Starting phenix.real_space_refine on Sun Jul 5 18:40:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iig_60594/07_2026/9iig_60594_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iig_60594/07_2026/9iig_60594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iig_60594/07_2026/9iig_60594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iig_60594/07_2026/9iig_60594.map" model { file = "/net/cci-nas-00/data/ceres_data/9iig_60594/07_2026/9iig_60594_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iig_60594/07_2026/9iig_60594_neut.cif" } resolution = 2.6 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= 0.026 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: 6 Type Number sf(0) Gaussians Fe 6 7.16 5 S 180 5.16 5 Na 6 4.78 5 C 19464 2.51 5 N 5232 2.21 5 O 5988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30876 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': 1, 'TRANS': 153} 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': 1, 'TRANS': 153} 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': 1, 'TRANS': 153} 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': 1, 'TRANS': 153} 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': 1, 'TRANS': 153} 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': 1, 'TRANS': 153} 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': 1, 'TRANS': 153} 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': 1, 'TRANS': 153} 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': 1, 'TRANS': 153} 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': 1, 'TRANS': 153} 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': 1, 'TRANS': 153} 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': 1, 'TRANS': 153} Chain: "M" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1289 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "N" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1289 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "O" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1289 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "P" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1289 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "Q" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1289 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "R" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1289 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "S" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1289 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "T" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1289 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "U" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1289 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "V" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1289 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "W" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1289 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "X" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1289 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "N" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "O" 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: "S" 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: 6.86, per 1000 atoms: 0.22 Number of scatterers: 30876 At special positions: 0 Unit cell: (139.035, 124.155, 134.385, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 S 180 16.00 Na 6 11.00 O 5988 8.00 N 5232 7.00 C 19464 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.2 seconds 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7128 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 0 sheets defined 85.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 4 through 35 Processing helix chain 'A' and resid 37 through 65 Processing helix chain 'A' and resid 82 through 111 Processing helix chain 'A' and resid 113 through 131 removed outlier: 3.846A pdb=" N HIS A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.545A pdb=" N LYS A 154 " --> pdb=" O TYR A 150 " (cutoff:3.500A) 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 111 Processing helix chain 'B' and resid 113 through 131 removed outlier: 3.846A pdb=" N HIS B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 146 Processing helix chain 'B' and resid 146 through 154 removed outlier: 3.545A pdb=" N LYS B 154 " --> pdb=" O TYR B 150 " (cutoff:3.500A) 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 111 Processing helix chain 'C' and resid 113 through 131 removed outlier: 3.847A pdb=" N HIS C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 146 Processing helix chain 'C' and resid 146 through 154 removed outlier: 3.545A pdb=" N LYS C 154 " --> pdb=" O TYR C 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 35 Processing helix chain 'D' and resid 37 through 65 Processing helix chain 'D' and resid 82 through 111 Processing helix chain 'D' and resid 113 through 131 removed outlier: 3.846A pdb=" N HIS D 131 " --> pdb=" O THR D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 146 Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.545A pdb=" N LYS D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 35 Processing helix chain 'E' and resid 37 through 65 Processing helix chain 'E' and resid 82 through 111 Processing helix chain 'E' and resid 113 through 131 removed outlier: 3.846A pdb=" N HIS E 131 " --> pdb=" O THR E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 146 Processing helix chain 'E' and resid 146 through 154 removed outlier: 3.544A pdb=" N LYS E 154 " --> pdb=" O TYR E 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 35 Processing helix chain 'F' and resid 37 through 65 Processing helix chain 'F' and resid 82 through 111 Processing helix chain 'F' and resid 113 through 131 removed outlier: 3.846A pdb=" N HIS F 131 " --> pdb=" O THR F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 146 Processing helix chain 'F' and resid 146 through 154 removed outlier: 3.544A pdb=" N LYS F 154 " --> pdb=" O TYR F 150 " (cutoff:3.500A) 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 111 Processing helix chain 'G' and resid 113 through 131 removed outlier: 3.846A pdb=" N HIS G 131 " --> pdb=" O THR G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 146 Processing helix chain 'G' and resid 146 through 154 removed outlier: 3.545A pdb=" N LYS G 154 " --> pdb=" O TYR G 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 35 Processing helix chain 'H' and resid 37 through 65 Processing helix chain 'H' and resid 82 through 111 Processing helix chain 'H' and resid 113 through 131 removed outlier: 3.846A pdb=" N HIS H 131 " --> pdb=" O THR H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 146 Processing helix chain 'H' and resid 146 through 154 removed outlier: 3.544A pdb=" N LYS H 154 " --> pdb=" O TYR H 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 35 Processing helix chain 'I' and resid 37 through 65 Processing helix chain 'I' and resid 82 through 111 Processing helix chain 'I' and resid 113 through 131 removed outlier: 3.847A pdb=" N HIS I 131 " --> pdb=" O THR I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 146 Processing helix chain 'I' and resid 146 through 154 removed outlier: 3.544A pdb=" N LYS I 154 " --> pdb=" O TYR I 150 " (cutoff:3.500A) 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 111 Processing helix chain 'J' and resid 113 through 131 removed outlier: 3.846A pdb=" N HIS J 131 " --> pdb=" O THR J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 146 Processing helix chain 'J' and resid 146 through 154 removed outlier: 3.544A pdb=" N LYS J 154 " --> pdb=" O TYR J 150 " (cutoff:3.500A) 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 111 Processing helix chain 'K' and resid 113 through 131 removed outlier: 3.846A pdb=" N HIS K 131 " --> pdb=" O THR K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 146 Processing helix chain 'K' and resid 146 through 154 removed outlier: 3.544A pdb=" N LYS K 154 " --> pdb=" O TYR K 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 35 Processing helix chain 'L' and resid 37 through 65 Processing helix chain 'L' and resid 82 through 111 Processing helix chain 'L' and resid 113 through 131 removed outlier: 3.846A pdb=" N HIS L 131 " --> pdb=" O THR L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 146 Processing helix chain 'L' and resid 146 through 154 removed outlier: 3.545A pdb=" N LYS L 154 " --> pdb=" O TYR L 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 35 Processing helix chain 'M' and resid 37 through 65 Processing helix chain 'M' and resid 82 through 111 Processing helix chain 'M' and resid 113 through 145 Processing helix chain 'M' and resid 145 through 152 Processing helix chain 'N' and resid 4 through 35 Processing helix chain 'N' and resid 37 through 65 Processing helix chain 'N' and resid 82 through 111 Processing helix chain 'N' and resid 113 through 145 Processing helix chain 'N' and resid 145 through 152 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 111 Processing helix chain 'O' and resid 113 through 145 Processing helix chain 'O' and resid 145 through 152 Processing helix chain 'P' and resid 4 through 35 Processing helix chain 'P' and resid 37 through 65 Processing helix chain 'P' and resid 82 through 111 Processing helix chain 'P' and resid 113 through 145 Processing helix chain 'P' and resid 145 through 152 Processing helix chain 'Q' and resid 4 through 35 Processing helix chain 'Q' and resid 37 through 65 Processing helix chain 'Q' and resid 82 through 111 Processing helix chain 'Q' and resid 113 through 145 Processing helix chain 'Q' and resid 145 through 152 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 111 Processing helix chain 'R' and resid 113 through 145 Processing helix chain 'R' and resid 145 through 152 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 111 Processing helix chain 'S' and resid 113 through 145 Processing helix chain 'S' and resid 145 through 152 Processing helix chain 'T' and resid 4 through 35 Processing helix chain 'T' and resid 37 through 65 Processing helix chain 'T' and resid 82 through 111 Processing helix chain 'T' and resid 113 through 145 Processing helix chain 'T' and resid 145 through 152 Processing helix chain 'U' and resid 4 through 35 Processing helix chain 'U' and resid 37 through 65 Processing helix chain 'U' and resid 82 through 111 Processing helix chain 'U' and resid 113 through 145 Processing helix chain 'U' and resid 145 through 152 Processing helix chain 'V' and resid 4 through 35 Processing helix chain 'V' and resid 37 through 65 Processing helix chain 'V' and resid 82 through 111 Processing helix chain 'V' and resid 113 through 145 Processing helix chain 'V' and resid 145 through 152 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 111 Processing helix chain 'W' and resid 113 through 145 Processing helix chain 'W' and resid 145 through 152 Processing helix chain 'X' and resid 4 through 35 Processing helix chain 'X' and resid 37 through 65 Processing helix chain 'X' and resid 82 through 111 Processing helix chain 'X' and resid 113 through 145 Processing helix chain 'X' and resid 145 through 152 2652 hydrogen bonds defined for protein. 