Starting phenix.real_space_refine on Thu Nov 20 06:00:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n5a_48919/11_2025/9n5a_48919.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n5a_48919/11_2025/9n5a_48919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n5a_48919/11_2025/9n5a_48919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n5a_48919/11_2025/9n5a_48919.map" model { file = "/net/cci-nas-00/data/ceres_data/9n5a_48919/11_2025/9n5a_48919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n5a_48919/11_2025/9n5a_48919.cif" } resolution = 2.96 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= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 12 7.16 5 S 168 5.16 5 C 19680 2.51 5 N 4968 2.21 5 O 5976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 232 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30804 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "B" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "C" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "D" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "E" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "F" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "G" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "H" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "I" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "J" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "K" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "L" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "M" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "N" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "O" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "P" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "Q" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "R" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "S" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "T" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "U" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "V" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "W" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "X" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1262 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.36, per 1000 atoms: 0.24 Number of scatterers: 30804 At special positions: 0 Unit cell: (125.45, 125.45, 125.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 12 26.01 S 168 16.00 O 5976 8.00 N 4968 7.00 C 19680 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6960 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 0 sheets defined 86.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 4 through 36 Processing helix chain 'A' and resid 37 through 65 Processing helix chain 'A' and resid 82 through 112 removed outlier: 3.560A pdb=" N LEU A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Proline residue: A 99 - end of helix Processing helix chain 'A' and resid 113 through 145 Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'B' and resid 4 through 35 Processing helix chain 'B' and resid 37 through 65 Processing helix chain 'B' and resid 82 through 112 Proline residue: B 99 - end of helix Processing helix chain 'B' and resid 113 through 145 Processing helix chain 'B' and resid 145 through 153 Processing helix chain 'C' and resid 4 through 35 Processing helix chain 'C' and resid 37 through 65 Processing helix chain 'C' and resid 82 through 112 Proline residue: C 99 - end of helix Processing helix chain 'C' and resid 113 through 145 Processing helix chain 'C' and resid 145 through 153 Processing helix chain 'D' and resid 4 through 35 removed outlier: 3.668A pdb=" N TRP D 35 " --> pdb=" O MET D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 65 Processing helix chain 'D' and resid 82 through 112 Proline residue: D 99 - end of helix Processing helix chain 'D' and resid 113 through 145 Processing helix chain 'D' and resid 145 through 153 Processing helix chain 'E' and resid 4 through 35 removed outlier: 3.622A pdb=" N TRP E 35 " --> pdb=" O MET E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 65 Processing helix chain 'E' and resid 82 through 96 Processing helix chain 'E' and resid 97 through 112 Processing helix chain 'E' and resid 113 through 145 removed outlier: 3.537A pdb=" N ASP E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 153 Processing helix chain 'F' and resid 4 through 36 removed outlier: 3.550A pdb=" N TRP F 35 " --> pdb=" O MET F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 65 Processing helix chain 'F' and resid 82 through 112 Proline residue: F 99 - end of helix Processing helix chain 'F' and resid 113 through 145 Processing helix chain 'F' and resid 145 through 153 Processing helix chain 'G' and resid 4 through 35 Processing helix chain 'G' and resid 37 through 65 Processing helix chain 'G' and resid 82 through 112 Proline residue: G 99 - end of helix Processing helix chain 'G' and resid 113 through 145 Processing helix chain 'G' and resid 145 through 153 Processing helix chain 'H' and resid 4 through 35 removed outlier: 3.504A pdb=" N TRP H 35 " --> pdb=" O MET H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 65 Processing helix chain 'H' and resid 82 through 112 Proline residue: H 99 - end of helix Processing helix chain 'H' and resid 113 through 145 Processing helix chain 'H' and resid 145 through 153 Processing helix chain 'I' and resid 4 through 36 Processing helix chain 'I' and resid 37 through 65 Processing helix chain 'I' and resid 82 through 112 removed outlier: 3.563A pdb=" N LEU I 98 " --> pdb=" O GLU I 94 " (cutoff:3.500A) Proline residue: I 99 - end of helix Processing helix chain 'I' and resid 113 through 145 Processing helix chain 'I' and resid 145 through 153 Processing helix chain 'J' and resid 4 through 35 Processing helix chain 'J' and resid 37 through 65 Processing helix chain 'J' and resid 82 through 112 Proline residue: J 99 - end of helix Processing helix chain 'J' and resid 113 through 145 Processing helix chain 'J' and resid 145 through 153 Processing helix chain 'K' and resid 4 through 35 Processing helix chain 'K' and resid 37 through 65 Processing helix chain 'K' and resid 82 through 112 Proline residue: K 99 - end of helix Processing helix chain 'K' and resid 113 through 145 Processing helix chain 'K' and resid 145 through 153 Processing helix chain 'L' and resid 4 through 35 removed outlier: 3.667A pdb=" N TRP L 35 " --> pdb=" O MET L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 65 Processing helix chain 'L' and resid 82 through 112 Proline residue: L 99 - end of helix Processing helix chain 'L' and resid 113 through 145 Processing helix chain 'L' and resid 145 through 153 Processing helix chain 'M' and resid 4 through 35 removed outlier: 3.600A pdb=" N TRP M 35 " --> pdb=" O MET M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 65 Processing helix chain 'M' and resid 82 through 96 Processing helix chain 'M' and resid 97 through 112 Processing helix chain 'M' and resid 113 through 145 removed outlier: 3.558A pdb=" N ASP M 142 " --> pdb=" O LEU M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 153 Processing helix chain 'N' and resid 4 through 35 removed outlier: 3.568A pdb=" N TRP N 35 " --> pdb=" O MET N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 65 Processing