 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C LYS K 67 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS K 67 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE K 68 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 14 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C LEU B 14 " 0.023 2.00e-02 2.50e+03 pdb=" O LEU B 14 " -0.009 2.00e-02 2.50e+03 pdb=" N GLU B 15 " -0.008 2.00e-02 2.50e+03 ... (remaining 2103 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2039 2.76 - 3.29: 12849 3.29 - 3.83: 20832 3.83 - 4.36: 26239 4.36 - 4.90: 43896 Nonbonded interactions: 105855 Sorted by model distance: nonbonded pdb=" O SER B 27 " pdb=" NZ LYS O 6 " model vdw 2.221 3.120 nonbonded pdb=" NZ LYS H 6 " pdb=" O SER M 27 " model vdw 2.255 3.120 nonbonded pdb=" NZ LYS L 6 " pdb=" O SER Q 27 " model vdw 2.257 3.120 nonbonded pdb=" NZ LYS I 6 " pdb=" O SER K 27 " model vdw 2.265 3.120 nonbonded pdb=" OD1 ASP D 50 " pdb=" OG SER H 27 " model vdw 2.280 3.040 ... (remaining 105850 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 1.710 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.280 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 : 0.002 0.029 12870 Z= 0.129 Angle : 0.495 5.819 17136 Z= 0.276 Chirality : 0.038 0.148 1980 Planarity : 0.003 0.052 2106 Dihedral : 14.842 89.996 5202 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.22), residues: 1512 helix: 1.59 (0.16), residues: 1134 sheet: None (None), residues: 0 loop : -1.55 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 40 TYR 0.021 0.001 TYR N 43 PHE 0.011 0.001 PHE O 56 HIS 0.002 0.001 HIS H 21 Details of bonding type rmsd covalent geometry : bond 0.00241 (12870) covalent geometry : angle 0.49460 (17136) hydrogen bonds : bond 0.11708 ( 766) hydrogen bonds : angle 6.29553 ( 2298) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: D 32 ASP cc_start: 0.8960 (m-30) cc_final: 0.8750 (m-30) REVERT: D 67 LYS cc_start: 0.8163 (mppt) cc_final: 0.7867 (mppt) REVERT: D 71 ASP cc_start: 0.8824 (m-30) cc_final: 0.8434 (m-30) REVERT: E 51 LEU cc_start: 0.8425 (tp) cc_final: 0.8160 (tp) REVERT: F 32 ASP cc_start: 0.9010 (m-30) cc_final: 0.8636 (m-30) REVERT: H 37 LEU cc_start: 0.9036 (tp) cc_final: 0.8672 (mp) REVERT: I 71 ASP cc_start: 0.8988 (m-30) cc_final: 0.8578 (m-30) REVERT: J 42 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8311 (mm-30) REVERT: K 24 MET cc_start: 0.9063 (ttp) cc_final: 0.8780 (ttm) REVERT: K 40 ARG cc_start: 0.8814 (tpp80) cc_final: 0.8332 (tpp80) REVERT: K 41 GLU cc_start: 0.8555 (pm20) cc_final: 0.8116 (pm20) REVERT: K 88 LYS cc_start: 0.9074 (tmtt) cc_final: 0.8783 (ttmt) REVERT: L 40 ARG cc_start: 0.8541 (tpp80) cc_final: 0.7982 (tpp80) REVERT: L 41 GLU cc_start: 0.8360 (pm20) cc_final: 0.7988 (pm20) REVERT: M 40 ARG cc_start: 0.8883 (ttm110) cc_final: 0.8613 (ttp-110) REVERT: M 71 ASP cc_start: 0.8893 (m-30) cc_final: 0.8617 (m-30) REVERT: Q 38 LYS cc_start: 0.4942 (mmtt) cc_final: 0.4458 (mmtm) REVERT: Q 41 GLU cc_start: 0.8212 (mp0) cc_final: 0.7980 (mp0) REVERT: R 39 MET cc_start: 0.9372 (mtm) cc_final: 0.8965 (mtp) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.1485 time to fit residues: 83.2170 Evaluate side-chains 401 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 47 GLN H 47 GLN K 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.112239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.099460 restraints weight = 18595.347| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.11 r_work: 0.3120 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12870 Z= 0.117 Angle : 0.467 6.951 17136 Z= 0.239 Chirality : 0.038 0.146 1980 Planarity : 0.003 0.043 2106 Dihedral : 3.514 13.549 1638 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.13 % Allowed : 11.60 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.22), residues: 1512 helix: 1.88 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.24 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 40 TYR 0.021 0.001 TYR I 43 PHE 0.009 0.001 PHE C 22 HIS 0.002 0.000 HIS M 21 Details of bonding type rmsd covalent geometry : bond 0.00282 (12870) covalent geometry : angle 0.46690 (17136) hydrogen bonds : bond 0.02435 ( 766) hydrogen bonds : angle 4.99672 ( 2298) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 427 time to evaluate : 0.439 Fit side-chains REVERT: A 37 LEU cc_start: 0.9087 (mp) cc_final: 0.8598 (mp) REVERT: A 41 GLU cc_start: 