7956 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: 5.62 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.40: 12864 1.40 - 1.59: 18168 1.59 - 1.78: 44 1.78 - 1.97: 268 1.97 - 2.16: 24 Bond restraints: 31368 Sorted by residual: bond pdb=" CG GLN U 97 " pdb=" CD GLN U 97 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.16e+00 bond pdb=" CG GLN X 97 " pdb=" CD GLN X 97 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.15e+00 bond pdb=" CG GLN N 97 " pdb=" CD GLN N 97 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.14e+00 bond pdb=" CG GLN Q 97 " pdb=" CD GLN Q 97 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.13e+00 bond pdb=" CG GLN S 97 " pdb=" CD GLN S 97 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.08e+00 ... (remaining 31363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 39500 1.28 - 2.57: 2175 2.57 - 3.85: 505 3.85 - 5.13: 110 5.13 - 6.41: 70 Bond angle restraints: 42360 Sorted by residual: angle pdb=" C GLU W 128 " pdb=" CA GLU W 128 " pdb=" CB GLU W 128 " ideal model delta sigma weight residual 109.55 115.96 -6.41 2.03e+00 2.43e-01 9.98e+00 angle pdb=" C GLU N 128 " pdb=" CA GLU N 128 " pdb=" CB GLU N 128 " ideal model delta sigma weight residual 109.55 115.90 -6.35 2.03e+00 2.43e-01 9.79e+00 angle pdb=" C GLU O 128 " pdb=" CA GLU O 128 " pdb=" CB GLU O 128 " ideal model delta sigma weight residual 109.55 115.90 -6.35 2.03e+00 2.43e-01 9.79e+00 angle pdb=" C GLU X 128 " pdb=" CA GLU X 128 " pdb=" CB GLU X 128 " ideal model delta sigma weight residual 109.55 115.89 -6.34 2.03e+00 2.43e-01 9.75e+00 angle pdb=" C GLU P 128 " pdb=" CA GLU P 128 " pdb=" CB GLU P 128 " ideal model delta sigma weight residual 109.55 115.89 -6.34 2.03e+00 2.43e-01 9.74e+00 ... (remaining 42355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 16881 17.43 - 34.86: 1772 34.86 - 52.29: 217 52.29 - 69.72: 54 69.72 - 87.14: 132 Dihedral angle restraints: 19056 sinusoidal: 8064 harmonic: 10992 Sorted by residual: dihedral pdb=" CA GLU V 128 " pdb=" C GLU V 128 " pdb=" N GLU V 129 " pdb=" CA GLU V 129 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA GLU R 128 " pdb=" C GLU R 128 " pdb=" N GLU R 129 " pdb=" CA GLU R 129 " ideal model delta harmonic sigma weight residual 180.00 162.22 17.78 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA GLU T 128 " pdb=" C GLU T 128 " pdb=" N GLU T 129 " pdb=" CA GLU T 129 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 19053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2444 0.031 - 0.063: 1604 0.063 - 0.094: 404 0.094 - 0.125: 186 0.125 - 0.156: 18 Chirality restraints: 4656 Sorted by residual: chirality pdb=" CA GLU E 118 " pdb=" N GLU E 118 " pdb=" C GLU E 118 " pdb=" CB GLU E 118 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CA GLU B 118 " pdb=" N GLU B 118 " pdb=" C GLU B 118 " pdb=" CB GLU B 118 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CA GLU D 118 " pdb=" N GLU D 118 " pdb=" C GLU D 118 " pdb=" CB GLU D 118 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.03e-01 ... (remaining 4653 not shown) Planarity restraints: 5484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG O 61 " -0.217 9.50e-02 1.11e+02 9.75e-02 6.06e+00 pdb=" NE ARG O 61 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG O 61 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG O 61 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG O 61 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG X 61 " 0.217 9.50e-02 1.11e+02 9.73e-02 6.04e+00 pdb=" NE ARG X 61 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG X 61 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG X 61 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG X 61 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 61 " -0.217 9.50e-02 1.11e+02 9.73e-02 6.04e+00 pdb=" NE ARG R 61 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG R 61 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG R 61 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG R 61 " -0.005 2.00e-02 2.50e+03 ... (remaining 5481 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2387 2.73 - 3.27: 32430 3.27 - 3.82: 58565 3.82 - 4.36: 71898 4.36 - 4.90: 117970 Nonbonded interactions: 283250 Sorted by model distance: nonbonded pdb=" OE1 GLN M 10 " pdb=" NH2 ARG M 13 " model vdw 2.189 3.120 nonbonded pdb=" OE1 GLN V 10 " pdb=" NH2 ARG V 13 " model vdw 2.189 3.120 nonbonded pdb=" OE1 GLN S 10 " pdb=" NH2 ARG S 13 " model vdw 2.189 3.120 nonbonded pdb=" OE1 GLN Q 10 " pdb=" NH2 ARG Q 13 " model vdw 2.189 3.120 nonbonded pdb=" OE1 GLN P 10 " pdb=" NH2 ARG P 13 " model vdw 2.189 3.120 ... (remaining 283245 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'X' } 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: 0.010 Normalize map: mean=0, sd=1: 7.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.290 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 27.830 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 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 : 0.008 0.174 31374 Z= 0.333 Angle : 0.741 6.413 42360 Z= 0.392 Chirality : 0.043 0.156 4656 Planarity : 0.008 0.097 5484 Dihedral : 15.760 87.144 11928 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.32 (0.11), residues: 3696 helix: 0.16 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -1.91 (0.17), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG I 117 TYR 0.022 0.004 TYR G 93 PHE 0.026 0.004 PHE B 26 TRP 0.032 0.003 TRP O 35 HIS 0.008 0.002 HIS P 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00817 / 0.33 (31368) covalent geometry : angle 0.74121 / 0.39 (42360) hydrogen bonds : bond 0.09209 / 6.10 ( 2652) hydrogen bonds : angle 5.14087 / 3.65 ( 7956) Misc. bond : bond 0.12702 / 6.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1122 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7212 (mm-30) REVERT: B 5 LYS cc_start: 0.7578 (tmtt) cc_final: 0.7377 (ttpp) REVERT: C 1 MET cc_start: 0.6785 (ptm) cc_final: 0.6543 (ptm) REVERT: C 52 LYS cc_start: 0.6757 (tptt) cc_final: 0.6023 (mttt) REVERT: C 66 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8109 (mt-10) REVERT: C 112 LYS cc_start: 0.8202 (mmtm) cc_final: 0.7711 (mmmt) REVERT: D 24 GLN cc_start: 0.8646 (tt0) cc_final: 0.8375 (tt0) REVERT: D 52 LYS cc_start: 0.6935 (tptt) cc_final: 0.5871 (mtmm) REVERT: D 88 ARG cc_start: 0.7913 (mtm110) cc_final: 0.7470 (mmt-90) REVERT: D 133 TYR cc_start: 0.7470 (t80) cc_final: 0.6825 (t80) REVERT: F 1 MET cc_start: 0.7408 (ptm) cc_final: 0.7186 (ptt) REVERT: F 22 MET cc_start: 0.7895 (ttp) cc_final: 0.7519 (ttm) REVERT: F 52 LYS cc_start: 0.6940 (tptt) cc_final: 0.6612 (tptt) REVERT: F 103 LYS cc_start: 0.7833 (mtmt) cc_final: 0.7597 (mtmt) REVERT: G 13 ARG cc_start: 0.7573 (mtm110) cc_final: 0.7356 (mtm-85) REVERT: G 66 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8057 (mp0) REVERT: G 96 LYS cc_start: 0.7997 (ttpp) cc_final: 0.7638 (tmtm) REVERT: G 125 ASP cc_start: 0.7601 (t70) cc_final: 0.7362 (t0) REVERT: H 47 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6949 (tp30) REVERT: I 1 MET cc_start: 0.6931 (ptm) cc_final: 0.6702 (ptm) REVERT: I 75 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7503 (mm-30) REVERT: I 103 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7746 (mmpt) REVERT: J 57 LYS cc_start: 0.7783 (mtmt) cc_final: 0.7545 (mttm) REVERT: J 93 TYR cc_start: 0.7288 (t80) cc_final: 0.6809 (t80) REVERT: J 96 LYS cc_start: 0.7976 (ttpp) cc_final: 0.7723 (ttpp) REVERT: J 103 LYS cc_start: 0.8112 (mtmt) cc_final: 0.7610 (mmtt) REVERT: J 110 GLN cc_start: 0.7573 (mt0) cc_final: 0.7272 (mt0) REVERT: K 1 MET cc_start: 0.6983 (ptm) cc_final: 0.6733 (ptm) REVERT: K 52 LYS cc_start: 0.6548 (tptt) cc_final: 0.5532 (mtmm) REVERT: K 57 LYS cc_start: 0.8166 (mtmt) cc_final: 0.7832 (mttt) REVERT: K 66 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7958 (mp0) REVERT: K 88 ARG cc_start: 0.7418 (mtm110) cc_final: 0.7180 (mmt180) REVERT: K 103 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7494 (mmtt) REVERT: L 1 MET cc_start: 0.6953 (ptm) cc_final: 0.6482 (ptm) REVERT: L 22 MET cc_start: 0.7603 (ttp) cc_final: 0.7217 (mtm) REVERT: L 42 GLU cc_start: 0.7594 (mt-10) cc_final: 0.6979 (tm-30) REVERT: L 52 LYS cc_start: 0.7095 (tptt) cc_final: 0.6885 (tptt) REVERT: L 125 ASP cc_start: 0.8347 (t70) cc_final: 0.8038 (t70) REVERT: N 76 LYS cc_start: 0.8423 (tmtt) cc_final: 0.8052 (tppt) REVERT: N 96 GLU cc_start: 0.7407 (tm-30) cc_final: 0.7207 (pt0) REVERT: O 10 GLN cc_start: 0.8174 (mm110) cc_final: 0.7836 (mm-40) REVERT: O 13 ARG cc_start: 0.7737 (ttm-80) cc_final: 0.7304 (ttm110) REVERT: O 51 ASP cc_start: 0.7847 (m-30) cc_final: 0.7535 (m-30) REVERT: O 68 LEU cc_start: 0.8548 (mt) cc_final: 0.8332 (mm) REVERT: O 96 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7165 (tm-30) REVERT: O 138 ARG cc_start: 0.7413 (ttm-80) cc_final: 0.6770 (ttm-80) REVERT: P 1 MET cc_start: 0.7250 (ttp) cc_final: 0.7034 (ttp) REVERT: P 17 CYS cc_start: 0.8143 (t) cc_final: 0.7684 (m) REVERT: P 38 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8078 (mm-30) REVERT: P 57 LYS cc_start: 0.7814 (mtmt) cc_final: 0.7590 (mttt) REVERT: Q 57 LYS cc_start: 0.8168 (mtmt) cc_final: 0.7965 (mttt) REVERT: Q 125 GLU cc_start: 0.7395 (pt0) cc_final: 0.6956 (mp0) REVERT: R 1 MET cc_start: 0.7159 (ttp) cc_final: 0.6936 (ttp) REVERT: S 6 LYS cc_start: 0.8389 (mmtp) cc_final: 0.8015 (mptt) REVERT: S 45 TYR cc_start: 0.7888 (t80) cc_final: 0.7659 (t80) REVERT: S 51 ASP cc_start: 0.7589 (m-30) cc_final: 0.7333 (m-30) REVERT: S 73 GLN cc_start: 0.7420 (mm110) cc_final: 0.7004 (tt0) REVERT: S 96 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7150 (tm-30) REVERT: T 6 LYS cc_start: 0.8087 (mmtp) cc_final: 0.7653 (mttp) REVERT: T 53 LYS cc_start: 0.8147 (mttp) cc_final: 0.7941 (mttt) REVERT: T 96 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7176 (tt0) REVERT: T 103 ASP cc_start: 0.8223 (m-30) cc_final: 0.7927 (m-30) REVERT: U 1 MET cc_start: 0.6441 (ttp) cc_final: 0.6205 (ptt) REVERT: U 10 GLN cc_start: 0.8068 (mm110) cc_final: 0.7724 (mm110) REVERT: U 68 LEU cc_start: 0.8876 (mt) cc_final: 0.8620 (mm) REVERT: U 113 ASP cc_start: 0.8394 (t0) cc_final: 0.8177 (t0) REVERT: U 126 ASP cc_start: 0.8174 (m-30) cc_final: 0.7940 (m-30) REVERT: V 33 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7796 (ttpp) REVERT: V 81 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7639 (mt-10) REVERT: V 129 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6535 (tm-30) REVERT: W 6 LYS cc_start: 0.8052 (mmtp) cc_final: 0.7451 (mtmm) REVERT: W 46 LYS cc_start: 0.7781 (pttt) cc_final: 0.7475 (mmmt) REVERT: W 66 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7700 (mm-30) REVERT: W 88 ASP cc_start: 0.8023 (m-30) cc_final: 0.7782 (m-30) REVERT: W 135 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7966 (mt-10) REVERT: X 1 MET cc_start: 0.7235 (ttp) cc_final: 0.7020 (ttp) REVERT: X 6 LYS cc_start: 0.8158 (mmtp) cc_final: 0.7567 (mmpt) REVERT: X 39 LYS cc_start: 0.7879 (ttpt) cc_final: 0.7672 (mtpt) outliers start: 0 outliers final: 1 residues processed: 1122 average time/residue: 0.7526 time to fit residues: 974.2106 Evaluate side-chains 837 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 836 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 148 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 GLN B 115 GLN B 149 ASN C 60 GLN C 149 ASN C 152 GLN D 78 ASN D 115 GLN E 89 ASN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 GLN F 149 ASN G 60 GLN G 149 ASN H 78 ASN H 115 GLN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 GLN I 149 ASN J 89 ASN J 149 ASN L 60 GLN L 110 GLN L 115 GLN L 149 ASN M 112 GLN N 70 ASN N 148 ASN N 151 GLN O 70 ASN O 130 HIS O 148 ASN P 73 GLN P 151 GLN Q 70 ASN Q 73 GLN Q 84 GLN Q 112 GLN Q 148 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 148 ASN S 151 GLN T 95 GLN T 148 ASN V 4 HIS V 10 GLN V 112 GLN V 148 ASN W 41 ASN ** X 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 130 HIS Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.148195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.136051 restraints weight = 28913.387| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.22 r_work: 0.3428 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.594 31374 Z= 0.129 Angle : 0.509 14.332 42360 Z= 0.246 Chirality : 0.033 0.118 4656 Planarity : 0.004 0.040 5484 Dihedral : 6.321 86.746 4118 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.20 % Allowed : 10.50 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.13), residues: 3696 helix: 2.46 (0.08), residues: 3228 sheet: None (None), residues: 0 loop : -2.07 (0.20), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 74 TYR 0.021 0.002 TYR D 133 PHE 0.024 0.002 PHE U 26 TRP 0.010 0.001 TRP I 35 HIS 0.006 0.001 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (31368) covalent geometry : angle 0.50896 / 0.25 (42360) hydrogen bonds : bond 0.04049 / 2.70 ( 2652) hydrogen bonds : angle 3.85680 / 2.74 ( 7956) Misc. bond : bond 0.46969 / 23.