helix chain 'N' and resid 82 through 112 Proline residue: N 99 - end of helix Processing helix chain 'N' and resid 113 through 145 Processing helix chain 'N' and resid 145 through 153 Processing helix chain 'O' and resid 4 through 35 Processing helix chain 'O' and resid 37 through 65 Processing helix chain 'O' and resid 82 through 112 Proline residue: O 99 - end of helix Processing helix chain 'O' and resid 113 through 145 Processing helix chain 'O' and resid 145 through 153 Processing helix chain 'P' and resid 4 through 35 removed outlier: 3.505A pdb=" N TRP P 35 " --> pdb=" O MET P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 65 Processing helix chain 'P' and resid 82 through 112 Proline residue: P 99 - end of helix Processing helix chain 'P' and resid 113 through 145 Processing helix chain 'P' and resid 145 through 153 Processing helix chain 'Q' and resid 4 through 36 Processing helix chain 'Q' and resid 37 through 65 Processing helix chain 'Q' and resid 82 through 112 removed outlier: 3.563A pdb=" N LEU Q 98 " --> pdb=" O GLU Q 94 " (cutoff:3.500A) Proline residue: Q 99 - end of helix Processing helix chain 'Q' and resid 113 through 145 Processing helix chain 'Q' and resid 145 through 153 Processing helix chain 'R' and resid 4 through 35 Processing helix chain 'R' and resid 37 through 65 Processing helix chain 'R' and resid 82 through 112 Proline residue: R 99 - end of helix Processing helix chain 'R' and resid 113 through 145 Processing helix chain 'R' and resid 145 through 153 Processing helix chain 'S' and resid 4 through 35 Processing helix chain 'S' and resid 37 through 65 Processing helix chain 'S' and resid 82 through 112 Proline residue: S 99 - end of helix Processing helix chain 'S' and resid 113 through 145 Processing helix chain 'S' and resid 145 through 153 Processing helix chain 'T' and resid 4 through 35 removed outlier: 3.617A pdb=" N TRP T 35 " --> pdb=" O MET T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 65 Processing helix chain 'T' and resid 82 through 112 Proline residue: T 99 - end of helix Processing helix chain 'T' and resid 113 through 145 Processing helix chain 'T' and resid 145 through 153 Processing helix chain 'U' and resid 4 through 35 removed outlier: 3.608A pdb=" N TRP U 35 " --> pdb=" O MET U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 65 Processing helix chain 'U' and resid 82 through 96 Processing helix chain 'U' and resid 97 through 112 Processing helix chain 'U' and resid 113 through 145 removed outlier: 3.536A pdb=" N ASP U 142 " --> pdb=" O LEU U 138 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 153 Processing helix chain 'V' and resid 4 through 35 removed outlier: 3.590A pdb=" N TRP V 35 " --> pdb=" O MET V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 37 through 65 Processing helix chain 'V' and resid 82 through 112 Proline residue: V 99 - end of helix Processing helix chain 'V' and resid 113 through 145 Processing helix chain 'V' and resid 145 through 153 Processing helix chain 'W' and resid 4 through 35 Processing helix chain 'W' and resid 37 through 65 Processing helix chain 'W' and resid 82 through 112 Proline residue: W 99 - end of helix Processing helix chain 'W' and resid 113 through 145 Processing helix chain 'W' and resid 145 through 153 Processing helix chain 'X' and resid 4 through 35 removed outlier: 3.505A pdb=" N TRP X 35 " --> pdb=" O MET X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 65 Processing helix chain 'X' and resid 82 through 112 Proline residue: X 99 - end of helix Processing helix chain 'X' and resid 113 through 145 Processing helix chain 'X' and resid 145 through 153 2647 hydrogen bonds defined for protein. 7941 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: 5.55 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 12648 1.40 - 1.58: 18384 1.58 - 1.76: 1 1.76 - 1.94: 287 1.94 - 2.13: 48 Bond restraints: 31368 Sorted by residual: bond pdb=" SD MET V 52 " pdb=" CE MET V 52 " ideal model delta sigma weight residual 1.791 1.740 0.051 2.50e-02 1.60e+03 4.17e+00 bond pdb=" C LEU B 98 " pdb=" N PRO B 99 " ideal model delta sigma weight residual 1.335 1.357 -0.021 1.36e-02 5.41e+03 2.49e+00 bond pdb=" C LEU J 98 " pdb=" N PRO J 99 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.29e+00 bond pdb=" C LEU R 98 " pdb=" N PRO R 99 " ideal model delta sigma weight residual 1.335 1.356 -0.020 1.36e-02 5.41e+03 2.26e+00 bond pdb=" CB GLU X 81 " pdb=" CG GLU X 81 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.22e+00 ... (remaining 31363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.30: 42330 5.30 - 10.60: 12 10.60 - 15.91: 6 15.91 - 21.21: 10 21.21 - 26.51: 2 Bond angle restraints: 42360 Sorted by residual: angle pdb=" N MET V 52 " pdb=" CA MET V 52 " pdb=" CB MET V 52 " ideal model delta sigma weight residual 110.07 104.54 5.53 1.45e+00 4.76e-01 1.46e+01 angle pdb=" C GLU V 51 " pdb=" N MET V 52 " pdb=" CA MET V 52 " ideal model delta sigma weight residual 120.44 124.69 -4.25 1.36e+00 5.41e-01 9.75e+00 angle pdb=" NB HEM U 201 " pdb="FE HEM U 201 " pdb=" ND HEM U 201 " ideal model delta sigma weight residual 180.00 153.49 26.51 1.00e+01 1.00e-02 7.03e+00 angle pdb=" CB GLU X 81 " pdb=" CG GLU X 81 " pdb=" CD GLU X 81 " ideal model delta sigma weight residual 112.60 116.89 -4.29 1.70e+00 3.46e-01 6.38e+00 angle pdb=" NA HEM U 201 " pdb="FE HEM U 201 " pdb=" NC HEM U 201 " ideal model delta sigma weight residual 180.00 154.82 25.18 1.00e+01 1.00e-02 6.34e+00 ... (remaining 42355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 16234 17.96 - 35.92: 1665 35.92 - 53.88: 667 53.88 - 71.84: 244 71.84 - 89.80: 78 Dihedral angle restraints: 18888 sinusoidal: 8088 harmonic: 10800 Sorted by residual: dihedral pdb=" C2D HEM M 201 " pdb=" C3D HEM M 201 " pdb=" CAD HEM M 201 " pdb=" CBD HEM M 201 " ideal model delta sinusoidal sigma weight residual -180.00 -90.52 -89.48 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C2D HEM E 201 " pdb=" C3D HEM E 201 " pdb=" CAD HEM E 201 " pdb=" CBD HEM E 201 " ideal model delta sinusoidal sigma weight residual -180.00 -90.62 -89.38 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA ASP S 4 " pdb=" CB ASP S 4 " pdb=" CG ASP S 4 " pdb=" OD1 ASP S 4 " ideal model delta sinusoidal sigma weight residual -30.00 -88.83 58.83 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 18885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 2756 0.023 - 0.047: 1108 0.047 - 0.070: 414 0.070 - 0.093: 168 0.093 - 0.116: 114 Chirality restraints: 4560 Sorted by residual: chirality pdb=" CA ILE P 20 " pdb=" N ILE P 20 " pdb=" C ILE P 20 " pdb=" CB ILE P 20 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 chirality pdb=" CA ILE I 22 " pdb=" N ILE I 22 " pdb=" C ILE I 22 " pdb=" CB ILE I 22 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.27e-01 chirality pdb=" CA MET K 31 " pdb=" N MET K 31 " pdb=" C MET K 31 " pdb=" CB MET K 31 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.26e-01 ... (remaining 4557 not shown) Planarity restraints: 5400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 130 " 0.012 2.00e-02 2.50e+03 1.57e-02 3.71e+00 pdb=" CG HIS D 130 " -0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS D 130 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 HIS D 130 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 