0.7930 (mp0) cc_final: 0.7387 (mp0) REVERT: C 41 GLU cc_start: 0.7923 (mp0) cc_final: 0.7260 (mp0) REVERT: D 67 LYS cc_start: 0.8461 (mppt) cc_final: 0.8203 (mppt) REVERT: E 51 LEU cc_start: 0.8762 (tp) cc_final: 0.8435 (tp) REVERT: F 32 ASP cc_start: 0.9046 (m-30) cc_final: 0.8753 (m-30) REVERT: G 67 LYS cc_start: 0.8548 (mppt) cc_final: 0.8296 (mppt) REVERT: I 56 PHE cc_start: 0.9023 (m-10) cc_final: 0.8644 (m-10) REVERT: I 71 ASP cc_start: 0.8913 (m-30) cc_final: 0.8661 (m-30) REVERT: K 41 GLU cc_start: 0.8357 (pm20) cc_final: 0.7907 (pm20) REVERT: K 88 LYS cc_start: 0.9118 (tmtt) cc_final: 0.8870 (ttmt) REVERT: M 15 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8697 (mm-30) REVERT: M 40 ARG cc_start: 0.9010 (ttm110) cc_final: 0.8742 (ttp-110) REVERT: M 71 ASP cc_start: 0.8869 (m-30) cc_final: 0.8627 (m-30) REVERT: O 11 LEU cc_start: 0.8894 (mm) cc_final: 0.8645 (mp) REVERT: Q 4 LYS cc_start: 0.7480 (tmtt) cc_final: 0.7213 (tmtt) REVERT: Q 41 GLU cc_start: 0.8257 (mp0) cc_final: 0.7903 (mp0) outliers start: 16 outliers final: 5 residues processed: 429 average time/residue: 0.1420 time to fit residues: 82.1368 Evaluate side-chains 424 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 419 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain Q residue 88 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 43 optimal weight: 0.0070 chunk 49 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 47 GLN I 47 GLN K 7 ASN M 7 ASN M 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.112275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 19)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.099773 restraints weight = 18585.630| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.06 r_work: 0.3132 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 12870 Z= 0.094 Angle : 0.430 4.447 17136 Z= 0.223 Chirality : 0.037 0.143 1980 Planarity : 0.002 0.037 2106 Dihedral : 3.423 13.717 1638 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.20 % Allowed : 14.91 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.22), residues: 1512 helix: 1.86 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -0.45 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 40 TYR 0.013 0.001 TYR I 43 PHE 0.009 0.001 PHE N 22 HIS 0.001 0.000 HIS M 21 Details of bonding type rmsd covalent geometry : bond 0.00226 (12870) covalent geometry : angle 0.42958 (17136) hydrogen bonds : bond 0.02163 ( 766) hydrogen bonds : angle 4.87215 ( 2298) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 429 time to evaluate : 0.433 Fit side-chains REVERT: A 37 LEU cc_start: 0.9104 (mp) cc_final: 0.8865 (mp) REVERT: A 41 GLU cc_start: 0.7953 (mp0) cc_final: 0.7698 (mp0) REVERT: C 41 GLU cc_start: 0.7964 (mp0) cc_final: 0.7262 (mp0) REVERT: D 67 LYS cc_start: 0.8558 (mppt) cc_final: 0.8214 (mppt) REVERT: E 51 LEU cc_start: 0.8732 (tp) cc_final: 0.8387 (tp) REVERT: F 32 ASP cc_start: 0.9023 (m-30) cc_final: 0.8742 (m-30) REVERT: H 52 MET cc_start: 0.8576 (mtt) cc_final: 0.8319 (mtt) REVERT: H 57 ARG cc_start: 0.8266 (ttm110) cc_final: 0.8043 (ttm110) REVERT: H 85 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8062 (mm-30) REVERT: H 88 LYS cc_start: 0.8957 (tmtt) cc_final: 0.8129 (ptmt) REVERT: I 56 PHE cc_start: 0.8985 (m-10) cc_final: 0.8643 (m-10) REVERT: I 67 LYS cc_start: 0.8774 (mppt) cc_final: 0.8449 (mppt) REVERT: I 71 ASP cc_start: 0.8906 (m-30) cc_final: 0.8644 (m-30) REVERT: J 67 LYS cc_start: 0.8540 (mppt) cc_final: 0.8312 (mppt) REVERT: K 41 GLU cc_start: 0.8291 (pm20) cc_final: 0.7923 (pm20) REVERT: M 15 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8660 (mm-30) REVERT: M 40 ARG cc_start: 0.8975 (ttm110) cc_final: 0.8755 (ttp-110) REVERT: M 71 ASP cc_start: 0.8861 (m-30) cc_final: 0.8596 (m-30) REVERT: N 85 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8564 (mm-30) REVERT: O 11 LEU cc_start: 0.8868 (mm) cc_final: 0.8639 (mp) REVERT: Q 4 LYS cc_start: 0.7281 (tmtt) cc_final: 0.6922 (tptp) REVERT: Q 38 LYS cc_start: 0.5304 (mmtt) cc_final: 0.4950 (mmtm) REVERT: Q 41 GLU cc_start: 0.8261 (mp0) cc_final: 0.7778 (mp0) REVERT: R 59 ASP cc_start: 0.8040 (p0) cc_final: 0.7793 (p0) outliers start: 17 outliers final: 10 residues processed: 430 average time/residue: 0.1335 time to fit residues: 77.4616 Evaluate side-chains 429 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 419 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain L residue 24 MET Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain Q residue 88 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 102 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN K 7 ASN M 7 ASN M 47 GLN P 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.098105 restraints weight = 18753.292| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.09 r_work: 0.3102 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12870 Z= 0.114 Angle : 0.430 4.574 17136 Z= 0.223 Chirality : 0.038 0.139 1980 Planarity : 0.002 0.034 2106 Dihedral : 3.423 13.792 1638 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.04 % Allowed : 15.33 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.22), residues: 1512 helix: 1.90 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -0.43 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 40 TYR 0.013 0.001 TYR I 43 PHE 0.007 0.001 PHE N 22 HIS 0.002 0.001 HIS R 21 Details of bonding type rmsd covalent geometry : bond 0.00285 (12870) covalent geometry : angle 0.43016 (17136) hydrogen bonds : bond 0.02095 ( 766) hydrogen bonds : angle 4.78718 ( 2298) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 434 time to evaluate : 0.429 Fit side-chains REVERT: A 37 LEU cc_start: 0.9124 (mp) cc_final: 0.8888 (mp) REVERT: A 41 GLU cc_start: 0.7913 (mp0) cc_final: 0.7639 (mp0) REVERT: A 67 LYS cc_start: 0.8592 (mppt) cc_final: 0.8335 (mppt) REVERT: C 41 GLU cc_start: 0.8002 (mp0) cc_final: 0.7290 (mp0) REVERT: D 67 LYS cc_start: 0.8602 (mppt) cc_final: 0.8220 (mppt) REVERT: D 71 ASP cc_start: 0.8840 (m-30) cc_final: 0.8488 (m-30) REVERT: E 51 LEU cc_start: 0.8803 (tp) cc_final: 0.8452 (tp) REVERT: F 32 ASP cc_start: 0.9025 (m-30) cc_final: 0.8767 (m-30) REVERT: G 67 LYS cc_start: 0.8551 (mppt) cc_final: 0.8259 (mppt) REVERT: H 88 LYS cc_start: 0.8993 (tmtt) cc_final: 0.8272 (ptmt) REVERT: I 56 PHE cc_start: 0.8992 (m-10) cc_final: 0.8686 (m-10) REVERT: I 67 LYS cc_start: 0.8776 (mppt) cc_final: 0.8434 (mppt) REVERT: I 71 ASP cc_start: 0.8932 (m-30) cc_final: 0.8663 (m-30) REVERT: J 42 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8546 (mm-30) REVERT: J 67 LYS cc_start: 0.8542 (mppt) cc_final: 0.8279 (mppt) REVERT: K 41 GLU cc_start: 0.8293 (pm20) cc_final: 0.7965 (pm20) REVERT: K 88 LYS cc_start: 0.9082 (tmtt) cc_final: 0.8784 (ttmt) REVERT: M 40 ARG cc_start: 0.9016 (ttm110) cc_final: 0.8776 (ttp-110) REVERT: M 71 ASP cc_start: 0.8873 (m-30) cc_final: 0.8618 (m-30) REVERT: O 11 LEU cc_start: 0.8933 (mm) cc_final: 0.8714 (mp) REVERT: Q 38 LYS cc_start: 0.5313 (mmtt) cc_final: 0.4783 (mmtt) REVERT: Q 41 GLU cc_start: 0.8325 (mp0) cc_final: 0.7767 (mp0) REVERT: R 59 ASP cc_start: 0.8101 (p0) cc_final: 0.7850 (p0) outliers start: 29 outliers final: 17 residues processed: 439 average time/residue: 0.1414 time to fit residues: 83.5331 Evaluate side-chains 444 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 427 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain L residue 24 MET Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain M residue 4 LYS Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain P residue 4 LYS Chi-restraints excluded: chain Q residue 88 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 111 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 107 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 47 GLN K 7 ASN M 7 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.098308 restraints weight = 18911.685| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.09 r_work: 0.3100 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12870 Z= 0.102 Angle : 0.420 4.571 17136 Z= 0.219 Chirality : 0.037 0.136 1980 Planarity : 0.002 0.032 2106 Dihedral : 3.369 13.293 1638 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.18 % Allowed : 16.67 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.22), residues: 1512 helix: 2.05 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.12 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 40 TYR 0.015 0.001 TYR N 43 PHE 0.007 0.001 PHE E 56 HIS 0.001 0.001 HIS R 21 Details of bonding type rmsd covalent geometry : bond 0.00251 (12870) covalent geometry : angle 0.42045 (17136) hydrogen bonds : bond 0.02028 ( 766) hydrogen bonds : angle 4.74422 ( 2298) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 439 time to evaluate : 0.532 Fit side-chains REVERT: A 37 LEU cc_start: 0.9115 (mp) cc_final: 0.8878 (mp) REVERT: A 41 GLU cc_start: 0.7975 (mp0) cc_final: 0.7668 (mp0) REVERT: A 67 LYS cc_start: 0.8617 (mppt) cc_final: 0.8361 (mppt) REVERT: B 47 GLN cc_start: 0.9192 (mt0) cc_final: 0.8790 (mt0) REVERT: C 41 GLU cc_start: 0.8047 (mp0) cc_final: 0.7307 (mp0) REVERT: C 85 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8567 (mm-30) REVERT: D 67 LYS cc_start: 0.8606 (mppt) cc_final: 0.8203 (mppt) REVERT: D 71 ASP cc_start: 0.8819 (m-30) cc_final: 0.8455 (m-30) REVERT: E 51 LEU cc_start: 0.8800 (tp) cc_final: 0.8446 (tp) REVERT: F 23 ARG cc_start: 0.8945 (mtp85) cc_final: 0.8641 (mtp180) REVERT: F 32 ASP cc_start: 0.9022 (m-30) cc_final: 0.8765 (m-30) REVERT: G 57 ARG cc_start: 0.8202 (mtm-85) cc_final: 0.7957 (tpp80) REVERT: H 88 LYS cc_start: 0.8986 (tmtt) cc_final: 0.8292 (ptmt) REVERT: I 56 PHE cc_start: 0.8977 (m-10) cc_final: 0.8670 (m-10) REVERT: I 67 LYS cc_start: 0.8782 (mppt) cc_final: 0.8426 (mppt) REVERT: I 71 ASP cc_start: 0.8900 (m-30) cc_final: 0.8632 (m-30) REVERT: J 42 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8544 (mm-30) REVERT: K 41 GLU cc_start: 0.8322 (pm20) cc_final: 0.8025 (pm20) REVERT: K 88 LYS cc_start: 0.9114 (tmtt) cc_final: 0.8820 (ttmt) REVERT: M 40 ARG cc_start: 0.9043 (ttm110) cc_final: 0.8756 (ttp-110) REVERT: M 71 ASP cc_start: 0.8822 (m-30) cc_final: 0.8539 (m-30) REVERT: N 11 LEU cc_start: 0.8944 (mm) cc_final: 0.8711 (mt) REVERT: N 24 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8867 (ttm) REVERT: O 11 LEU cc_start: 0.8947 (mm) cc_final: 0.8716 (mp) REVERT: Q 38 LYS cc_start: 0.5217 (mmtt) cc_final: 0.4748 (mmtm) REVERT: Q 41 GLU cc_start: 0.8405 (mp0) cc_final: 0.7813 (mp0) REVERT: R 59 ASP cc_start: 0.8102 (p0) cc_final: 0.7813 (p0) outliers start: 31 outliers final: 16 residues processed: 446 average time/residue: 0.1376 time to fit residues: 83.3628 Evaluate side-chains 451 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 434 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain F residue 4 LYS Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain L residue 24 MET Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain Q residue 88 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 52 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 0.0470 chunk 136 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 0.0970 chunk 123 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 7 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.099805 restraints weight = 18549.575| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.06 r_work: 0.3128 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12870 Z= 0.087 Angle : 0.421 4.572 17136 Z= 0.220 Chirality : 0.037 0.141 1980 Planarity : 0.002 0.030 2106 Dihedral : 3.325 12.842 1638 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.25 % Allowed : 16.95 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.22), residues: 1512 helix: 2.08 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.11 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 40 TYR 0.021 0.001 TYR N 43 PHE 0.007 0.001 PHE C 22 HIS 0.001 0.000 HIS I 21 Details of bonding type rmsd covalent geometry : bond 0.00212 (12870) covalent geometry : angle 0.42062 (17136) hydrogen bonds : bond 0.01982 ( 766) hydrogen bonds : angle 4.73396 ( 2298) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 435 time to evaluate : 0.531 Fit side-chains REVERT: A 37 LEU cc_start: 0.9134 (mp) cc_final: 0.8893 (mp) REVERT: A 41 GLU cc_start: 0.7923 (mp0) cc_final: 0.7622 (mp0) REVERT: A 67 LYS cc_start: 0.8604 (mppt) cc_final: 0.8323 (mppt) REVERT: B 47 GLN cc_start: 0.9197 (mt0) cc_final: 0.8806 (mt0) REVERT: C 41 GLU cc_start: 0.8038 (mp0) cc_final: 0.7292 (mp0) REVERT: C 85 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8552 (mm-30) REVERT: D 67 LYS cc_start: 0.8551 (mppt) cc_final: 0.8114 (mppt) REVERT: D 71 ASP cc_start: 0.8775 (m-30) cc_final: 0.8420 (m-30) REVERT: E 11 LEU cc_start: 0.8908 (mm) cc_final: 0.8582 (mt) REVERT: E 51 LEU cc_start: 0.8803 (tp) cc_final: 0.8444 (tp) REVERT: F 32 ASP cc_start: 0.8978 (m-30) cc_final: 0.8772 (m-30) REVERT: G 67 LYS cc_start: 0.8512 (mppt) cc_final: 0.8294 (mppt) REVERT: H 88 LYS cc_start: 0.8889 (tmtt) cc_final: 0.8266 (ptmt) REVERT: I 56 PHE cc_start: 0.8956 (m-10) cc_final: 0.8664 (m-10) REVERT: I 67 LYS cc_start: 0.8800 (mppt) cc_final: 0.8456 (mppt) REVERT: I 71 ASP cc_start: 0.8856 (m-30) cc_final: 0.8579 (m-30) REVERT: J 67 LYS cc_start: 0.8545 (mppt) cc_final: 0.8312 (mppt) REVERT: K 41 GLU cc_start: 0.8322 (pm20) cc_final: 0.8039 (pm20) REVERT: M 40 ARG cc_start: 0.8995 (ttm110) cc_final: 0.8718 (ttp-110) REVERT: M 71 ASP cc_start: 0.8839 (m-30) cc_final: 0.8558 (m-30) REVERT: N 24 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8802 (ttm) REVERT: N 85 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8574 (mm-30) REVERT: O 11 LEU cc_start: 0.8921 (mm) cc_final: 0.8698 (mp) REVERT: Q 38 LYS cc_start: 0.5288 (mmtt) cc_final: 0.5031 (mmtt) REVERT: Q 41 GLU cc_start: 0.8355 (mp0) cc_final: 0.7728 (mp0) REVERT: R 39 MET cc_start: 0.9170 (mtm) cc_final: 0.8745 (mtp) REVERT: R 59 ASP cc_start: 0.8046 (p0) cc_final: 0.7778 (p0) outliers start: 32 outliers final: 20 residues processed: 441 average time/residue: 0.1327 time to fit residues: 78.8980 Evaluate side-chains 448 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 427 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain F residue 4 LYS Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain L residue 24 MET Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain P residue 4 LYS Chi-restraints excluded: chain R residue 15 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 124 optimal weight: 0.0970 chunk 117 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.111790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.099149 restraints weight = 18786.863| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.08 r_work: 0.3121 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12870 Z= 0.097 Angle : 0.426 4.616 17136 Z= 0.222 Chirality : 0.037 0.133 1980 Planarity : 0.002 0.029 2106 Dihedral : 3.316 13.260 1638 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.90 % Allowed : 18.14 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.22), residues: 1512 helix: 2.10 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.09 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 40 TYR 0.022 0.001 TYR G 43 PHE 0.007 0.001 PHE B 56 HIS 0.001 0.001 HIS F 21 Details of bonding type rmsd covalent geometry : bond 0.00240 (12870) covalent geometry : angle 0.42562 (17136) hydrogen bonds : bond 0.01982 ( 766) hydrogen bonds : angle 4.70720 ( 2298) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 431 time to evaluate : 0.576 Fit side-chains REVERT: A 37 LEU cc_start: 0.9134 (mp) cc_final: 0.8895 (mp) REVERT: A 41 GLU cc_start: 0.7973 (mp0) cc_final: 0.7644 (mp0) REVERT: A 67 LYS cc_start: 0.8615 (mppt) cc_final: 0.8333 (mppt) REVERT: B 47 GLN cc_start: 0.9186 (mt0) cc_final: 0.8764 (mt0) REVERT: C 34 LYS cc_start: 0.8833 (mtmm) cc_final: 0.8575 (mmtp) REVERT: C 41 GLU cc_start: 0.8104 (mp0) cc_final: 0.7328 (mp0) REVERT: C 85 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8556 (mm-30) REVERT: D 67 LYS cc_start: 0.8543 (mppt) cc_final: 0.8094 (mppt) REVERT: D 71 ASP cc_start: 0.8784 (m-30) cc_final: 0.8412 (m-30) REVERT: E 51 LEU cc_start: 0.8808 (tp) cc_final: 0.8441 (tp) REVERT: F 7 ASN cc_start: 0.8875 (t0) cc_final: 0.8657 (t0) REVERT: G 41 GLU cc_start: 0.7981 (mp0) cc_final: 0.7418 (mp0) REVERT: G 57 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7901 (tpp80) REVERT: G 67 LYS cc_start: 0.8551 (mppt) cc_final: 0.8292 (mppt) REVERT: H 39 MET cc_start: 0.9261 (mtm) cc_final: 0.8776 (mtp) REVERT: H 88 LYS cc_start: 0.8886 (tmtt) cc_final: 0.8271 (ptmt) REVERT: I 56 PHE cc_start: 0.8923 (m-10) cc_final: 0.8623 (m-10) REVERT: I 67 LYS cc_start: 0.8803 (mppt) cc_final: 0.8458 (mppt) REVERT: I 71 ASP cc_start: 0.8849 (m-30) cc_final: 0.8570 (m-30) REVERT: J 42 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8575 (mm-30) REVERT: J 67 LYS cc_start: 0.8548 (mppt) cc_final: 0.8310 (mppt) REVERT: K 41 GLU cc_start: 0.8368 (pm20) cc_final: 0.8098 (pm20) REVERT: K 67 LYS cc_start: 0.8515 (ttmm) cc_final: 0.8231 (ttmm) REVERT: K 88 LYS cc_start: 0.9061 (tmtt) cc_final: 0.8801 (ttmt) REVERT: M 40 ARG cc_start: 0.9007 (ttm110) cc_final: 0.8702 (ttp-110) REVERT: M 71 ASP cc_start: 0.8838 (m-30) cc_final: 0.8583 (m-30) REVERT: N 24 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8834 (ttm) REVERT: N 85 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8579 (mm-30) REVERT: O 11 LEU cc_start: 0.8948 (mm) cc_final: 0.8719 (mp) REVERT: Q 38 LYS cc_start: 0.5302 (mmtt) cc_final: 0.5000 (mmtt) REVERT: Q 41 GLU cc_start: 0.8370 (mp0) cc_final: 0.7745 (mp0) REVERT: R 59 ASP cc_start: 0.8079 (p0) cc_final: 0.7814 (p0) outliers start: 27 outliers final: 20 residues processed: 436 average time/residue: 0.1504 time to fit residues: 88.6349 Evaluate side-chains 449 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 428 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain F residue 4 LYS Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain L residue 24 MET Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain P residue 4 LYS Chi-restraints excluded: chain R residue 15 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 1.9990 chunk 126 optimal weight: 0.2980 chunk 50 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 102 optimal weight: 0.0870 chunk 56 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 GLN M 47 GLN P 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.112002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.099374 restraints weight = 18543.858| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.07 r_work: 0.3123 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12870 Z= 0.092 Angle : 0.427 4.615 17136 Z= 0.223 Chirality : 0.037 0.135 1980 Planarity : 0.002 0.029 2106 Dihedral : 3.303 13.203 1638 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.83 % Allowed : 18.64 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.22), residues: 1512 helix: 2.09 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.10 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 40 TYR 0.029 0.001 TYR G 43 PHE 0.009 0.001 PHE O 56 HIS 0.001 0.001 HIS P 21 Details of bonding type rmsd covalent geometry : bond 0.00226 (12870) covalent geometry : angle 0.42725 (17136) hydrogen bonds : bond 0.01956 ( 766) hydrogen bonds : angle 4.69184 ( 2298) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 428 time to evaluate : 0.558 Fit side-chains REVERT: A 67 LYS cc_start: 0.8608 (mppt) cc_final: 0.8325 (mppt) REVERT: B 47 GLN cc_start: 0.9182 (mt0) cc_final: 0.8788 (mt0) REVERT: C 34 LYS cc_start: 0.8809 (mtmm) cc_final: 0.8605 (mmtp) REVERT: C 41 GLU cc_start: 0.8083 (mp0) cc_final: 0.7299 (mp0) REVERT: C 85 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8556 (mm-30) REVERT: D 67 LYS cc_start: 0.8543 (mppt) cc_final: 0.8081 (mppt) REVERT: D 71 ASP cc_start: 0.8782 (m-30) cc_final: 0.8413 (m-30) REVERT: E 51 LEU cc_start: 0.8801 (tp) cc_final: 0.8437 (tp) REVERT: F 7 ASN cc_start: 0.8883 (t0) cc_final: 0.8669 (t0) REVERT: G 41 GLU cc_start: 0.7966 (mp0) cc_final: 0.7416 (mp0) REVERT: G 57 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7921 (tpp80) REVERT: G 67 LYS cc_start: 0.8505 (mppt) cc_final: 0.8271 (mppt) REVERT: H 34 LYS cc_start: 0.8791 (mtmm) cc_final: 0.8514 (mmmm) REVERT: H 39 MET cc_start: 0.9272 (mtm) cc_final: 0.8835 (mtp) REVERT: H 52 MET cc_start: 0.8706 (mtt) cc_final: 0.8460 (mtt) REVERT: H 88 LYS cc_start: 0.8889 (tmtt) cc_final: 0.8254 (ptmt) REVERT: I 56 PHE cc_start: 0.8901 (m-10) cc_final: 0.8614 (m-10) REVERT: I 67 LYS cc_start: 0.8811 (mppt) cc_final: 0.8444 (mppt) REVERT: I 71 ASP cc_start: 0.8853 (m-30) cc_final: 0.8569 (m-30) REVERT: J 42 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8517 (mm-30) REVERT: K 41 GLU cc_start: 0.8363 (pm20) cc_final: 0.8063 (pm20) REVERT: K 67 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8251 (ttmm) REVERT: K 88 LYS cc_start: 0.9040 (tmtt) cc_final: 0.8765 (ttmt) REVERT: M 39 MET cc_start: 0.9231 (mtm) cc_final: 0.9009 (mtm) REVERT: M 40 ARG cc_start: 0.9004 (ttm110) cc_final: 0.8732 (ttp-110) REVERT: M 71 ASP cc_start: 0.8841 (m-30) cc_final: 0.8575 (m-30) REVERT: N 24 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8842 (ttm) REVERT: N 85 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8566 (mm-30) REVERT: O 11 LEU cc_start: 0.8961 (mm) cc_final: 0.8718 (mp) REVERT: Q 38 LYS cc_start: 0.5290 (mmtt) cc_final: 0.5018 (mmtt) REVERT: Q 41 GLU cc_start: 0.8322 (mp0) cc_final: 0.7689 (mp0) REVERT: R 59 ASP cc_start: 0.8071 (p0) cc_final: 0.7810 (p0) outliers start: 26 outliers final: 19 residues processed: 431 average time/residue: 0.1485 time to fit residues: 86.9386 Evaluate side-chains 446 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 426 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain F residue 4 LYS Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain L residue 24 MET Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain P residue 4 LYS Chi-restraints excluded: chain Q residue 4 LYS Chi-restraints excluded: chain R residue 15 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.098035 restraints weight = 18861.765| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.07 r_work: 0.3097 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12870 Z= 0.112 Angle : 0.449 4.685 17136 Z= 0.232 Chirality : 0.038 0.138 1980 Planarity : 0.002 0.028 2106 Dihedral : 3.335 13.660 1638 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.97 % Allowed : 18.50 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.22), residues: 1512 helix: 2.08 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.12 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 40 TYR 0.023 0.001 TYR M 43 PHE 0.009 0.001 PHE O 56 HIS 0.001 0.001 HIS P 21 Details of bonding type rmsd covalent geometry : bond 0.00280 (12870) covalent geometry : angle 0.44869 (17136) hydrogen bonds : bond 0.02039 ( 766) hydrogen bonds : angle 4.67982 ( 2298) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 434 time to evaluate : 0.528 Fit side-chains REVERT: A 67 LYS cc_start: 0.8623 (mppt) cc_final: 0.8342 (mppt) REVERT: C 34 LYS cc_start: 0.8882 (mtmm) cc_final: 0.8615 (mmtp) REVERT: C 41 GLU cc_start: 0.8126 (mp0) cc_final: 0.7365 (mp0) REVERT: C 42 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8844 (mm-30) REVERT: C 85 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8599 (mm-30) REVERT: D 67 LYS cc_start: 0.8610 (mppt) cc_final: 0.8130 (mppt) REVERT: D 71 ASP cc_start: 0.8834 (m-30) cc_final: 0.8421 (m-30) REVERT: E 51 LEU cc_start: 0.8826 (tp) cc_final: 0.8459 (tp) REVERT: F 7 ASN cc_start: 0.8903 (t0) cc_final: 0.8699 (t0) REVERT: G 41 GLU cc_start: 0.8044 (mp0) cc_final: 0.7483 (mp0) REVERT: G 57 ARG cc_start: 0.8197 (mtm-85) cc_final: 0.7942 (tpp80) REVERT: G 67 LYS cc_start: 0.8514 (mppt) cc_final: 0.8261 (mppt) REVERT: H 34 LYS cc_start: 0.8812 (mtmm) cc_final: 0.8521 (mmmm) REVERT: H 39 MET cc_start: 0.9285 (mtm) cc_final: 0.8899 (mtp) REVERT: H 52 MET cc_start: 0.8757 (mtt) cc_final: 0.8502 (mtt) REVERT: H 88 LYS cc_start: 0.8881 (tmtt) cc_final: 0.8304 (ptmt) REVERT: I 56 PHE cc_start: 0.8925 (m-10) cc_final: 0.8634 (m-10) REVERT: I 67 LYS cc_start: 0.8814 (mppt) cc_final: 0.8483 (mppt) REVERT: I 71 ASP cc_start: 0.8855 (m-30) cc_final: 0.8584 (m-30) REVERT: I 76 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8131 (mm-30) REVERT: K 40 ARG cc_start: 0.9024 (tpp80) cc_final: 0.8759 (tpp80) REVERT: K 41 GLU cc_start: 0.8441 (pm20) cc_final: 0.8151 (pm20) REVERT: K 67 LYS cc_start: 0.8649 (ttmm) cc_final: 0.8382 (ttmm) REVERT: L 47 GLN cc_start: 0.9019 (mt0) cc_final: 0.8768 (mt0) REVERT: M 15 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8823 (mm-30) REVERT: M 40 ARG cc_start: 0.8985 (ttm110) cc_final: 0.8698 (ttp-110) REVERT: M 71 ASP cc_start: 0.8860 (m-30) cc_final: 0.8600 (m-30) REVERT: N 24 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8834 (ttm) REVERT: N 85 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8565 (mm-30) REVERT: O 11 LEU cc_start: 0.8970 (mm) cc_final: 0.8688 (mp) REVERT: Q 38 LYS cc_start: 0.5523 (mmtt) cc_final: 0.5063 (mmtm) REVERT: R 59 ASP cc_start: 0.8123 (p0) cc_final: 0.7863 (p0) outliers start: 28 outliers final: 21 residues processed: 438 average time/residue: 0.1479 time to fit residues: 87.3639 Evaluate side-chains 455 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 433 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain F residue 4 LYS Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain L residue 24 MET Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain M residue 4 LYS Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain P residue 4 LYS Chi-restraints excluded: chain Q residue 4 LYS Chi-restraints excluded: chain R residue 15 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 120 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 57 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 7 ASN ** N 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.109745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.097354 restraints weight = 18942.687| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.05 r_work: 0.3086 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12870 Z= 0.128 Angle : 0.475 5.146 17136 Z= 0.243 Chirality : 0.039 0.139 1980 Planarity : 0.002 0.029 2106 Dihedral : 3.411 13.916 1638 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.69 % Allowed : 18.92 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.22), residues: 1512 helix: 2.03 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.11 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 40 TYR 0.043 0.001 TYR N 43 PHE 0.010 0.001 PHE O 56 HIS 0.001 0.001 HIS P 21 Details of bonding type rmsd covalent geometry : bond 0.00320 (12870) covalent geometry : angle 0.47545 (17136) hydrogen bonds : bond 0.02099 ( 766) hydrogen bonds : angle 4.70815 ( 2298) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 441 time to evaluate : 0.562 Fit side-chains REVERT: A 39 MET cc_start: 0.9148 (mtm) cc_final: 0.8837 (mtp) REVERT: A 67 LYS cc_start: 0.8651 (mppt) cc_final: 0.8363 (mppt) REVERT: B 47 GLN cc_start: 0.9131 (mt0) cc_final: 0.8845 (mt0) REVERT: C 42 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8893 (mm-30) REVERT: D 67 LYS cc_start: 0.8621 (mppt) cc_final: 0.8125 (mppt) REVERT: D 71 ASP cc_start: 0.8850 (m-30) cc_final: 0.8426 (m-30) REVERT: E 51 LEU cc_start: 0.8833 (tp) cc_final: 0.8463 (tp) REVERT: F 7 ASN cc_start: 0.8929 (t0) cc_final: 0.8727 (t0) REVERT: G 41 GLU cc_start: 0.8079 (mp0) cc_final: 0.7550 (mp0) REVERT: H 52 MET cc_start: 0.8711 (mtt) cc_final: 0.8445 (mtt) REVERT: H 88 LYS cc_start: 0.8968 (tmtt) cc_final: 0.8290 (ptmt) REVERT: I 56 PHE cc_start: 0.8987 (m-10) cc_final: 0.8660 (m-10) REVERT: I 67 LYS cc_start: 0.8838 (mppt) cc_final: 0.8511 (mppt) REVERT: I 71 ASP cc_start: 0.8848 (m-30) cc_final: 0.8556 (m-30) REVERT: K 40 ARG cc_start: 0.9023 (tpp80) cc_final: 0.8761 (tpp80) REVERT: K 41 GLU cc_start: 0.8437 (pm20) cc_final: 0.8144 (pm20) REVERT: K 67 LYS cc_start: 0.8626 (ttmm) cc_final: 0.8360 (ttmm) REVERT: K 88 LYS cc_start: 0.9087 (tmtt) cc_final: 0.8806 (ttmt) REVERT: L 47 GLN cc_start: 0.9057 (mt0) cc_final: 0.8781 (mt0) REVERT: L 67 LYS cc_start: 0.8672 (ttmm) cc_final: 0.8468 (ttmm) REVERT: L 85 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8793 (mm-30) REVERT: M 15 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8791 (mm-30) REVERT: M 40 ARG cc_start: 0.8930 (ttm110) cc_final: 0.8649 (ttp-110) REVERT: M 71 ASP cc_start: 0.8847 (m-30) cc_final: 0.8567 (m-30) REVERT: N 24 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8839 (ttm) REVERT: N 41 GLU cc_start: 0.8055 (mp0) cc_final: 0.7705 (mp0) REVERT: N 85 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8561 (mm-30) REVERT: O 11 LEU cc_start: 0.9041 (mm) cc_final: 0.8766 (mp) REVERT: Q 38 LYS cc_start: 0.5301 (mmtt) cc_final: 0.4934 (mmtm) REVERT: Q 41 GLU cc_start: 0.8299 (mp0) cc_final: 0.7839 (mp0) REVERT: R 59 ASP cc_start: 0.8155 (p0) cc_final: 0.7878 (p0) outliers start: 24 outliers final: 21 residues processed: 444 average time/residue: 0.1483 time to fit residues: 88.8228 Evaluate side-chains 460 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 438 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain F residue 4 LYS Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain L residue 24 MET Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain M residue 4 LYS Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain P residue 4 LYS Chi-restraints excluded: chain R residue 15 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 114 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 47 GLN M 7 ASN M 47 GLN N 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.111129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.098634 restraints weight = 18820.016| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.09 r_work: 0.3105 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12870 Z= 0.103 Angle : 0.469 6.551 17136 Z= 0.242 Chirality : 0.038 0.136 1980 Planarity : 0.002 0.032 2106 Dihedral : 3.412 13.852 1638 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.48 % Allowed : 19.34 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.22), residues: 1512 helix: 2.00 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.11 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 40 TYR 0.034 0.001 TYR M 43 PHE 0.010 0.001 PHE O 56 HIS 0.001 0.001 HIS P 21 Details of bonding type rmsd covalent geometry : bond 0.00255 (12870) covalent geometry : angle 0.46919 (17136) hydrogen bonds : bond 0.02045 ( 766) hydrogen bonds : angle 4.71592 ( 2298) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2964.84 seconds wall clock time: 51 minutes 56.37 seconds (3116.37 seconds total)