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 902 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7108 (mm-30) REVERT: A 115 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7220 (tm-30) REVERT: B 39 GLU cc_start: 0.7759 (tt0) cc_final: 0.7409 (tt0) REVERT: B 43 ARG cc_start: 0.7608 (tpt170) cc_final: 0.7215 (tpt170) REVERT: B 112 LYS cc_start: 0.8139 (mptt) cc_final: 0.7399 (mmmt) REVERT: C 1 MET cc_start: 0.6711 (ptm) cc_final: 0.6298 (ptm) REVERT: C 43 ARG cc_start: 0.7407 (tpt170) cc_final: 0.7148 (tpt170) REVERT: C 50 ASP cc_start: 0.7307 (m-30) cc_final: 0.6824 (t0) REVERT: C 52 LYS cc_start: 0.6833 (tptt) cc_final: 0.5960 (mtmm) REVERT: C 66 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7557 (mp0) REVERT: C 112 LYS cc_start: 0.8020 (mmtm) cc_final: 0.7415 (mmmt) REVERT: D 1 MET cc_start: 0.7852 (ptp) cc_final: 0.7026 (ptt) REVERT: D 52 LYS cc_start: 0.6950 (tptt) cc_final: 0.5734 (mtmm) REVERT: D 66 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8082 (mp0) REVERT: D 115 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7561 (tm130) REVERT: D 117 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7807 (ttt90) REVERT: E 115 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.6378 (tm-30) REVERT: E 122 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.8014 (m) REVERT: F 22 MET cc_start: 0.7840 (ttp) cc_final: 0.7369 (ttm) REVERT: F 47 GLU cc_start: 0.7419 (tp30) cc_final: 0.6804 (tp30) REVERT: F 52 LYS cc_start: 0.6911 (tptt) cc_final: 0.6645 (tptt) REVERT: F 103 LYS cc_start: 0.7910 (mtmt) cc_final: 0.7432 (ttpt) REVERT: G 13 ARG cc_start: 0.7501 (mtm110) cc_final: 0.7246 (mtm-85) REVERT: G 66 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7866 (mp0) REVERT: G 96 LYS cc_start: 0.7934 (ttpp) cc_final: 0.7468 (tmtm) REVERT: G 115 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: G 125 ASP cc_start: 0.7899 (t70) cc_final: 0.7623 (t0) REVERT: I 1 MET cc_start: 0.6538 (ptm) cc_final: 0.6336 (ptm) REVERT: I 9 ASP cc_start: 0.7996 (m-30) cc_final: 0.7705 (m-30) REVERT: I 50 ASP cc_start: 0.6479 (m-30) cc_final: 0.5892 (t0) REVERT: I 75 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7433 (mm-30) REVERT: J 50 ASP cc_start: 0.7215 (m-30) cc_final: 0.6995 (m-30) REVERT: J 57 LYS cc_start: 0.7706 (mtmt) cc_final: 0.7408 (mttm) REVERT: J 96 LYS cc_start: 0.7938 (ttpp) cc_final: 0.7514 (ttpp) REVERT: J 103 LYS cc_start: 0.7929 (mtmt) cc_final: 0.7319 (mmtt) REVERT: J 110 GLN cc_start: 0.7591 (mt0) cc_final: 0.7223 (mt0) REVERT: K 1 MET cc_start: 0.6910 (ptm) cc_final: 0.6659 (ptm) REVERT: K 66 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7871 (mp0) REVERT: K 88 ARG cc_start: 0.7198 (mtm110) cc_final: 0.6770 (mmt180) REVERT: K 103 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7152 (mmtt) REVERT: L 1 MET cc_start: 0.6943 (ptm) cc_final: 0.6597 (ptp) REVERT: L 22 MET cc_start: 0.7356 (ttp) cc_final: 0.6911 (mtp) REVERT: L 51 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7873 (mm-30) REVERT: L 112 LYS cc_start: 0.8456 (mppt) cc_final: 0.7557 (mmmt) REVERT: L 152 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8413 (tt0) REVERT: O 1 MET cc_start: 0.6822 (ttp) cc_final: 0.6235 (ptp) REVERT: O 13 ARG cc_start: 0.7410 (ttm-80) cc_final: 0.7139 (ttm110) REVERT: O 51 ASP cc_start: 0.7777 (m-30) cc_final: 0.7547 (m-30) REVERT: O 68 LEU cc_start: 0.8436 (mt) cc_final: 0.8155 (mm) REVERT: O 75 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7423 (mt-10) REVERT: O 96 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7082 (tm-30) REVERT: O 138 ARG cc_start: 0.7523 (ttm-80) cc_final: 0.6781 (ttm-80) REVERT: P 1 MET cc_start: 0.7130 (ttp) cc_final: 0.6734 (ttp) REVERT: P 38 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8062 (mm-30) REVERT: P 57 LYS cc_start: 0.7609 (mtmt) cc_final: 0.7319 (mttt) REVERT: P 76 LYS cc_start: 0.7709 (mmtt) cc_final: 0.7242 (tmtt) REVERT: Q 57 LYS cc_start: 0.7841 (mtmt) cc_final: 0.7575 (mttt) REVERT: Q 81 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: Q 125 GLU cc_start: 0.7246 (pt0) cc_final: 0.6738 (mt-10) REVERT: R 1 MET cc_start: 0.6977 (ttp) cc_final: 0.6725 (ttp) REVERT: R 6 LYS cc_start: 0.8007 (mmtp) cc_final: 0.7725 (mttp) REVERT: R 97 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7128 (tm-30) REVERT: R 129 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6836 (mt-10) REVERT: S 6 LYS cc_start: 0.8221 (mmtp) cc_final: 0.7818 (mptt) REVERT: S 45 TYR cc_start: 0.7878 (t80) cc_final: 0.7641 (t80) REVERT: S 73 GLN cc_start: 0.6906 (mm110) cc_final: 0.6643 (tt0) REVERT: S 96 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6986 (tm-30) REVERT: T 6 LYS cc_start: 0.7920 (mmtp) cc_final: 0.7378 (mtmm) REVERT: T 13 ARG cc_start: 0.7400 (ttm-80) cc_final: 0.6940 (mtm-85) REVERT: T 53 LYS cc_start: 0.8006 (mttp) cc_final: 0.7679 (mttt) REVERT: T 73 GLN cc_start: 0.7408 (mm-40) cc_final: 0.6736 (tp40) REVERT: T 75 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7615 (mm-30) REVERT: T 96 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7243 (tt0) REVERT: T 103 ASP cc_start: 0.8098 (m-30) cc_final: 0.7716 (m-30) REVERT: T 127 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6345 (mm-30) REVERT: U 10 GLN cc_start: 0.8077 (mm110) cc_final: 0.7837 (mm110) REVERT: U 68 LEU cc_start: 0.8736 (mt) cc_final: 0.8468 (mm) REVERT: U 96 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: U 126 ASP cc_start: 0.7980 (m-30) cc_final: 0.7707 (m-30) REVERT: V 13 ARG cc_start: 0.7698 (ttm110) cc_final: 0.7271 (mtm-85) REVERT: V 33 LYS cc_start: 0.8306 (ttmt) cc_final: 0.7705 (ttpp) REVERT: V 81 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7492 (mt-10) REVERT: V 85 GLU cc_start: 0.8624 (tt0) cc_final: 0.8423 (tt0) REVERT: V 96 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7150 (pt0) REVERT: V 129 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6349 (tm-30) REVERT: W 6 LYS cc_start: 0.7847 (mmtp) cc_final: 0.7379 (mtmm) REVERT: W 13 ARG cc_start: 0.7874 (mtm-85) cc_final: 0.7546 (mtt90) REVERT: W 46 LYS cc_start: 0.7545 (pttt) cc_final: 0.7210 (mmmt) REVERT: W 66 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7611 (mm-30) REVERT: W 88 ASP cc_start: 0.8164 (m-30) cc_final: 0.7885 (m-30) REVERT: W 100 LEU cc_start: 0.8358 (tt) cc_final: 0.8061 (tp) REVERT: W 129 GLU cc_start: 0.6698 (mt-10) cc_final: 0.6118 (pt0) REVERT: W 135 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7903 (mt-10) REVERT: W 151 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: X 6 LYS cc_start: 0.7860 (mmtp) cc_final: 0.7177 (mmpt) outliers start: 73 outliers final: 9 residues processed: 932 average time/residue: 0.7393 time to fit residues: 800.8189 Evaluate side-chains 840 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 816 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 152 GLN Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain R residue 97 GLN Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 96 GLU Chi-restraints excluded: chain V residue 96 GLU Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 151 GLN Chi-restraints excluded: chain X residue 94 VAL Chi-restraints excluded: chain X residue 96 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 339 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 322 optimal weight: 10.0000 chunk 297 optimal weight: 0.9990 chunk 272 optimal weight: 8.9990 chunk 299 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN D 138 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 GLN F 138 GLN G 60 GLN G 149 ASN H 115 GLN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 149 ASN L 60 GLN L 115 GLN M 70 ASN M 148 ASN N 70 ASN O 148 ASN P 73 GLN P 130 HIS ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 ASN T 42 HIS V 4 HIS V 148 ASN X 97 GLN ** X 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.146672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.134586 restraints weight = 29255.263| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.23 r_work: 0.3408 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.569 31374 Z= 0.122 Angle : 0.484 15.136 42360 Z= 0.231 Chirality : 0.032 0.113 4656 Planarity : 0.003 0.032 5484 Dihedral : 5.942 89.098 4116 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.44 % Allowed : 12.61 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.90 (0.13), residues: 3696 helix: 3.11 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.85 (0.20), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 74 TYR 0.017 0.001 TYR D 133 PHE 0.022 0.002 PHE S 26 TRP 0.006 0.001 TRP I 35 HIS 0.008 0.001 HIS T 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (31368) covalent geometry : angle 0.48397 / 0.23 (42360) hydrogen bonds : bond 0.03970 / 2.65 ( 2652) hydrogen bonds : angle 3.62614 / 2.58 ( 7956) Misc. bond : bond 0.47119 / 22.