HIS D 130 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS D 130 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS L 130 " -0.012 2.00e-02 2.50e+03 1.56e-02 3.65e+00 pdb=" CG HIS L 130 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS L 130 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS L 130 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 HIS L 130 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS L 130 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS T 130 " 0.012 2.00e-02 2.50e+03 1.54e-02 3.54e+00 pdb=" CG HIS T 130 " -0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS T 130 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS T 130 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 HIS T 130 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS T 130 " -0.000 2.00e-02 2.50e+03 ... (remaining 5397 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1116 2.73 - 3.27: 31083 3.27 - 3.82: 56477 3.82 - 4.36: 64692 4.36 - 4.90: 113520 Nonbonded interactions: 266888 Sorted by model distance: nonbonded pdb=" NH1 ARG B 117 " pdb=" OE2 GLU C 109 " model vdw 2.188 3.120 nonbonded pdb=" OE1 GLN U 137 " pdb=" OH TYR U 149 " model vdw 2.300 3.040 nonbonded pdb=" OE1 GLN M 137 " pdb=" OH TYR M 149 " model vdw 2.300 3.040 nonbonded pdb=" OE1 GLN D 137 " pdb=" OH TYR D 149 " model vdw 2.301 3.040 nonbonded pdb=" OE1 GLN E 137 " pdb=" OH TYR E 149 " model vdw 2.302 3.040 ... (remaining 266883 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 155) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 1 through 155) selection = (chain 'E' and resid 1 through 155) selection = chain 'F' selection = chain 'G' selection = (chain 'H' and resid 1 through 155) selection = (chain 'I' and resid 1 through 155) selection = chain 'J' selection = chain 'K' selection = (chain 'L' and resid 1 through 155) selection = (chain 'M' and resid 1 through 155) selection = chain 'N' selection = chain 'O' selection = (chain 'P' and resid 1 through 155) selection = (chain 'Q' and resid 1 through 155) selection = chain 'R' selection = chain 'S' selection = (chain 'T' and resid 1 through 155) selection = (chain 'U' and resid 1 through 155) selection = chain 'V' selection = chain 'W' selection = (chain 'X' and resid 1 through 155) } 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: 12.670 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.810 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 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:7.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.005 0.310 31380 Z= 0.141 Angle : 0.677 26.511 42360 Z= 0.310 Chirality : 0.034 0.116 4560 Planarity : 0.002 0.022 5400 Dihedral : 18.955 89.796 11928 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.61 % Allowed : 18.07 % Favored : 80.32 % 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: 4.32 (0.13), residues: 3672 helix: 3.35 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.67 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG V 117 TYR 0.013 0.002 TYR H 107 PHE 0.014 0.002 PHE J 26 TRP 0.012 0.001 TRP I 35 HIS 0.020 0.003 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00301 (31368) covalent geometry : angle 0.67658 (42360) hydrogen bonds : bond 0.11401 ( 2647) hydrogen bonds : angle 4.49844 ( 7941) Misc. bond : bond 0.23113 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 319 time to evaluate : 1.226 Fit side-chains REVERT: B 57 LYS cc_start: 0.7524 (mtpt) cc_final: 0.7215 (mttt) REVERT: J 57 LYS cc_start: 0.7529 (mtpt) cc_final: 0.7221 (mttt) REVERT: K 109 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7263 (tm-30) REVERT: L 57 LYS cc_start: 0.7515 (mtpt) cc_final: 0.7198 (mttt) REVERT: R 57 LYS cc_start: 0.7519 (mtpt) cc_final: 0.7198 (mttt) REVERT: S 109 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7283 (tm-30) outliers start: 53 outliers final: 13 residues processed: 349 average time/residue: 0.6273 time to fit residues: 262.2675 Evaluate side-chains 313 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 298 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain R residue 50 ASP Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 152 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS D 130 HIS F 130 HIS G 130 HIS I 130 HIS J 130 HIS L 130 HIS M 130 HIS N 130 HIS R 130 HIS T 130 HIS U 130 HIS V 130 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.167579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.153569 restraints weight = 32349.823| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.46 r_work: 0.3643 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.265 31380 Z= 0.144 Angle : 0.603 19.705 42360 Z= 0.253 Chirality : 0.034 0.116 4560 Planarity : 0.002 0.022 5400 Dihedral : 7.283 85.430 4060 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 4.17 % Allowed : 13.69 % Favored : 82.15 % 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: 4.71 (0.13), residues: 3672 helix: 3.62 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.62 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG V 117 TYR 0.012 0.002 TYR E 107 PHE 0.013 0.002 PHE J 26 TRP 0.007 0.001 TRP A 35 HIS 0.008 0.002 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00335 (31368) covalent geometry : angle 0.60252 (42360) hydrogen bonds : bond 0.04961 ( 2647) hydrogen bonds : angle 3.73219 ( 7941) Misc. bond : bond 0.17611 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 401 time to evaluate : 1.000 Fit side-chains REVERT: B 42 LYS cc_start: 0.7615 (mttt) cc_final: 0.7121 (tttt) REVERT: B 57 LYS cc_start: 0.7985 (mtpt) cc_final: 0.7698 (mttt) REVERT: C 13 LYS cc_start: 0.8435 (ttpt) cc_final: 0.8000 (ttmm) REVERT: D 1 MET cc_start: 0.6491 (OUTLIER) cc_final: 0.6205 (ttt) REVERT: D 42 LYS cc_start: 0.7907 (ttmt) cc_final: 0.7113 (tttt) REVERT: E 4 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7978 (t70) REVERT: H 42 LYS cc_start: 0.7867 (ttmt) cc_final: 0.7094 (tttt) REVERT: H 65 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8554 (mp) REVERT: H 102 LYS cc_start: 0.7744 (mttt) cc_final: 0.7372 (mtpp) REVERT: H 127 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6373 (mp0) REVERT: I 57 LYS cc_start: 0.7906 (mtmt) cc_final: 0.7668 (mtmt) REVERT: I 127 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: J 57 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7699 (mttt) REVERT: K 13 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8022 (ttmm) REVERT: L 1 MET cc_start: 0.6489 (OUTLIER) cc_final: 0.6206 (ttt) REVERT: L 42 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7122 (tttt) REVERT: M 4 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7972 (t70) REVERT: N 42 LYS cc_start: 0.7771 (ttpt) cc_final: 0.7556 (tttt) REVERT: P 42 LYS cc_start: 0.7854 (ttmt) cc_final: 0.7079 (tttt) REVERT: P 65 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8554 (mp) REVERT: P 102 LYS cc_start: 0.7733 (mttt) cc_final: 0.7364 (mtpp) REVERT: P 127 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6392 (mp0) REVERT: Q 57 LYS cc_start: 0.7916 (mtmt) cc_final: 0.7681 (mtmt) REVERT: Q 127 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6549 (mp0) REVERT: R 57 LYS cc_start: 0.7976 (mtpt) cc_final: 0.7692 (mttt) REVERT: T 1 MET cc_start: 0.6512 (OUTLIER) cc_final: 0.6221 (ttt) REVERT: T 42 LYS cc_start: 0.7913 (ttmt) cc_final: 0.7116 (tttt) REVERT: U 4 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7980 (t70) REVERT: V 57 LYS cc_start: 0.7962 (mtmt) cc_final: 0.7735 (mtmt) REVERT: X 42 LYS cc_start: 0.7883 (ttmt) cc_final: 0.7111 (tttt) REVERT: X 65 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8559 (mp) REVERT: X 102 LYS cc_start: 0.7726 (mttt) cc_final: 0.7360 (mtpp) REVERT: X 127 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6376 (mp0) outliers start: 137 outliers final: 34 residues processed: 505 average time/residue: 0.7490 time to fit residues: 439.9814 Evaluate side-chains 390 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 342 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 94 GLU Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 127 GLU Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 127 GLU Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 50 ASP Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 94 GLU Chi-restraints excluded: chain U residue 4 ASP Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 122 ASP Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 127 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 221 optimal weight: 3.9990 chunk 310 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 306 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 321 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 314 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS D 130 HIS E 130 HIS F 130 HIS G 130 HIS H 130 HIS I 130 HIS J 130 HIS L 130 HIS N 130 HIS O 130 HIS P 130 HIS R 130 HIS T 130 HIS V 130 HIS W 130 HIS X 130 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.162006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.148841 restraints weight = 32079.368| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.38 r_work: 0.3611 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.283 31380 Z= 0.172 Angle : 0.587 19.211 42360 Z= 0.261 Chirality : 0.035 0.122 4560 Planarity : 0.002 0.026 5400 Dihedral : 6.916 82.796 4046 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 4.68 % Allowed : 15.02 % Favored : 80.29 % 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: 4.64 (0.13), residues: 3672 helix: 3.56 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.52 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 117 TYR 0.013 0.002 TYR E 107 PHE 0.014 0.002 PHE B 26 TRP 0.005 0.001 TRP H 35 HIS 0.007 0.002 HIS T 130 Details of bonding type rmsd covalent geometry : bond 0.00419 (31368) covalent geometry : angle 0.58682 (42360) hydrogen bonds : bond 0.05292 ( 2647) hydrogen bonds : angle 3.70023 ( 7941) Misc. bond : bond 0.15186 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 359 time to evaluate : 0.900 Fit side-chains REVERT: B 42 LYS cc_start: 0.7595 (mttt) cc_final: 0.7098 (tttt) REVERT: C 13 LYS cc_start: 0.8425 (ttpt) cc_final: 0.7986 (ttmm) REVERT: D 1 MET cc_start: 0.6636 (OUTLIER) cc_final: 0.6336 (ttt) REVERT: D 42 LYS cc_start: 0.7915 (ttmt) cc_final: 0.7148 (tttt) REVERT: D 88 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8399 (mt-10) REVERT: E 4 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7980 (t70) REVERT: F 42 LYS cc_start: 0.7759 (ttpt) cc_final: 0.7554 (tttt) REVERT: F 102 LYS cc_start: 0.7759 (mttt) cc_final: 0.7532 (mtpp) REVERT: H 42 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7165 (tttt) REVERT: H 65 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8569 (mp) REVERT: H 102 LYS cc_start: 0.7738 (mttt) cc_final: 0.7378 (mtpp) REVERT: I 127 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6434 (mp0) REVERT: K 13 LYS cc_start: 0.8441 (ttpt) cc_final: 0.8000 (ttmm) REVERT: L 1 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6361 (ttt) REVERT: L 42 LYS cc_start: 0.7915 (ttmt) cc_final: 0.7142 (tttt) REVERT: L 88 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8425 (mt-10) REVERT: M 4 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7953 (t70) REVERT: N 42 LYS cc_start: 0.7769 (ttpt) cc_final: 0.7564 (tttt) REVERT: N 102 LYS cc_start: 0.7762 (mttt) cc_final: 0.7538 (mtpp) REVERT: P 42 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7141 (tttt) REVERT: P 65 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8552 (mp) REVERT: P 102 LYS cc_start: 0.7735 (mttt) cc_final: 0.7378 (mtpp) REVERT: Q 127 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6446 (mp0) REVERT: S 13 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8011 (ttmm) REVERT: T 1 MET cc_start: 0.6656 (OUTLIER) cc_final: 0.6351 (ttt) REVERT: T 42 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7157 (tttt) REVERT: T 88 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8381 (mt-10) REVERT: V 42 LYS cc_start: 0.7784 (ttpt) cc_final: 0.7576 (tttt) REVERT: X 42 LYS cc_start: 0.7929 (ttmt) cc_final: 0.7177 (tttt) REVERT: X 65 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8576 (mp) REVERT: X 102 LYS cc_start: 0.7729 (mttt) cc_final: 0.7372 (mtpp) outliers start: 154 outliers final: 64 residues processed: 488 average time/residue: 0.7375 time to fit residues: 420.2589 Evaluate side-chains 390 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 313 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 152 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain L residue 110 SER Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 94 GLU Chi-restraints excluded: chain N residue 152 SER Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 152 SER Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain P residue 152 SER Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 127 GLU Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 152 SER Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 88 GLU Chi-restraints excluded: chain T residue 94 GLU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 122 ASP Chi-restraints excluded: chain U residue 123 ILE Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain W residue 152 SER Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 79 ILE Chi-restraints excluded: chain X residue 94 GLU Chi-restraints excluded: chain X residue 152 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 38 optimal weight: 0.8980 chunk 136 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 120 optimal weight: 0.0370 chunk 181 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 353 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS B 130 HIS C 130 HIS D 130 HIS E 130 HIS ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 HIS G 130 HIS H 130 HIS I 130 HIS J 130 HIS K 130 HIS L 130 HIS M 130 HIS ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 HIS O 130 HIS P 130 HIS Q 130 HIS R 130 HIS S 130 HIS T 130 HIS U 130 HIS ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 130 HIS W 130 HIS X 130 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.167648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.154019 restraints weight = 32151.928| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.44 r_work: 0.3646 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.242 31380 Z= 0.123 Angle : 0.522 18.305 42360 Z= 0.230 Chirality : 0.033 0.117 4560 Planarity : 0.002 0.019 5400 Dihedral : 6.694 84.288 4040 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 4.35 % Allowed : 16.36 % Favored : 79.29 % 