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 869 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7048 (mm-30) REVERT: A 115 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7263 (tm-30) REVERT: C 50 ASP cc_start: 0.7344 (m-30) cc_final: 0.6678 (t0) REVERT: C 52 LYS cc_start: 0.6808 (tptt) cc_final: 0.5943 (mtmm) REVERT: C 66 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7506 (mp0) REVERT: C 112 LYS cc_start: 0.8005 (mmtm) cc_final: 0.7402 (mmmt) REVERT: C 118 GLU cc_start: 0.7420 (mp0) cc_final: 0.7209 (mp0) REVERT: D 1 MET cc_start: 0.7866 (ptp) cc_final: 0.7198 (ptt) REVERT: D 5 LYS cc_start: 0.7374 (mppt) cc_final: 0.6433 (tttp) REVERT: D 24 GLN cc_start: 0.8570 (tt0) cc_final: 0.8188 (tt0) REVERT: D 52 LYS cc_start: 0.6970 (tptt) cc_final: 0.5736 (mtmm) REVERT: D 66 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: D 100 ASP cc_start: 0.7524 (t0) cc_final: 0.7252 (m-30) REVERT: D 118 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6493 (mt-10) REVERT: D 133 TYR cc_start: 0.7173 (t80) cc_final: 0.6964 (t80) REVERT: E 113 ASP cc_start: 0.8782 (t0) cc_final: 0.8555 (t70) REVERT: E 115 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.6320 (tm-30) REVERT: E 122 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.8009 (m) REVERT: F 47 GLU cc_start: 0.7431 (tp30) cc_final: 0.6882 (tp30) REVERT: F 103 LYS cc_start: 0.7878 (mtmt) cc_final: 0.7397 (ttmt) REVERT: F 115 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7716 (tm130) REVERT: G 50 ASP cc_start: 0.6957 (m-30) cc_final: 0.6010 (t0) REVERT: G 66 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7851 (mp0) REVERT: G 96 LYS cc_start: 0.7922 (ttpp) cc_final: 0.7441 (tmtm) REVERT: G 115 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: G 125 ASP cc_start: 0.7954 (t70) cc_final: 0.7709 (t0) REVERT: H 103 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7777 (tttm) REVERT: I 1 MET cc_start: 0.6613 (ptm) cc_final: 0.6276 (ptm) REVERT: I 9 ASP cc_start: 0.7966 (m-30) cc_final: 0.7652 (m-30) REVERT: I 50 ASP cc_start: 0.6461 (m-30) cc_final: 0.5808 (t70) REVERT: I 75 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7416 (mm-30) REVERT: I 112 LYS cc_start: 0.8112 (mmtm) cc_final: 0.7386 (mmmt) REVERT: J 1 MET cc_start: 0.6866 (ptm) cc_final: 0.6522 (ptt) REVERT: J 50 ASP cc_start: 0.7157 (m-30) cc_final: 0.6896 (m-30) REVERT: J 57 LYS cc_start: 0.7699 (mtmt) cc_final: 0.7413 (mttm) REVERT: J 96 LYS cc_start: 0.7937 (ttpp) cc_final: 0.7565 (ttpp) REVERT: J 103 LYS cc_start: 0.7958 (mtmt) cc_final: 0.7319 (mmtt) REVERT: J 110 GLN cc_start: 0.7537 (mt0) cc_final: 0.7215 (mt0) REVERT: K 1 MET cc_start: 0.6923 (ptm) cc_final: 0.6715 (ptm) REVERT: K 66 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7875 (mp0) REVERT: K 88 ARG cc_start: 0.7269 (mtm110) cc_final: 0.6798 (mmt180) REVERT: K 103 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7179 (mmtt) REVERT: L 1 MET cc_start: 0.6922 (ptm) cc_final: 0.6465 (ptm) REVERT: L 52 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.5923 (mtmm) REVERT: L 112 LYS cc_start: 0.8511 (mppt) cc_final: 0.7655 (mmmt) REVERT: N 76 LYS cc_start: 0.8541 (tmtt) cc_final: 0.8303 (tmtt) REVERT: O 1 MET cc_start: 0.6778 (ttp) cc_final: 0.6106 (ptp) REVERT: O 13 ARG cc_start: 0.7437 (ttm-80) cc_final: 0.7028 (mtm110) REVERT: O 51 ASP cc_start: 0.7801 (m-30) cc_final: 0.7540 (m-30) REVERT: O 68 LEU cc_start: 0.8445 (mt) cc_final: 0.8158 (mm) REVERT: O 75 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7494 (mt-10) REVERT: O 96 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7047 (tm-30) REVERT: O 138 ARG cc_start: 0.7524 (ttm-80) cc_final: 0.6763 (ttm-80) REVERT: P 1 MET cc_start: 0.7253 (ttp) cc_final: 0.6901 (ttp) REVERT: P 38 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8080 (mm-30) REVERT: P 57 LYS cc_start: 0.7598 (mtmt) cc_final: 0.7312 (mttt) REVERT: Q 53 LYS cc_start: 0.8082 (mttp) cc_final: 0.7702 (mttp) REVERT: Q 57 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7551 (mttt) REVERT: Q 81 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: Q 139 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: R 6 LYS cc_start: 0.7999 (mmtp) cc_final: 0.7689 (mttp) REVERT: R 85 GLU cc_start: 0.8135 (tt0) cc_final: 0.7809 (tt0) REVERT: R 97 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: R 129 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6943 (mt-10) REVERT: S 6 LYS cc_start: 0.8203 (mmtp) cc_final: 0.7770 (mmtm) REVERT: S 45 TYR cc_start: 0.7879 (t80) cc_final: 0.7620 (t80) REVERT: S 96 GLU cc_start: 0.7312 (tm-30) cc_final: 0.7006 (tm-30) REVERT: T 6 LYS cc_start: 0.7887 (mmtp) cc_final: 0.7403 (mttp) REVERT: T 13 ARG cc_start: 0.7410 (ttm-80) cc_final: 0.6976 (mtm-85) REVERT: T 53 LYS cc_start: 0.8039 (mttp) cc_final: 0.7712 (mttt) REVERT: T 73 GLN cc_start: 0.7455 (mm-40) cc_final: 0.6858 (tp-100) REVERT: T 75 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7432 (mm-30) REVERT: T 96 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7160 (tt0) REVERT: T 103 ASP cc_start: 0.8163 (m-30) cc_final: 0.7786 (m-30) REVERT: U 10 GLN cc_start: 0.8075 (mm110) cc_final: 0.7836 (mm110) REVERT: U 68 LEU cc_start: 0.8728 (mt) cc_final: 0.8477 (mm) REVERT: U 126 ASP cc_start: 0.8012 (m-30) cc_final: 0.7747 (m-30) REVERT: V 13 ARG cc_start: 0.7686 (ttm110) cc_final: 0.7358 (ttm110) REVERT: V 33 LYS cc_start: 0.8330 (tttt) cc_final: 0.7632 (ttpp) REVERT: V 81 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7470 (mt-10) REVERT: V 85 GLU cc_start: 0.8565 (tt0) cc_final: 0.8339 (tt0) REVERT: V 129 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6400 (tm-30) REVERT: W 6 LYS cc_start: 0.7827 (mmtp) cc_final: 0.7334 (mtmm) REVERT: W 46 LYS cc_start: 0.7532 (pttt) cc_final: 0.7185 (mmmt) REVERT: W 66 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7633 (mm-30) REVERT: W 88 ASP cc_start: 0.8140 (m-30) cc_final: 0.7856 (m-30) REVERT: W 100 LEU cc_start: 0.8333 (tt) cc_final: 0.8059 (tp) REVERT: W 135 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7903 (mt-10) REVERT: X 6 LYS cc_start: 0.7811 (mmtp) cc_final: 0.7116 (mmpt) REVERT: X 39 LYS cc_start: 0.8339 (ttmt) cc_final: 0.8087 (mttt) REVERT: X 66 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: X 112 GLN cc_start: 0.8179 (mp10) cc_final: 0.7971 (mt0) outliers start: 81 outliers final: 19 residues processed: 899 average time/residue: 0.7660 time to fit residues: 801.7248 Evaluate side-chains 834 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 801 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain C residue 4 ASP Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 139 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 97 GLN Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain X residue 94 VAL Chi-restraints excluded: chain X residue 96 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 34 optimal weight: 3.9990 chunk 182 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 297 optimal weight: 0.8980 chunk 287 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN D 115 GLN E 149 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 GLN G 60 GLN G 149 ASN H 115 GLN H 149 ASN H 152 GLN K 115 GLN L 60 GLN L 115 GLN M 148 ASN N 70 ASN O 10 GLN O 148 ASN P 73 GLN R 148 ASN S 137 GLN ** X 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.132635 restraints weight = 29177.330| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.22 r_work: 0.3379 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.580 31374 Z= 0.132 Angle : 0.499 17.977 42360 Z= 0.233 Chirality : 0.033 0.115 4656 Planarity : 0.003 0.036 5484 Dihedral : 5.772 89.622 4116 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.26 % Allowed : 13.57 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.18 (0.13), residues: 3696 helix: 3.29 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.76 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 74 TYR 0.019 0.002 TYR K 133 PHE 0.023 0.002 PHE S 26 TRP 0.004 0.001 TRP P 133 HIS 0.007 0.001 HIS T 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (31368) covalent geometry : angle 0.49889 / 0.23 (42360) hydrogen bonds : bond 0.04074 / 2.72 ( 2652) hydrogen bonds : angle 3.56065 / 2.53 ( 7956) Misc. bond : bond 0.48433 / 23.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 835 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7138 (mm-30) REVERT: A 115 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7192 (tm-30) REVERT: B 43 ARG cc_start: 0.7679 (tpt170) cc_final: 0.7334 (tpt170) REVERT: B 112 LYS cc_start: 0.8144 (mptt) cc_final: 0.7493 (mtmt) REVERT: C 50 ASP cc_start: 0.7388 (m-30) cc_final: 0.6689 (t0) REVERT: C 52 LYS cc_start: 0.6851 (tptt) cc_final: 0.5971 (mtmm) REVERT: C 66 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7568 (mp0) REVERT: C 112 LYS cc_start: 0.7986 (mmtm) cc_final: 0.7386 (mmmt) REVERT: D 1 MET cc_start: 0.7900 (ptp) cc_final: 0.7229 (ptt) REVERT: D 5 LYS cc_start: 0.7338 (mppt) cc_final: 0.6436 (tttp) REVERT: D 52 LYS cc_start: 0.7053 (tptt) cc_final: 0.5779 (mtmm) REVERT: D 66 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: D 88 ARG cc_start: 0.7890 (mtm110) cc_final: 0.7303 (mmt-90) REVERT: D 117 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7960 (ttt90) REVERT: D 118 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6487 (mt-10) REVERT: E 115 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.6340 (tm-30) REVERT: E 122 VAL cc_start: 0.8265 (OUTLIER) cc_final: 0.8005 (m) REVERT: F 22 MET cc_start: 0.7771 (ttp) cc_final: 0.7305 (ttm) REVERT: F 47 GLU cc_start: 0.7494 (tp30) cc_final: 0.6938 (tp30) REVERT: F 103 LYS cc_start: 0.7900 (mtmt) cc_final: 0.7427 (ttmt) REVERT: G 50 ASP cc_start: 0.6976 (m-30) cc_final: 0.6037 (t0) REVERT: G 66 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7886 (mp0) REVERT: G 96 LYS cc_start: 0.7952 (ttpp) cc_final: 0.7263 (tmtm) REVERT: G 100 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7393 (m-30) REVERT: G 112 LYS cc_start: 0.8214 (mmtm) cc_final: 0.7787 (mmmt) REVERT: G 115 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: H 57 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7788 (mtpt) REVERT: H 96 LYS cc_start: 0.8198 (tttm) cc_final: 0.7748 (ttpt) REVERT: H 103 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7777 (tttm) REVERT: I 1 MET cc_start: 0.6689 (ptm) cc_final: 0.6354 (ptt) REVERT: I 9 ASP cc_start: 0.8003 (m-30) cc_final: 0.7665 (m-30) REVERT: I 50 ASP cc_start: 0.6496 (m-30) cc_final: 0.5839 (t70) REVERT: I 75 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7428 (mm-30) REVERT: I 112 LYS cc_start: 0.8197 (mmtm) cc_final: 0.7489 (mmmt) REVERT: J 1 MET cc_start: 0.6937 (ptm) cc_final: 0.6613 (ptt) REVERT: J 50 ASP cc_start: 0.7181 (m-30) cc_final: 0.6940 (m-30) REVERT: J 57 LYS cc_start: 0.7738 (mtmt) cc_final: 0.7456 (mttm) REVERT: J 96 LYS cc_start: 0.7972 (ttpp) cc_final: 0.7694 (ttpp) REVERT: J 103 LYS cc_start: 0.7993 (mtmt) cc_final: 0.7361 (mmtt) REVERT: J 110 GLN cc_start: 0.7575 (mt0) cc_final: 0.7241 (mt0) REVERT: K 1 MET cc_start: 0.6986 (ptm) cc_final: 0.6092 (ptp) REVERT: K 66 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7905 (mp0) REVERT: K 88 ARG cc_start: 0.7333 (mtm110) cc_final: 0.6899 (mmt180) REVERT: K 96 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7467 (mtmm) REVERT: K 103 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7255 (mmtt) REVERT: L 1 MET cc_start: 0.6939 (ptm) cc_final: 0.6513 (ptm) REVERT: L 42 GLU cc_start: 0.7690 (mt-10) cc_final: 0.6841 (pp20) REVERT: L 52 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.5982 (mtmm) REVERT: L 112 LYS cc_start: 0.8541 (mppt) cc_final: 0.7735 (mmmt) REVERT: M 66 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7394 (mm-30) REVERT: O 1 MET cc_start: 0.6854 (ttp) cc_final: 0.6093 (ptp) REVERT: O 52 MET cc_start: 0.6459 (mtt) cc_final: 0.6189 (mtp) REVERT: O 68 LEU cc_start: 0.8454 (mt) cc_final: 0.8157 (mm) REVERT: O 75 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7424 (mt-10) REVERT: O 96 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7023 (tm-30) REVERT: O 125 GLU cc_start: 0.7275 (pt0) cc_final: 0.7046 (pt0) REVERT: O 138 ARG cc_start: 0.7572 (ttm-80) cc_final: 0.6769 (ttm-80) REVERT: P 1 MET cc_start: 0.7316 (ttp) cc_final: 0.7010 (ttp) REVERT: P 38 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8082 (mm-30) REVERT: P 39 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7208 (mtmt) REVERT: P 57 LYS cc_start: 0.7652 (mtmt) cc_final: 0.7372 (mttm) REVERT: Q 39 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8226 (mtpt) REVERT: Q 57 LYS cc_start: 0.7860 (mtmt) cc_final: 0.7582 (mttt) REVERT: Q 81 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: Q 125 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6903 (mt-10) REVERT: Q 139 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: R 6 LYS cc_start: 0.8034 (mmtp) cc_final: 0.7719 (mttp) REVERT: R 81 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: R 85 GLU cc_start: 0.8171 (tt0) cc_final: 0.7668 (tt0) REVERT: R 129 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6814 (tm-30) REVERT: S 1 MET cc_start: 0.6679 (ptm) cc_final: 0.6254 (ptt) REVERT: S 45 TYR cc_start: 0.7961 (t80) cc_final: 0.7698 (t80) REVERT: S 96 GLU cc_start: 0.7393 (tm-30) cc_final: 0.7049 (tm-30) REVERT: T 6 LYS cc_start: 0.7924 (mmtp) cc_final: 0.7391 (mtmm) REVERT: T 13 ARG cc_start: 0.7502 (ttm-80) cc_final: 0.7056 (mtm-85) REVERT: T 53 LYS cc_start: 0.8070 (mttp) cc_final: 0.7737 (mttt) REVERT: T 73 GLN cc_start: 0.7502 (mm-40) cc_final: 0.6892 (tp40) REVERT: T 74 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.6993 (mp) REVERT: T 75 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7323 (mm-30) REVERT: T 96 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7242 (mt-10) REVERT: T 103 ASP cc_start: 0.8207 (m-30) cc_final: 0.7834 (m-30) REVERT: U 10 GLN cc_start: 0.8050 (mm110) cc_final: 0.7827 (mm110) REVERT: U 68 LEU cc_start: 0.8757 (mt) cc_final: 0.8519 (mm) REVERT: U 91 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7664 (tp) REVERT: V 33 LYS cc_start: 0.8373 (tttt) cc_final: 0.7694 (ttpp) REVERT: V 81 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7522 (mt-10) REVERT: V 129 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6450 (tm-30) REVERT: W 6 LYS cc_start: 0.7817 (mmtp) cc_final: 0.7377 (mtmm) REVERT: W 46 LYS cc_start: 0.7569 (pttt) cc_final: 0.7228 (mmmt) REVERT: W 66 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7622 (mm-30) REVERT: W 88 ASP cc_start: 0.8180 (m-30) cc_final: 0.7905 (m-30) REVERT: W 100 LEU cc_start: 0.8397 (tt) cc_final: 0.8095 (tp) REVERT: W 135 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7948 (mt-10) REVERT: W 151 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: X 6 LYS cc_start: 0.7833 (mmtp) cc_final: 0.7119 (mmpt) REVERT: X 51 ASP cc_start: 0.7556 (m-30) cc_final: 0.7311 (m-30) outliers start: 75 outliers final: 24 residues processed: 865 average time/residue: 0.7756 time to fit residues: 777.6582 Evaluate side-chains 829 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 786 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain C residue 4 ASP Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 139 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 155 SER Chi-restraints excluded: chain W residue 74 LEU Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 119 LEU Chi-restraints excluded: chain W residue 151 GLN Chi-restraints excluded: chain X residue 94 VAL Chi-restraints excluded: chain X residue 96 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 213 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 296 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 330 optimal weight: 8.9990 chunk 287 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 339 optimal weight: 5.9990 chunk 329 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN E 115 GLN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 GLN F 138 GLN G 60 GLN J 131 HIS K 115 GLN L 60 GLN L 115 GLN M 148 ASN N 70 ASN O 10 GLN O 148 ASN P 73 GLN P 148 ASN R 148 ASN V 10 GLN W 41 ASN ** X 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.140267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.129067 restraints weight = 29427.177| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.10 r_work: 0.3353 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.661 31374 Z= 0.201 Angle : 0.571 17.595 42360 Z= 0.270 Chirality : 0.036 0.147 4656 Planarity : 0.004 0.050 5484 Dihedral : 5.888 87.085 4116 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.92 % Allowed : 13.33 % Favored : 83.75 % 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: 3.97 (0.13), residues: 3696 helix: 3.15 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.77 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG X 30 TYR 0.024 0.002 TYR F 93 PHE 0.034 0.002 PHE U 26 TRP 0.008 0.001 TRP S 35 HIS 0.009 0.001 HIS T 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (31368) covalent geometry : angle 0.57139 / 0.27 (42360) hydrogen bonds : bond 0.04689 / 3.15 ( 2652) hydrogen bonds : angle 3.72819 / 2.66 ( 7956) Misc. bond : bond 0.53802 / 26.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 840 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7013 (tm-30) REVERT: B 112 LYS cc_start: 0.8156 (mptt) cc_final: 0.7414 (mtmt) REVERT: C 50 ASP cc_start: 0.7275 (m-30) cc_final: 0.6552 (t0) REVERT: C 52 LYS cc_start: 0.6766 (tptt) cc_final: 0.5849 (mtmm) REVERT: C 66 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7419 (mp0) REVERT: C 112 LYS cc_start: 0.7902 (mmtm) cc_final: 0.7265 (mmmt) REVERT: D 1 MET cc_start: 0.7883 (ptp) cc_final: 0.7173 (ptt) REVERT: D 5 LYS cc_start: 0.7306 (mppt) cc_final: 0.6394 (tttp) REVERT: D 66 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: D 88 ARG cc_start: 0.7786 (mtm110) cc_final: 0.7175 (mmt180) REVERT: D 117 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7728 (ttt90) REVERT: D 118 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6324 (mt-10) REVERT: D 125 ASP cc_start: 0.8053 (t70) cc_final: 0.7832 (t70) REVERT: E 113 ASP cc_start: 0.8759 (t0) cc_final: 0.8404 (t70) REVERT: E 136 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7856 (mp0) REVERT: F 22 MET cc_start: 0.7743 (ttp) cc_final: 0.7226 (ttp) REVERT: F 52 LYS cc_start: 0.6842 (tptt) cc_final: 0.6315 (tptt) REVERT: F 96 LYS cc_start: 0.7865 (ttpp) cc_final: 0.7568 (tttm) REVERT: F 100 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7182 (t0) REVERT: F 103 LYS cc_start: 0.7825 (mtmt) cc_final: 0.7291 (ttmt) REVERT: F 111 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.6974 (mptm) REVERT: F 115 GLN cc_start: 0.8436 (tp40) cc_final: 0.8150 (mm-40) REVERT: G 66 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7815 (mp0) REVERT: G 96 LYS cc_start: 0.7858 (ttpp) cc_final: 0.7247 (tmtm) REVERT: G 100 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7301 (m-30) REVERT: G 112 LYS cc_start: 0.8232 (mmtm) cc_final: 0.7746 (mmmt) REVERT: G 115 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: H 57 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7622 (mtpt) REVERT: H 96 LYS cc_start: 0.8077 (tttm) cc_final: 0.7620 (ttpt) REVERT: H 103 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7659 (tttm) REVERT: I 1 MET cc_start: 0.6720 (ptm) cc_final: 0.6387 (ptt) REVERT: I 9 ASP cc_start: 0.7942 (m-30) cc_final: 0.7726 (m-30) REVERT: I 42 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7020 (mt-10) REVERT: I 50 ASP cc_start: 0.6388 (m-30) cc_final: 0.5710 (t0) REVERT: I 75 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7447 (mm-30) REVERT: I 112 LYS cc_start: 0.8207 (mmtm) cc_final: 0.7350 (mtpm) REVERT: I 118 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7035 (pt0) REVERT: J 1 MET cc_start: 0.6967 (ptm) cc_final: 0.6715 (ptt) REVERT: J 50 ASP cc_start: 0.7092 (m-30) cc_final: 0.6825 (m-30) REVERT: J 57 LYS cc_start: 0.7627 (mtmt) cc_final: 0.7309 (mttm) REVERT: J 103 LYS cc_start: 0.7920 (mtmt) cc_final: 0.7221 (mmtt) REVERT: J 110 GLN cc_start: 0.7402 (mt0) cc_final: 0.7104 (mt0) REVERT: K 1 MET cc_start: 0.6884 (ptm) cc_final: 0.6571 (ptm) REVERT: K 42 GLU cc_start: 0.7556 (mt-10) cc_final: 0.6570 (tm-30) REVERT: K 66 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7865 (mp0) REVERT: K 88 ARG cc_start: 0.7240 (mtm110) cc_final: 0.6799 (mmt180) REVERT: K 103 LYS cc_start: 0.8124 (mtmt) cc_final: 0.7143 (mmtt) REVERT: K 110 GLN cc_start: 0.7610 (tt0) cc_final: 0.7376 (tt0) REVERT: L 1 MET cc_start: 0.6905 (ptm) cc_final: 0.6526 (ptt) REVERT: L 42 GLU cc_start: 0.7715 (mt-10) cc_final: 0.6831 (pp20) REVERT: L 52 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.5820 (mtmm) REVERT: L 57 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7712 (mptm) REVERT: L 112 LYS cc_start: 0.8472 (mppt) cc_final: 0.7591 (mmmt) REVERT: L 125 ASP cc_start: 0.8058 (t0) cc_final: 0.7666 (t70) REVERT: L 152 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8438 (tt0) REVERT: M 46 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7556 (ptpt) REVERT: N 76 LYS cc_start: 0.8480 (tmtt) cc_final: 0.8131 (tptp) REVERT: N 100 LEU cc_start: 0.8590 (tp) cc_final: 0.8372 (tp) REVERT: O 68 LEU cc_start: 0.8400 (mt) cc_final: 0.8070 (mm) REVERT: O 75 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7342 (mt-10) REVERT: O 138 ARG cc_start: 0.7531 (ttm-80) cc_final: 0.6659 (ttm-80) REVERT: P 38 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8074 (mm-30) REVERT: P 39 LYS cc_start: 0.7884 (ttpt) cc_final: 0.7095 (mtmt) REVERT: P 57 LYS cc_start: 0.7514 (mtmt) cc_final: 0.7215 (mttm) REVERT: P 127 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6944 (mm-30) REVERT: Q 38 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7615 (mm-30) REVERT: Q 52 MET cc_start: 0.8129 (mtt) cc_final: 0.7922 (mtt) REVERT: Q 57 LYS cc_start: 0.7794 (mtmt) cc_final: 0.7461 (mttt) REVERT: Q 81 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: Q 98 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7460 (mp) REVERT: Q 125 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6761 (mt-10) REVERT: Q 139 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.6892 (tm-30) REVERT: R 6 LYS cc_start: 0.7934 (mmtp) cc_final: 0.7587 (mttp) REVERT: R 13 ARG cc_start: 0.7603 (ttm-80) cc_final: 0.7327 (mtp85) REVERT: R 81 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: R 129 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6718 (mt-10) REVERT: S 1 MET cc_start: 0.6679 (ptm) cc_final: 0.6302 (ptt) REVERT: S 6 LYS cc_start: 0.8073 (mmtp) cc_final: 0.7652 (mptt) REVERT: S 96 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6973 (tm-30) REVERT: T 6 LYS cc_start: 0.7829 (mmtp) cc_final: 0.7282 (mtmm) REVERT: T 53 LYS cc_start: 0.7986 (mttp) cc_final: 0.7647 (mttt) REVERT: T 73 GLN cc_start: 0.7510 (mm-40) cc_final: 0.6914 (tp40) REVERT: T 74 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7056 (mp) REVERT: T 75 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7254 (mm-30) REVERT: T 96 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7110 (mt-10) REVERT: T 103 ASP cc_start: 0.8120 (m-30) cc_final: 0.7742 (m-30) REVERT: U 10 GLN cc_start: 0.7948 (mm110) cc_final: 0.7644 (mm110) REVERT: U 45 TYR cc_start: 0.8091 (t80) cc_final: 0.7361 (t80) REVERT: U 68 LEU cc_start: 0.8757 (mt) cc_final: 0.8479 (mm) REVERT: U 91 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7561 (tt) REVERT: V 33 LYS cc_start: 0.8361 (tttt) cc_final: 0.7657 (ttpp) REVERT: V 81 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7573 (mt-10) REVERT: V 129 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6249 (tm-30) REVERT: W 6 LYS cc_start: 0.7692 (mmtp) cc_final: 0.7282 (mtmm) REVERT: W 46 LYS cc_start: 0.7574 (pttt) cc_final: 0.7168 (mmmt) REVERT: W 88 ASP cc_start: 0.8052 (m-30) cc_final: 0.7793 (m-30) REVERT: W 100 LEU cc_start: 0.8342 (tt) cc_final: 0.8061 (tp) REVERT: W 135 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7890 (mt-10) REVERT: W 151 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: X 1 MET cc_start: 0.6613 (ttp) cc_final: 0.6232 (ptt) REVERT: X 6 LYS cc_start: 0.7745 (mmtp) cc_final: 0.7068 (mmpt) REVERT: X 51 ASP cc_start: 0.7743 (m-30) cc_final: 0.7507 (m-30) outliers start: 97 outliers final: 29 residues processed: 886 average time/residue: 0.7580 time to fit residues: 777.0541 Evaluate side-chains 871 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 817 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 4 ASP Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 57 LYS Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 152 GLN Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 17 CYS Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 139 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 155 SER Chi-restraints excluded: chain W residue 74 LEU Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 119 LEU Chi-restraints excluded: chain W residue 151 GLN Chi-restraints excluded: chain X residue 94 VAL Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 106 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 273 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 296 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 302 optimal weight: 6.9990 chunk 224 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 89 ASN A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN D 115 GLN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 GLN G 60 GLN G 149 ASN H 149 ASN I 149 ASN J 89 ASN K 60 GLN K 89 ASN K 115 GLN L 60 GLN L 115 GLN M 148 ASN N 70 ASN O 10 GLN O 148 ASN P 73 GLN P 97 GLN P 148 ASN Q 148 ASN R 148 ASN T 42 HIS V 10 GLN ** W 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129985 restraints weight = 29380.170| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.10 r_work: 0.3362 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.655 31374 Z= 0.170 Angle : 0.535 17.590 42360 Z= 0.254 Chirality : 0.035 0.144 4656 Planarity : 0.003 0.045 5484 Dihedral : 5.772 86.045 4116 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.89 % Allowed : 14.17 % Favored : 82.94 % 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: 4.05 (0.13), residues: 3696 helix: 3.20 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.75 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG V 13 TYR 0.023 0.002 TYR K 133 PHE 0.028 0.002 PHE U 26 TRP 0.005 0.001 TRP X 133 HIS 0.009 0.001 HIS T 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (31368) covalent geometry : angle 0.53465 / 0.25 (42360) hydrogen bonds : bond 0.04455 / 2.99 ( 2652) hydrogen bonds : angle 3.65517 / 2.60 ( 7956) Misc. bond : bond 0.48958 / 24.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 828 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: B 43 ARG cc_start: 0.7554 (tpt170) cc_final: 0.7238 (tpt170) REVERT: B 112 LYS cc_start: 0.8163 (mptt) cc_final: 0.7421 (mtmt) REVERT: C 50 ASP cc_start: 0.7229 (m-30) cc_final: 0.6510 (t0) REVERT: C 52 LYS cc_start: 0.6744 (tptt) cc_final: 0.5816 (mtmm) REVERT: C 66 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7451 (mp0) REVERT: C 75 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7796 (mt-10) REVERT: C 112 LYS cc_start: 0.7878 (mmtm) cc_final: 0.7305 (mtmt) REVERT: D 1 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7176 (ptt) REVERT: D 5 LYS cc_start: 0.7308 (mppt) cc_final: 0.6405 (tttp) REVERT: D 42 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7081 (mt-10) REVERT: D 52 LYS cc_start: 0.7341 (tptp) cc_final: 0.5858 (mtmm) REVERT: D 66 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: D 88 ARG cc_start: 0.7807 (mtm110) cc_final: 0.7209 (mmt-90) REVERT: D 117 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7709 (ttt90) REVERT: D 118 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6326 (mt-10) REVERT: E 115 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.6330 (tm-30) REVERT: E 122 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7913 (m) REVERT: E 136 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7844 (mp0) REVERT: F 22 MET cc_start: 0.7712 (ttp) cc_final: 0.7258 (ttp) REVERT: F 52 LYS cc_start: 0.6930 (tptt) cc_final: 0.6499 (tptt) REVERT: F 96 LYS cc_start: 0.7873 (ttpp) cc_final: 0.7577 (tttm) REVERT: F 103 LYS cc_start: 0.7782 (mtmt) cc_final: 0.7281 (ttmt) REVERT: F 118 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.5830 (mp0) REVERT: F 132 MET cc_start: 0.8250 (ttp) cc_final: 0.8022 (ttp) REVERT: G 66 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7810 (mp0) REVERT: G 96 LYS cc_start: 0.7841 (ttpp) cc_final: 0.7221 (tmtm) REVERT: G 100 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7260 (m-30) REVERT: G 112 LYS cc_start: 0.8215 (mmtm) cc_final: 0.7745 (mmmt) REVERT: G 115 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: H 57 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7640 (mtpt) REVERT: H 96 LYS cc_start: 0.8082 (tttm) cc_final: 0.7644 (ttpt) REVERT: H 103 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7633 (tttm) REVERT: I 1 MET cc_start: 0.6725 (ptm) cc_final: 0.6389 (ptt) REVERT: I 9 ASP cc_start: 0.7969 (m-30) cc_final: 0.7748 (m-30) REVERT: I 42 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7003 (mt-10) REVERT: I 50 ASP cc_start: 0.6373 (m-30) cc_final: 0.5707 (t0) REVERT: I 75 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7440 (mm-30) REVERT: I 112 LYS cc_start: 0.8236 (mmtm) cc_final: 0.7400 (mtpm) REVERT: I 118 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7021 (pt0) REVERT: J 1 MET cc_start: 0.6943 (ptm) cc_final: 0.6656 (ptt) REVERT: J 50 ASP cc_start: 0.7065 (m-30) cc_final: 0.6770 (m-30) REVERT: J 57 LYS cc_start: 0.7600 (mtmt) cc_final: 0.7281 (mttm) REVERT: J 103 LYS cc_start: 0.7894 (mtmt) cc_final: 0.7186 (mmtt) REVERT: J 110 GLN cc_start: 0.7398 (mt0) cc_final: 0.7124 (mt0) REVERT: K 42 GLU cc_start: 0.7516 (mt-10) cc_final: 0.6547 (tm-30) REVERT: K 66 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7865 (mp0) REVERT: K 88 ARG cc_start: 0.7214 (mtm110) cc_final: 0.6778 (mmt180) REVERT: K 103 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7141 (mmtt) REVERT: K 110 GLN cc_start: 0.7584 (tt0) cc_final: 0.7361 (tt0) REVERT: L 1 MET cc_start: 0.6856 (ptm) cc_final: 0.6506 (ptt) REVERT: L 42 GLU cc_start: 0.7664 (mt-10) cc_final: 0.6789 (pp20) REVERT: L 52 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.5764 (mtmm) REVERT: L 57 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7670 (mptm) REVERT: L 112 LYS cc_start: 0.8493 (mppt) cc_final: 0.7610 (mmmt) REVERT: L 125 ASP cc_start: 0.8078 (t0) cc_final: 0.7730 (t70) REVERT: L 152 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8442 (tt0) REVERT: M 46 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7418 (ptpt) REVERT: N 1 MET cc_start: 0.5967 (ptt) cc_final: 0.5681 (ptt) REVERT: N 76 LYS cc_start: 0.8499 (tmtt) cc_final: 0.8129 (tptp) REVERT: O 1 MET cc_start: 0.6930 (ttp) cc_final: 0.5929 (ptp) REVERT: O 68 LEU cc_start: 0.8385 (mt) cc_final: 0.8068 (mm) REVERT: O 75 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7318 (mt-10) REVERT: O 138 ARG cc_start: 0.7518 (ttm-80) cc_final: 0.6636 (ttm-80) REVERT: P 39 LYS cc_start: 0.7891 (ttpt) cc_final: 0.7089 (mttt) REVERT: P 57 LYS cc_start: 0.7503 (mtmt) cc_final: 0.7198 (mttm) REVERT: P 127 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6980 (mm-30) REVERT: Q 38 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7599 (mm-30) REVERT: Q 39 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8160 (mtpt) REVERT: Q 57 LYS cc_start: 0.7788 (mtmt) cc_final: 0.7455 (mttt) REVERT: Q 81 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: Q 98 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7443 (mp) REVERT: Q 125 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6772 (mt-10) REVERT: Q 139 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.6878 (tm-30) REVERT: R 6 LYS cc_start: 0.7918 (mmtp) cc_final: 0.7582 (mttp) REVERT: R 13 ARG cc_start: 0.7583 (ttm-80) cc_final: 0.7315 (mtp85) REVERT: R 81 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: R 85 GLU cc_start: 0.8218 (tt0) cc_final: 0.7927 (tt0) REVERT: R 96 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7094 (pt0) REVERT: R 129 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6564 (tm-30) REVERT: S 1 MET cc_start: 0.6622 (ptm) cc_final: 0.6224 (ptt) REVERT: S 6 LYS cc_start: 0.8068 (mmtp) cc_final: 0.7647 (mptt) REVERT: S 96 GLU cc_start: 0.7385 (tm-30) cc_final: 0.6969 (tm-30) REVERT: T 6 LYS cc_start: 0.7824 (mmtp) cc_final: 0.7287 (mtmm) REVERT: T 53 LYS cc_start: 0.7975 (mttp) cc_final: 0.7649 (mttt) REVERT: T 73 GLN cc_start: 0.7499 (mm-40) cc_final: 0.6897 (tp40) REVERT: T 74 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7058 (mp) REVERT: T 75 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7255 (mm-30) REVERT: T 96 GLU cc_start: 0.7347 (tm-30) cc_final: 0.7106 (mt-10) REVERT: T 103 ASP cc_start: 0.8110 (m-30) cc_final: 0.7726 (m-30) REVERT: U 10 GLN cc_start: 0.7941 (mm110) cc_final: 0.7666 (mm110) REVERT: U 33 LYS cc_start: 0.8237 (ttpp) cc_final: 0.7576 (ttpp) REVERT: U 45 TYR cc_start: 0.8093 (t80) cc_final: 0.7312 (t80) REVERT: U 68 LEU cc_start: 0.8760 (mt) cc_final: 0.8493 (mm) REVERT: U 91 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7544 (tt) REVERT: V 13 ARG cc_start: 0.7755 (ttm-80) cc_final: 0.7407 (mtm-85) REVERT: V 33 LYS cc_start: 0.8350 (tttt) cc_final: 0.7653 (ttpp) REVERT: V 76 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7603 (tmmt) REVERT: V 81 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7563 (mt-10) REVERT: V 129 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6249 (tm-30) REVERT: W 6 LYS cc_start: 0.7714 (mmtp) cc_final: 0.7278 (mtmm) REVERT: W 46 LYS cc_start: 0.7537 (pttt) cc_final: 0.7140 (mmmt) REVERT: W 75 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7305 (mt-10) REVERT: W 88 ASP cc_start: 0.8059 (m-30) cc_final: 0.7788 (m-30) REVERT: W 100 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8021 (tp) REVERT: W 135 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7886 (mt-10) REVERT: W 151 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: X 1 MET cc_start: 0.6533 (ttp) cc_final: 0.6225 (ptt) REVERT: X 6 LYS cc_start: 0.7721 (mmtp) cc_final: 0.7051 (mmpt) REVERT: X 66 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: X 119 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7970 (tp) outliers start: 96 outliers final: 24 residues processed: 869 average time/residue: 0.7605 time to fit residues: 765.9872 Evaluate side-chains 858 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 801 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 57 LYS Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 152 GLN Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 17 CYS Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 97 GLN Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 139 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 76 LYS Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 100 LEU Chi-restraints excluded: chain W residue 119 LEU Chi-restraints excluded: chain W residue 151 GLN Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain X residue 94 VAL Chi-restraints excluded: chain X residue 119 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 78 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 342 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 358 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 247 optimal weight: 0.8980 chunk 142 optimal weight: 0.0970 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 ASN A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN D 115 GLN E 70 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 GLN F 138 GLN G 149 ASN I 149 ASN J 89 ASN J 149 ASN K 60 GLN K 115 GLN L 60 GLN L 115 GLN M 148 ASN N 70 ASN O 10 GLN O 148 ASN P 73 GLN P 148 ASN Q 148 ASN R 148 ASN T 42 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.142246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.130037 restraints weight = 29312.787| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.22 r_work: 0.3354 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.656 31374 Z= 0.141 Angle : 0.515 18.345 42360 Z= 0.242 Chirality : 0.034 0.127 4656 Planarity : 0.003 0.039 5484 Dihedral : 5.614 87.465 4116 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.44 % Allowed : 15.04 % Favored : 82.52 % 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: 4.19 (0.13), residues: 3696 helix: 3.29 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.71 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 74 TYR 0.023 0.002 TYR K 133 PHE 0.025 0.002 PHE U 26 TRP 0.005 0.001 TRP X 133 HIS 0.009 0.001 HIS T 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (31368) covalent geometry : angle 0.51523 / 0.24 (42360) hydrogen bonds : bond 0.04217 / 2.83 ( 2652) hydrogen bonds : angle 3.56872 / 2.54 ( 7956) Misc. bond : bond 0.49681 / 25.