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: 4.87 (0.13), residues: 3672 helix: 3.71 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.48 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 117 TYR 0.011 0.002 TYR E 107 PHE 0.012 0.002 PHE R 26 TRP 0.006 0.001 TRP Q 35 HIS 0.008 0.002 HIS P 130 Details of bonding type rmsd covalent geometry : bond 0.00285 (31368) covalent geometry : angle 0.52191 (42360) hydrogen bonds : bond 0.04581 ( 2647) hydrogen bonds : angle 3.51674 ( 7941) Misc. bond : bond 0.11984 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 295 time to evaluate : 1.216 Fit side-chains REVERT: D 1 MET cc_start: 0.6524 (OUTLIER) cc_final: 0.6229 (ttt) REVERT: D 42 LYS cc_start: 0.7898 (ttmt) cc_final: 0.7132 (tttt) REVERT: D 88 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8419 (mt-10) REVERT: E 4 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7886 (t70) REVERT: F 102 LYS cc_start: 0.7789 (mttt) cc_final: 0.7550 (mtpp) REVERT: H 42 LYS cc_start: 0.7890 (ttmt) cc_final: 0.7134 (tttt) REVERT: H 65 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8512 (mp) REVERT: J 92 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7759 (mtpt) REVERT: L 1 MET cc_start: 0.6564 (OUTLIER) cc_final: 0.6247 (ttt) REVERT: L 42 LYS cc_start: 0.7890 (ttmt) cc_final: 0.7127 (tttt) REVERT: L 88 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8422 (mt-10) REVERT: M 4 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7894 (t70) REVERT: P 42 LYS cc_start: 0.7880 (ttmt) cc_final: 0.7126 (tttt) REVERT: P 65 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8509 (mp) REVERT: R 92 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7767 (mtpt) REVERT: T 1 MET cc_start: 0.6538 (OUTLIER) cc_final: 0.6232 (ttt) REVERT: T 42 LYS cc_start: 0.7894 (ttmt) cc_final: 0.7134 (tttt) REVERT: T 88 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8418 (mt-10) REVERT: X 42 LYS cc_start: 0.7916 (ttmt) cc_final: 0.7161 (tttt) REVERT: X 65 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8502 (mp) outliers start: 143 outliers final: 57 residues processed: 410 average time/residue: 0.6788 time to fit residues: 330.2741 Evaluate side-chains 354 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 284 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 152 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain L residue 110 SER Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 94 GLU Chi-restraints excluded: chain N residue 152 SER Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 152 SER Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 152 SER Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 92 LYS Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 152 SER Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 88 GLU Chi-restraints excluded: chain T residue 94 GLU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 122 ASP Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain V residue 30 ARG Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain W residue 152 SER Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 152 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 286 optimal weight: 0.9990 chunk 295 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 268 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 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 130 HIS C 130 HIS D 130 HIS ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 HIS G 130 HIS H 130 HIS I 130 HIS J 130 HIS K 130 HIS L 130 HIS ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 HIS O 130 HIS P 130 HIS Q 130 HIS R 130 HIS S 130 HIS T 130 HIS ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 130 HIS W 130 HIS X 130 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.166315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.152914 restraints weight = 32175.447| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.42 r_work: 0.3648 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.294 31380 Z= 0.123 Angle : 0.510 18.253 42360 Z= 0.229 Chirality : 0.033 0.119 4560 Planarity : 0.002 0.020 5400 Dihedral : 6.657 86.221 4040 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 4.14 % Allowed : 17.00 % Favored : 78.86 % 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: 4.92 (0.13), residues: 3672 helix: 3.74 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.42 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 117 TYR 0.011 0.002 TYR E 107 PHE 0.012 0.002 PHE R 26 TRP 0.004 0.001 TRP A 35 HIS 0.010 0.002 HIS P 130 Details of bonding type rmsd covalent geometry : bond 0.00285 (31368) covalent geometry : angle 0.50971 (42360) hydrogen bonds : bond 0.04501 ( 2647) hydrogen bonds : angle 3.47639 ( 7941) Misc. bond : bond 0.14569 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 283 time to evaluate : 1.244 Fit side-chains REVERT: D 1 MET cc_start: 0.6515 (OUTLIER) cc_final: 0.6228 (ttt) REVERT: D 42 LYS cc_start: 0.7892 (ttmt) cc_final: 0.7125 (tttt) REVERT: D 88 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8424 (mt-10) REVERT: H 42 LYS cc_start: 0.7897 (ttmt) cc_final: 0.7140 (tttt) REVERT: H 65 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8506 (mp) REVERT: J 92 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7626 (mtpp) REVERT: L 1 MET cc_start: 0.6510 (OUTLIER) cc_final: 0.6184 (ttt) REVERT: L 42 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7131 (tttt) REVERT: L 88 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8440 (mt-10) REVERT: P 42 LYS cc_start: 0.7880 (ttmt) cc_final: 0.7113 (tttt) REVERT: P 65 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8502 (mp) REVERT: R 92 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7621 (mtpp) REVERT: T 1 MET cc_start: 0.6559 (OUTLIER) cc_final: 0.6269 (ttt) REVERT: T 42 LYS cc_start: 0.7909 (ttmt) cc_final: 0.7146 (tttt) REVERT: T 88 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8420 (mt-10) REVERT: V 102 LYS cc_start: 0.7764 (mttt) cc_final: 0.7547 (mtpp) REVERT: X 42 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7165 (tttt) REVERT: X 65 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8496 (mp) outliers start: 136 outliers final: 73 residues processed: 394 average time/residue: 0.6694 time to fit residues: 312.2279 Evaluate side-chains 364 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 280 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 152 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain L residue 110 SER Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 94 GLU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 152 SER Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 152 SER Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 152 SER Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 92 LYS Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 152 SER Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 30 ARG Chi-restraints excluded: chain T residue 88 GLU Chi-restraints excluded: chain T residue 94 GLU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 122 ASP Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain V residue 30 ARG Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain W residue 152 SER Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 152 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 154 