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 832 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7115 (mm-30) REVERT: A 115 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7244 (tm-30) REVERT: B 43 ARG cc_start: 0.7661 (tpt170) cc_final: 0.7316 (tpt170) REVERT: B 112 LYS cc_start: 0.8256 (mptt) cc_final: 0.7564 (mtmt) REVERT: C 50 ASP cc_start: 0.7344 (m-30) cc_final: 0.6645 (t0) REVERT: C 66 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7566 (mp0) REVERT: C 75 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7866 (mt-10) REVERT: C 112 LYS cc_start: 0.7924 (mmtm) cc_final: 0.7376 (mtpt) REVERT: D 1 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7204 (ptt) REVERT: D 5 LYS cc_start: 0.7348 (mppt) cc_final: 0.6954 (mptp) REVERT: D 24 GLN cc_start: 0.8615 (tt0) cc_final: 0.8224 (tt0) REVERT: D 42 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7159 (mt-10) REVERT: D 52 LYS cc_start: 0.7402 (tptp) cc_final: 0.6051 (mtmm) REVERT: D 66 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: D 88 ARG cc_start: 0.7978 (mtm110) cc_final: 0.7385 (mmt-90) REVERT: D 117 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7900 (ttt90) REVERT: D 118 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6442 (mt-10) REVERT: E 113 ASP cc_start: 0.8772 (t0) cc_final: 0.8477 (t70) REVERT: E 122 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.8036 (m) REVERT: E 136 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7937 (mp0) REVERT: F 22 MET cc_start: 0.7859 (ttp) cc_final: 0.7376 (ttp) REVERT: F 52 LYS cc_start: 0.7034 (tptt) cc_final: 0.6644 (tptt) REVERT: F 96 LYS cc_start: 0.7997 (ttpp) cc_final: 0.7713 (tttm) REVERT: F 103 LYS cc_start: 0.7892 (mtmt) cc_final: 0.7430 (ttmt) REVERT: F 115 GLN cc_start: 0.8491 (tp40) cc_final: 0.8253 (tp-100) REVERT: F 118 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.6204 (mt-10) REVERT: F 132 MET cc_start: 0.8288 (ttp) cc_final: 0.8064 (ttp) REVERT: G 50 ASP cc_start: 0.6957 (m-30) cc_final: 0.6000 (t0) REVERT: G 66 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7877 (mp0) REVERT: G 96 LYS cc_start: 0.7938 (ttpp) cc_final: 0.7340 (tmtm) REVERT: G 100 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7395 (m-30) REVERT: G 112 LYS cc_start: 0.8285 (mmtm) cc_final: 0.7864 (mmmt) REVERT: G 115 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: H 57 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7790 (mtpt) REVERT: H 96 LYS cc_start: 0.8175 (tttm) cc_final: 0.7770 (ttpt) REVERT: H 103 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7779 (tttm) REVERT: H 125 ASP cc_start: 0.8129 (t0) cc_final: 0.7785 (t70) REVERT: I 1 MET cc_start: 0.6789 (ptm) cc_final: 0.6458 (ptt) REVERT: I 42 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7064 (mt-10) REVERT: I 50 ASP cc_start: 0.6468 (m-30) cc_final: 0.5788 (t70) REVERT: I 60 GLN cc_start: 0.8497 (mt0) cc_final: 0.8292 (mt0) REVERT: I 75 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7489 (mm-30) REVERT: I 112 LYS cc_start: 0.8274 (mmtm) cc_final: 0.7533 (mtpm) REVERT: I 113 ASP cc_start: 0.8529 (t0) cc_final: 0.8317 (t0) REVERT: J 1 MET cc_start: 0.6988 (ptm) cc_final: 0.6768 (ptt) REVERT: J 50 ASP cc_start: 0.7188 (m-30) cc_final: 0.6888 (m-30) REVERT: J 57 LYS cc_start: 0.7752 (mtmt) cc_final: 0.7465 (mttm) REVERT: J 103 LYS cc_start: 0.7992 (mtmt) cc_final: 0.7342 (mmtt) REVERT: J 110 GLN cc_start: 0.7509 (mt0) cc_final: 0.7242 (mt0) REVERT: K 1 MET cc_start: 0.7241 (ptm) cc_final: 0.6797 (ptt) REVERT: K 42 GLU cc_start: 0.7584 (mt-10) cc_final: 0.6663 (tm-30) REVERT: K 66 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7979 (mp0) REVERT: K 88 ARG cc_start: 0.7354 (mtm110) cc_final: 0.6942 (mmt180) REVERT: K 103 LYS cc_start: 0.8237 (mtmt) cc_final: 0.7298 (mmtt) REVERT: K 110 GLN cc_start: 0.7659 (tt0) cc_final: 0.7438 (tt0) REVERT: L 1 MET cc_start: 0.6932 (ptm) cc_final: 0.6382 (ptt) REVERT: L 42 GLU cc_start: 0.7748 (mt-10) cc_final: 0.6895 (pp20) REVERT: L 52 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.5933 (mtmm) REVERT: L 57 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7800 (mptm) REVERT: L 66 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7603 (mp0) REVERT: L 112 LYS cc_start: 0.8566 (mppt) cc_final: 0.7678 (mtmt) REVERT: L 125 ASP cc_start: 0.8137 (t0) cc_final: 0.7848 (t70) REVERT: M 46 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7516 (ptpt) REVERT: N 1 MET cc_start: 0.6037 (ptt) cc_final: 0.5795 (ptt) REVERT: O 1 MET cc_start: 0.6985 (ttp) cc_final: 0.6009 (ptp) REVERT: O 68 LEU cc_start: 0.8434 (mt) cc_final: 0.8128 (mm) REVERT: O 75 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7358 (mt-10) REVERT: O 138 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.6770 (ttm-80) REVERT: P 39 LYS cc_start: 0.7972 (ttpt) cc_final: 0.7216 (mttt) REVERT: P 57 LYS cc_start: 0.7649 (mtmt) cc_final: 0.7360 (mttm) REVERT: P 127 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7123 (mm-30) REVERT: Q 38 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7681 (mm-30) REVERT: Q 39 LYS cc_start: 0.8712 (ttmm) cc_final: 0.8201 (mtpt) REVERT: Q 52 MET cc_start: 0.8133 (mtt) cc_final: 0.7773 (ttm) REVERT: Q 53 LYS cc_start: 0.8168 (mttp) cc_final: 0.7796 (mttt) REVERT: Q 57 LYS cc_start: 0.7875 (mtmt) cc_final: 0.7569 (mttt) REVERT: Q 81 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: Q 125 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6938 (mt-10) REVERT: Q 139 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: R 6 LYS cc_start: 0.8017 (mmtp) cc_final: 0.7693 (mttp) REVERT: R 13 ARG cc_start: 0.7686 (ttm-80) cc_final: 0.7456 (mtp85) REVERT: R 96 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7167 (pt0) REVERT: R 129 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6724 (tm-30) REVERT: S 1 MET cc_start: 0.6677 (ptm) cc_final: 0.6350 (ptt) REVERT: S 96 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7093 (tm-30) REVERT: T 6 LYS cc_start: 0.7931 (mmtp) cc_final: 0.7399 (mtmm) REVERT: T 53 LYS cc_start: 0.8065 (mttp) cc_final: 0.7761 (mttt) REVERT: T 73 GLN cc_start: 0.7547 (mm-40) cc_final: 0.6972 (tp40) REVERT: T 74 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7129 (mp) REVERT: T 75 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7327 (mm-30) REVERT: T 96 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7243 (mt-10) REVERT: T 103 ASP cc_start: 0.8211 (m-30) cc_final: 0.7873 (m-30) REVERT: U 6 LYS cc_start: 0.8092 (mptm) cc_final: 0.7640 (mtmm) REVERT: U 10 GLN cc_start: 0.8045 (mm110) cc_final: 0.7793 (mm110) REVERT: U 33 LYS cc_start: 0.8303 (ttpp) cc_final: 0.7666 (ttpp) REVERT: U 45 TYR cc_start: 0.8159 (t80) cc_final: 0.7378 (t80) REVERT: U 68 LEU cc_start: 0.8789 (mt) cc_final: 0.8546 (mm) REVERT: U 91 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7619 (tt) REVERT: V 13 ARG cc_start: 0.7821 (ttm-80) cc_final: 0.7406 (mtm-85) REVERT: V 33 LYS cc_start: 0.8435 (tttt) cc_final: 0.7782 (ttpp) REVERT: V 76 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7623 (tmmt) REVERT: V 81 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7599 (mt-10) REVERT: V 129 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6423 (tm-30) REVERT: W 6 LYS cc_start: 0.7803 (mmtp) cc_final: 0.7425 (mtmm) REVERT: W 46 LYS cc_start: 0.7593 (pttt) cc_final: 0.7253 (mmmt) REVERT: W 52 MET cc_start: 0.7493 (ttm) cc_final: 0.7051 (ttt) REVERT: W 75 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7336 (mt-10) REVERT: W 88 ASP cc_start: 0.8184 (m-30) cc_final: 0.7915 (m-30) REVERT: W 135 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7958 (mt-10) REVERT: W 151 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: X 1 MET cc_start: 0.6566 (ttp) cc_final: 0.6272 (ptt) REVERT: X 66 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8138 (mt-10) outliers start: 81 outliers final: 27 residues processed: 865 average time/residue: 0.7330 time to fit residues: 735.5641 Evaluate side-chains 856 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 803 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 57 LYS Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 17 CYS Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 139 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 74 LEU Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 76 LYS Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 119 LEU Chi-restraints excluded: chain W residue 151 GLN Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain X residue 94 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 243 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 190 optimal weight: 0.5980 chunk 39 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 ASN A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN D 115 GLN E 70 ASN E 115 GLN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 HIS F 138 GLN G 149 ASN I 149 ASN J 89 ASN K 60 GLN K 89 ASN K 115 GLN L 60 GLN L 115 GLN M 148 ASN N 70 ASN O 10 GLN O 148 ASN P 73 GLN P 148 ASN Q 148 ASN R 148 ASN T 42 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.144231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.131997 restraints weight = 29416.664| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.22 r_work: 0.3378 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.618 31374 Z= 0.123 Angle : 0.498 16.857 42360 Z= 0.236 Chirality : 0.033 0.146 4656 Planarity : 0.002 0.033 5484 Dihedral : 5.423 88.768 4116 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.38 % Allowed : 15.43 % Favored : 82.19 % 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: 4.31 (0.13), residues: 3696 helix: 3.37 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.66 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 74 TYR 0.024 0.001 TYR K 133 PHE 0.025 0.002 PHE U 26 TRP 0.005 0.001 TRP S 133 HIS 0.009 0.001 HIS T 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (31368) covalent geometry : angle 0.49818 / 0.24 (42360) hydrogen bonds : bond 0.04019 / 2.70 ( 2652) hydrogen bonds : angle 3.49068 / 2.49 ( 7956) Misc. bond : bond 0.46752 / 23.