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 182 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS B 130 HIS C 130 HIS D 130 HIS E 130 HIS ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 HIS G 130 HIS H 130 HIS I 130 HIS J 130 HIS K 130 HIS L 130 HIS M 130 HIS ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 HIS O 130 HIS P 130 HIS Q 130 HIS R 130 HIS S 130 HIS T 130 HIS U 130 HIS ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 130 HIS W 130 HIS X 130 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.168430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.154824 restraints weight = 32293.641| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.44 r_work: 0.3653 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.327 31380 Z= 0.118 Angle : 0.497 16.539 42360 Z= 0.224 Chirality : 0.033 0.123 4560 Planarity : 0.002 0.018 5400 Dihedral : 6.634 87.972 4040 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 4.44 % Allowed : 17.31 % Favored : 78.25 % 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: 4.97 (0.13), residues: 3672 helix: 3.77 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.39 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 117 TYR 0.010 0.001 TYR P 107 PHE 0.011 0.002 PHE K 26 TRP 0.005 0.001 TRP J 35 HIS 0.011 0.002 HIS T 130 Details of bonding type rmsd covalent geometry : bond 0.00271 (31368) covalent geometry : angle 0.49695 (42360) hydrogen bonds : bond 0.04402 ( 2647) hydrogen bonds : angle 3.44366 ( 7941) Misc. bond : bond 0.16025 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 283 time to evaluate : 1.159 Fit side-chains REVERT: D 1 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.6226 (ttt) REVERT: D 42 LYS cc_start: 0.7881 (ttmt) cc_final: 0.7106 (tttt) REVERT: D 88 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8396 (mt-10) REVERT: H 42 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7136 (tttt) REVERT: H 65 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8480 (mp) REVERT: J 92 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7588 (mtpp) REVERT: L 1 MET cc_start: 0.6504 (OUTLIER) cc_final: 0.6189 (ttt) REVERT: L 42 LYS cc_start: 0.7884 (ttmt) cc_final: 0.7114 (tttt) REVERT: L 88 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8413 (mt-10) REVERT: P 42 LYS cc_start: 0.7891 (ttmt) cc_final: 0.7122 (tttt) REVERT: P 65 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8481 (mp) REVERT: R 92 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7563 (mtpp) REVERT: S 92 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7831 (mtpt) REVERT: T 1 MET cc_start: 0.6562 (OUTLIER) cc_final: 0.6277 (ttt) REVERT: T 42 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7134 (tttt) REVERT: T 81 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7089 (mm-30) REVERT: T 88 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8416 (mm-30) REVERT: X 42 LYS cc_start: 0.7924 (ttmt) cc_final: 0.7161 (tttt) REVERT: X 65 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8478 (mp) REVERT: X 127 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6198 (mp0) outliers start: 146 outliers final: 81 residues processed: 397 average time/residue: 0.6605 time to fit residues: 310.4393 Evaluate side-chains 373 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 279 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 152 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain L residue 110 SER Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain N residue 30 ARG Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 94 GLU Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 152 SER Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 152 SER Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 152 SER Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 92 LYS Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 92 LYS Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 142 ASP Chi-restraints excluded: chain S residue 152 SER Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 30 ARG Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain T residue 88 GLU Chi-restraints excluded: chain T residue 94 GLU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 122 ASP Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain V residue 30 ARG Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain W residue 152 SER Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 127 GLU Chi-restraints excluded: chain X residue 152 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 316 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 262 optimal weight: 6.9990 chunk 263 optimal weight: 0.7980 chunk 281 optimal weight: 3.9990 chunk 273 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 342 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS B 130 HIS C 130 HIS D 130 HIS E 130 HIS ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 HIS G 130 HIS H 130 HIS I 130 HIS J 130 HIS K 130 HIS L 130 HIS M 130 HIS ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 HIS O 130 HIS P 130 HIS Q 130 HIS R 130 HIS S 130 HIS T 130 HIS U 130 HIS ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 130 HIS W 130 HIS X 130 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.169284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.155621 restraints weight = 32422.686| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.46 r_work: 0.3660 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.342 31380 Z= 0.113 Angle : 0.495 17.339 42360 Z= 0.222 Chirality : 0.033 0.144 4560 Planarity : 0.002 0.018 5400 Dihedral : 6.624 89.990 4040 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 4.50 % Allowed : 17.64 % Favored : 77.86 % 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: 5.01 (0.13), residues: 3672 helix: 3.80 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.37 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 117 TYR 0.009 0.001 TYR L 32 PHE 0.011 0.002 PHE K 26 TRP 0.004 0.001 TRP B 35 HIS 0.013 0.002 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00256 (31368) covalent geometry : angle 0.49548 (42360) hydrogen bonds : bond 0.04280 ( 2647) hydrogen bonds : angle 3.41366 ( 7941) Misc. bond : bond 0.17168 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 285 time to evaluate : 1.221 Fit side-chains REVERT: D 42 LYS cc_start: 0.7869 (ttmt) cc_final: 0.7087 (tttt) REVERT: H 42 LYS cc_start: 0.7889 (ttmt) cc_final: 0.7129 (tttt) REVERT: H 65 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8466 (mp) REVERT: L 42 LYS cc_start: 0.7878 (ttmt) cc_final: 0.7111 (tttt) REVERT: L 88 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8413 (mm-30) REVERT: P 42 LYS cc_start: 0.7862 (ttmt) cc_final: 0.7094 (tttt) REVERT: P 65 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8457 (mp) REVERT: S 92 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7753 (mtpt) REVERT: X 42 LYS cc_start: 0.7904 (ttmt) cc_final: 0.7142 (tttt) REVERT: X 65 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8499 (mp) outliers start: 148 outliers final: 81 residues processed: 391 average time/residue: 0.6652 time to fit residues: 308.6930 Evaluate side-chains 362 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 276 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 152 SER Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain L residue 110 SER Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 94 GLU Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 152 SER Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 152 SER Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 152 SER Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 92 LYS Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 142 ASP Chi-restraints excluded: chain S residue 152 SER Chi-restraints excluded: chain T residue 30 ARG Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain T residue 94 GLU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 122 ASP Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain V residue 30 ARG Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain W residue 110 SER Chi-restraints excluded: chain W residue 152 SER Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 152 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 128 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 65 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 342 optimal weight: 1.9990 chunk 293 optimal weight: 0.6980 chunk 323 optimal weight: 5.9990 chunk 311 optimal weight: 3.9990 chunk 335 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS B 130 HIS C 130 HIS C 153 GLN D 130 HIS E 130 HIS ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 HIS G 130 HIS H 130 HIS I 130 HIS J 130 HIS K 130 HIS K 153 GLN L 130 HIS M 130 HIS ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 HIS O 130 HIS P 130 HIS Q 130 HIS R 130 HIS S 130 HIS S 153 GLN T 130 HIS U 130 HIS ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 130 HIS W 130 HIS X 130 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.170422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157000 restraints weight = 32350.814| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.43 r_work: 0.3678 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.324 31380 Z= 0.107 Angle : 0.484 16.688 42360 Z= 0.219 Chirality : 0.032 0.193 4560 Planarity : 0.002 0.019 5400 Dihedral : 6.567 87.367 4040 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.71 % Allowed : 18.83 % Favored : 77.46 % 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: 5.06 (0.13), residues: 3672 helix: 3.84 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.36 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 117 TYR 0.011 0.001 TYR T 32 PHE 0.010 0.002 PHE R 26 TRP 0.005 0.000 TRP B 35 HIS 0.015 0.002 HIS T 130 Details of bonding type rmsd covalent geometry : bond 0.00238 (31368) covalent geometry : angle 0.48438 (42360) hydrogen bonds : bond 0.04124 ( 2647) hydrogen bonds : angle 3.38094 ( 7941) Misc. bond : bond 0.16761 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 291 time to evaluate : 1.239 Fit side-chains REVERT: A 57 LYS cc_start: 0.7862 (mttt) cc_final: 0.7618 (mtmt) REVERT: H 42 LYS cc_start: 0.7865 (ttmt) cc_final: 0.7103 (tttt) REVERT: H 65 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8449 (mp) REVERT: I 57 LYS cc_start: 0.7830 (mttt) cc_final: 0.7583 (mtmt) REVERT: P 65 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8442 (mp) REVERT: Q 57 LYS cc_start: 0.7825 (mttt) cc_final: 0.7575 (mtmt) REVERT: V 86 MET cc_start: 0.8284 (mtp) cc_final: 0.8083 (mtt) REVERT: X 42 LYS cc_start: 0.7885 (ttmt) cc_final: 0.7118 (tttt) REVERT: X 65 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8474 (mp) outliers start: 122 outliers final: 70 residues processed: 369 average time/residue: 0.6121 time to fit residues: 271.1793 Evaluate side-chains 364 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 291 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 152 SER Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain L residue 110 SER Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 94 GLU Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 152 SER Chi-restraints excluded: chain O residue 152 SER Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 152 SER Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 142 ASP Chi-restraints excluded: chain S residue 152 SER Chi-restraints excluded: chain T residue 30 ARG Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain T residue 94 GLU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 111 VAL Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 122 ASP Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain V residue 30 ARG Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain W residue 142 ASP Chi-restraints excluded: chain W residue 152 SER Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 152 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 342 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 338 optimal weight: 0.2980 chunk 329 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 267 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS E 130 HIS ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 HIS H 130 HIS I 130 HIS J 130 HIS L 130 HIS M 130 HIS ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 HIS O 130 HIS P 130 HIS Q 130 HIS R 130 HIS T 130 HIS U 130 HIS ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 130 HIS W 130 HIS X 130 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.165787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.152900 restraints weight = 32022.021| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.36 r_work: 0.3659 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.360 31380 Z= 0.124 Angle : 0.510 17.555 42360 Z= 0.233 Chirality : 0.034 0.189 4560 Planarity : 0.002 0.026 5400 Dihedral : 6.553 83.641 4040 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.68 % Allowed : 19.01 % Favored : 77.31 % 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: 4.96 (0.13), residues: 3672 helix: 3.77 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.37 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 117 TYR 0.010 0.002 TYR V 107 PHE 0.011 0.002 PHE K 26 TRP 0.009 0.001 TRP N 35 HIS 0.017 0.002 HIS T 130 Details of bonding type rmsd covalent geometry : bond 0.00288 (31368) covalent geometry : angle 0.50957 (42360) hydrogen bonds : bond 0.04435 ( 2647) hydrogen bonds : angle 3.44641 ( 7941) Misc. bond : bond 0.19840 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 289 time to evaluate : 1.259 Fit side-chains REVERT: A 92 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7680 (mtpp) REVERT: D 42 LYS cc_start: 0.7910 (ttmt) cc_final: 0.7128 (tttt) REVERT: H 42 LYS cc_start: 0.7890 (ttmt) cc_final: 0.7132 (tttt) REVERT: H 65 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8497 (mp) REVERT: I 57 LYS cc_start: 0.7842 (mttt) cc_final: 0.7605 (mtmt) REVERT: I 92 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7652 (mtpp) REVERT: I 127 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7500 (mm-30) REVERT: L 42 LYS cc_start: 0.7896 (ttmt) cc_final: 0.7134 (tttt) REVERT: L 88 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8375 (mt-10) REVERT: P 42 LYS cc_start: 0.7861 (ttmt) cc_final: 0.7095 (tttt) REVERT: P 65 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8494 (mp) REVERT: Q 127 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7531 (mm-30) REVERT: T 42 LYS cc_start: 0.7918 (ttmt) cc_final: 0.7140 (tttt) REVERT: X 42 LYS cc_start: 0.7912 (ttmt) cc_final: 0.7143 (tttt) REVERT: X 65 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8481 (mp) REVERT: X 127 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6275 (mp0) outliers start: 121 outliers final: 69 residues processed: 380 average time/residue: 0.6549 time to fit residues: 296.4263 Evaluate side-chains 363 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 285 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 152 SER Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain L residue 110 SER Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 94 GLU Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 152 SER Chi-restraints excluded: chain O residue 152 SER Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 152 SER Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 127 GLU Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 142 ASP Chi-restraints excluded: chain S residue 152 SER Chi-restraints excluded: chain T residue 30 ARG Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain T residue 94 GLU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 111 VAL Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 122 ASP Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain V residue 30 ARG Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain W residue 142 ASP Chi-restraints excluded: chain W residue 152 SER Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 127 GLU Chi-restraints excluded: chain X residue 152 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 111 optimal weight: 0.8980 chunk 331 optimal weight: 2.9990 chunk 277 optimal weight: 5.9990 chunk 251 optimal weight: 0.8980 chunk 216 optimal weight: 0.5980 chunk 349 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 314 optimal weight: 0.7980 chunk 276 optimal weight: 0.6980 chunk 332 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS E 130 HIS ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 HIS I 130 HIS J 130 HIS M 130 HIS ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 HIS P 130 HIS Q 130 HIS R 130 HIS U 130 HIS ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 130 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.166751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.153993 restraints weight = 31833.022| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.35 r_work: 0.3670 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.378 31380 Z= 0.116 Angle : 0.506 17.657 42360 Z= 0.234 Chirality : 0.033 0.210 4560 Planarity : 0.002 0.023 5400 Dihedral : 6.535 79.688 4040 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.10 % Allowed : 19.56 % Favored : 77.34 % 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: 4.99 (0.13), residues: 3672 helix: 3.78 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.37 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 117 TYR 0.011 0.002 TYR T 32 PHE 0.011 0.002 PHE B 26 TRP 0.004 0.001 TRP J 35 HIS 0.020 0.002 HIS T 130 Details of bonding type rmsd covalent geometry : bond 0.00265 (31368) covalent geometry : angle 0.50621 (42360) hydrogen bonds : bond 0.04325 ( 2647) hydrogen bonds : angle 3.43640 ( 7941) Misc. bond : bond 0.21064 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 290 time to evaluate : 1.451 Fit side-chains REVERT: A 92 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7685 (mtpp) REVERT: H 42 LYS cc_start: 0.7873 (ttmt) cc_final: 0.7115 (tttt) REVERT: H 65 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8463 (mp) REVERT: I 57 LYS cc_start: 0.7822 (mttt) cc_final: 0.7586 (mtmt) REVERT: I 127 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7499 (mm-30) REVERT: L 42 LYS cc_start: 0.7894 (ttmt) cc_final: 0.7125 (tttt) REVERT: P 42 LYS cc_start: 0.7873 (ttmt) cc_final: 0.7112 (tttt) REVERT: P 65 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8454 (mp) REVERT: Q 57 LYS cc_start: 0.7811 (mttt) cc_final: 0.7572 (mtmt) REVERT: Q 127 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7542 (mm-30) REVERT: T 42 LYS cc_start: 0.7902 (ttmt) cc_final: 0.7115 (tttt) REVERT: X 42 LYS cc_start: 0.7886 (ttmt) cc_final: 0.7128 (tttt) REVERT: X 65 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8448 (mp) outliers start: 102 outliers final: 71 residues processed: 366 average time/residue: 0.5804 time to fit residues: 255.9355 Evaluate side-chains 366 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 289 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 127 GLU Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 152 SER Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain L residue 110 SER Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 94 GLU Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 152 SER Chi-restraints excluded: chain O residue 152 SER Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 152 SER Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 127 GLU Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 142 ASP Chi-restraints excluded: chain S residue 152 SER Chi-restraints excluded: chain T residue 30 ARG Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain T residue 94 GLU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 122 ASP Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain V residue 30 ARG Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain W residue 142 ASP Chi-restraints excluded: chain W residue 152 SER Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 152 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 81 optimal weight: 0.0470 chunk 235 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 239 optimal weight: 0.0980 chunk 315 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 chunk 359 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 232 optimal weight: 0.4980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN B 130 HIS E 130 HIS ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 HIS F 151 GLN G 130 HIS G 151 GLN H 130 HIS H 151 GLN I 130 HIS I 151 GLN J 130 HIS M 130 HIS ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 HIS N 151 GLN O 130 HIS O 151 GLN P 130 HIS P 151 GLN Q 130 HIS Q 151 GLN R 130 HIS U 130 HIS ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 130 HIS V 151 GLN W 130 HIS W 151 GLN X 151 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.171416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157857 restraints weight = 32491.245| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.46 r_work: 0.3682 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.407 31380 Z= 0.104 Angle : 0.496 16.831 42360 Z= 0.227 Chirality : 0.033 0.195 4560 Planarity : 0.002 0.020 5400 Dihedral : 6.480 74.020 4040 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.52 % Allowed : 20.26 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 5.06 (0.13), residues: 3672 helix: 3.84 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.35 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 117 TYR 0.013 0.001 TYR E 32 PHE 0.011 0.002 PHE N 26 TRP 0.006 0.000 TRP I 35 HIS 0.019 0.002 HIS T 130 Details of bonding type rmsd covalent geometry : bond 0.00230 (31368) covalent geometry : angle 0.49552 (42360) hydrogen bonds : bond 0.04038 ( 2647) hydrogen bonds : angle 3.37079 ( 7941) Misc. bond : bond 0.21591 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8860.62 seconds wall clock time: 152 minutes 22.32 seconds (9142.32 seconds total)