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 842 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7997 (mt-10) REVERT: A 47 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7171 (mm-30) REVERT: A 115 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: A 126 ASP cc_start: 0.7894 (m-30) cc_final: 0.7651 (t0) REVERT: B 43 ARG cc_start: 0.7649 (tpt170) cc_final: 0.7294 (tpt170) REVERT: B 112 LYS cc_start: 0.8197 (mptt) cc_final: 0.7545 (mtmt) REVERT: C 22 MET cc_start: 0.7693 (ttp) cc_final: 0.7344 (ttm) REVERT: C 50 ASP cc_start: 0.7343 (m-30) cc_final: 0.6617 (t0) REVERT: C 66 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7575 (mp0) REVERT: C 75 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7840 (mt-10) REVERT: D 1 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7209 (ptt) REVERT: D 5 LYS cc_start: 0.7301 (mppt) cc_final: 0.6942 (mptp) REVERT: D 24 GLN cc_start: 0.8610 (tt0) cc_final: 0.8270 (tt0) REVERT: D 42 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7142 (mt-10) REVERT: D 52 LYS cc_start: 0.7461 (tptp) cc_final: 0.6017 (mtmm) REVERT: D 66 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: D 88 ARG cc_start: 0.7995 (mtm110) cc_final: 0.7387 (mmt-90) REVERT: D 115 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8147 (mm-40) REVERT: D 117 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7870 (ttt90) REVERT: D 118 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6409 (mt-10) REVERT: D 125 ASP cc_start: 0.8067 (t70) cc_final: 0.7831 (t0) REVERT: E 122 VAL cc_start: 0.8291 (OUTLIER) cc_final: 0.8017 (m) REVERT: E 136 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7945 (mp0) REVERT: F 22 MET cc_start: 0.7846 (ttp) cc_final: 0.7350 (ttp) REVERT: F 52 LYS cc_start: 0.7049 (tptt) cc_final: 0.6705 (tptt) REVERT: F 96 LYS cc_start: 0.7975 (ttpp) cc_final: 0.7685 (tttm) REVERT: F 103 LYS cc_start: 0.7865 (mtmt) cc_final: 0.7411 (ttmt) REVERT: F 118 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6198 (mt-10) REVERT: F 132 MET cc_start: 0.8272 (ttp) cc_final: 0.8054 (ttp) REVERT: G 50 ASP cc_start: 0.6941 (m-30) cc_final: 0.5963 (t0) REVERT: G 66 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7871 (mp0) REVERT: G 96 LYS cc_start: 0.7927 (ttpp) cc_final: 0.7256 (tmtm) REVERT: G 100 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7428 (m-30) REVERT: G 112 LYS cc_start: 0.8228 (mmtm) cc_final: 0.7840 (mmmt) REVERT: G 115 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: H 57 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7811 (mtpt) REVERT: H 96 LYS cc_start: 0.8185 (tttm) cc_final: 0.7798 (ttpt) REVERT: H 103 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7779 (tttm) REVERT: H 125 ASP cc_start: 0.8120 (t0) cc_final: 0.7822 (t70) REVERT: I 1 MET cc_start: 0.6784 (ptm) cc_final: 0.6446 (ptt) REVERT: I 42 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6998 (mt-10) REVERT: I 50 ASP cc_start: 0.6293 (m-30) cc_final: 0.5657 (t70) REVERT: I 75 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7432 (mm-30) REVERT: I 112 LYS cc_start: 0.8284 (mmtm) cc_final: 0.7576 (mtpm) REVERT: J 1 MET cc_start: 0.6947 (ptm) cc_final: 0.6710 (ptt) REVERT: J 50 ASP cc_start: 0.7174 (m-30) cc_final: 0.6866 (m-30) REVERT: J 57 LYS cc_start: 0.7726 (mtmt) cc_final: 0.7444 (mttm) REVERT: J 103 LYS cc_start: 0.7998 (mtmt) cc_final: 0.7347 (mmtt) REVERT: J 110 GLN cc_start: 0.7543 (mt0) cc_final: 0.7285 (mt0) REVERT: K 1 MET cc_start: 0.7219 (ptm) cc_final: 0.6733 (ptt) REVERT: K 42 GLU cc_start: 0.7559 (mt-10) cc_final: 0.6622 (tm-30) REVERT: K 66 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7985 (mp0) REVERT: K 88 ARG cc_start: 0.7316 (mtm110) cc_final: 0.6907 (mmt180) REVERT: K 103 LYS cc_start: 0.8230 (mtmt) cc_final: 0.7297 (mmtt) REVERT: K 110 GLN cc_start: 0.7646 (tt0) cc_final: 0.7414 (tt0) REVERT: L 1 MET cc_start: 0.6874 (ptm) cc_final: 0.6379 (ptt) REVERT: L 42 GLU cc_start: 0.7699 (mt-10) cc_final: 0.6850 (pp20) REVERT: L 52 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.5892 (mtmm) REVERT: L 66 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7559 (mp0) REVERT: L 112 LYS cc_start: 0.8560 (mppt) cc_final: 0.7695 (mtmt) REVERT: N 1 MET cc_start: 0.6023 (ptt) cc_final: 0.5791 (ptt) REVERT: N 76 LYS cc_start: 0.8481 (tmtt) cc_final: 0.8090 (tptp) REVERT: O 1 MET cc_start: 0.6952 (ttp) cc_final: 0.5982 (ptp) REVERT: O 68 LEU cc_start: 0.8419 (mt) cc_final: 0.8116 (mm) REVERT: O 75 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7376 (mt-10) REVERT: O 138 ARG cc_start: 0.7595 (ttm-80) cc_final: 0.6754 (ttm-80) REVERT: P 39 LYS cc_start: 0.7977 (ttpt) cc_final: 0.7221 (mtmt) REVERT: P 57 LYS cc_start: 0.7633 (mtmt) cc_final: 0.7342 (mttm) REVERT: P 138 ARG cc_start: 0.8071 (ttm170) cc_final: 0.7863 (ttp-170) REVERT: Q 38 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7671 (mm-30) REVERT: Q 39 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8182 (mtpt) REVERT: Q 53 LYS cc_start: 0.8137 (mttp) cc_final: 0.7745 (mttp) REVERT: Q 57 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7556 (mttt) REVERT: Q 81 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: Q 139 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.6906 (tm-30) REVERT: R 6 LYS cc_start: 0.8027 (mmtp) cc_final: 0.7708 (mttp) REVERT: R 13 ARG cc_start: 0.7681 (ttm-80) cc_final: 0.7461 (mtp85) REVERT: R 96 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7194 (pt0) REVERT: R 129 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6735 (tm-30) REVERT: S 1 MET cc_start: 0.6627 (ptm) cc_final: 0.6319 (ptt) REVERT: S 96 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7085 (tm-30) REVERT: T 6 LYS cc_start: 0.7970 (mmtp) cc_final: 0.7453 (mttp) REVERT: T 53 LYS cc_start: 0.8031 (mttp) cc_final: 0.7681 (mtmt) REVERT: T 57 LYS cc_start: 0.8222 (mtmt) cc_final: 0.7674 (mmtt) REVERT: T 73 GLN cc_start: 0.7516 (mm-40) cc_final: 0.6960 (tp40) REVERT: T 75 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7290 (mm-30) REVERT: T 96 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7217 (mt-10) REVERT: T 103 ASP cc_start: 0.8209 (m-30) cc_final: 0.7860 (m-30) REVERT: U 6 LYS cc_start: 0.8068 (mptm) cc_final: 0.7646 (mtmm) REVERT: U 10 GLN cc_start: 0.8032 (mm110) cc_final: 0.7790 (mm110) REVERT: U 33 LYS cc_start: 0.8260 (ttpp) cc_final: 0.7629 (ttpp) REVERT: U 45 TYR cc_start: 0.8092 (t80) cc_final: 0.7310 (t80) REVERT: U 68 LEU cc_start: 0.8768 (mt) cc_final: 0.8524 (mm) REVERT: U 91 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7572 (tt) REVERT: U 112 GLN cc_start: 0.8325 (mp10) cc_final: 0.7808 (mt0) REVERT: U 113 ASP cc_start: 0.8397 (t0) cc_final: 0.8012 (t0) REVERT: V 33 LYS cc_start: 0.8417 (tttt) cc_final: 0.7773 (ttpp) REVERT: V 76 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7633 (tmmt) REVERT: V 81 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7557 (mt-10) REVERT: V 129 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6426 (tm-30) REVERT: W 6 LYS cc_start: 0.7776 (mmtp) cc_final: 0.7374 (mtmm) REVERT: W 46 LYS cc_start: 0.7548 (pttt) cc_final: 0.7243 (mmmt) REVERT: W 75 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7328 (mt-10) REVERT: W 88 ASP cc_start: 0.8199 (m-30) cc_final: 0.7909 (m-30) REVERT: W 135 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7960 (mt-10) REVERT: W 151 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: X 1 MET cc_start: 0.6475 (ttp) cc_final: 0.6200 (ptt) REVERT: X 13 ARG cc_start: 0.7323 (mtm-85) cc_final: 0.6880 (mtm-85) REVERT: X 66 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8117 (mt-10) outliers start: 79 outliers final: 25 residues processed: 879 average time/residue: 0.7346 time to fit residues: 748.8169 Evaluate side-chains 858 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 809 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 17 CYS Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 139 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 74 LEU Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 76 LYS Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 119 LEU Chi-restraints excluded: chain W residue 151 GLN Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain X residue 94 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 136 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 281 optimal weight: 10.0000 chunk 240 optimal weight: 1.9990 chunk 284 optimal weight: 5.9990 chunk 209 optimal weight: 0.8980 chunk 298 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 349 optimal weight: 1.9990 chunk 327 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN C 131 HIS D 115 GLN E 70 ASN E 115 GLN E 152 GLN F 115 GLN G 60 GLN G 149 ASN I 60 GLN I 149 ASN J 89 ASN J 149 ASN K 60 GLN L 60 GLN ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 ASN N 70 ASN O 10 GLN O 148 ASN P 97 GLN P 148 ASN Q 148 ASN R 148 ASN T 42 HIS W 148 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.143560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.131237 restraints weight = 29304.948| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.22 r_work: 0.3363 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.652 31374 Z= 0.142 Angle : 0.525 17.391 42360 Z= 0.251 Chirality : 0.034 0.190 4656 Planarity : 0.003 0.041 5484 Dihedral : 5.384 88.172 4116 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.87 % Allowed : 16.46 % Favored : 81.68 % 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: 4.23 (0.13), residues: 3696 helix: 3.31 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.65 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 13 TYR 0.025 0.002 TYR K 133 PHE 0.027 0.002 PHE S 26 TRP 0.005 0.001 TRP X 133 HIS 0.009 0.001 HIS T 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (31368) covalent geometry : angle 0.52486 / 0.25 (42360) hydrogen bonds : bond 0.04196 / 2.82 ( 2652) hydrogen bonds : angle 3.55256 / 2.53 ( 7956) Misc. bond : bond 0.47350 / 24.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 809 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7186 (mm-30) REVERT: A 115 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: A 126 ASP cc_start: 0.7899 (m-30) cc_final: 0.7665 (t0) REVERT: B 43 ARG cc_start: 0.7679 (tpt170) cc_final: 0.7313 (tpt170) REVERT: B 112 LYS cc_start: 0.8216 (mptt) cc_final: 0.7558 (mtmt) REVERT: C 22 MET cc_start: 0.7702 (ttp) cc_final: 0.7365 (ttm) REVERT: C 50 ASP cc_start: 0.7367 (m-30) cc_final: 0.6644 (t0) REVERT: C 66 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7562 (mp0) REVERT: C 75 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7852 (mt-10) REVERT: D 1 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7183 (ptt) REVERT: D 5 LYS cc_start: 0.7298 (mppt) cc_final: 0.6957 (mptp) REVERT: D 24 GLN cc_start: 0.8634 (tt0) cc_final: 0.8286 (tt0) REVERT: D 42 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7186 (mt-10) REVERT: D 52 LYS cc_start: 0.7362 (tptp) cc_final: 0.6022 (mtmm) REVERT: D 66 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: D 88 ARG cc_start: 0.7969 (mtm110) cc_final: 0.7369 (mmt-90) REVERT: D 117 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7832 (ttt90) REVERT: D 118 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6480 (mt-10) REVERT: E 113 ASP cc_start: 0.8763 (t0) cc_final: 0.8455 (t70) REVERT: E 122 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.8033 (m) REVERT: E 136 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7948 (mp0) REVERT: F 22 MET cc_start: 0.7853 (ttp) cc_final: 0.7365 (ttp) REVERT: F 52 LYS cc_start: 0.7048 (tptt) cc_final: 0.6713 (tptt) REVERT: F 96 LYS cc_start: 0.7990 (ttpp) cc_final: 0.7713 (tttm) REVERT: F 103 LYS cc_start: 0.7882 (mtmt) cc_final: 0.7409 (ttmt) REVERT: F 115 GLN cc_start: 0.8503 (tp40) cc_final: 0.8179 (mm-40) REVERT: F 118 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6223 (mt-10) REVERT: G 50 ASP cc_start: 0.6978 (m-30) cc_final: 0.6010 (t0) REVERT: G 66 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7849 (mp0) REVERT: G 96 LYS cc_start: 0.7944 (ttpp) cc_final: 0.7346 (tmtm) REVERT: G 100 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7412 (m-30) REVERT: G 112 LYS cc_start: 0.8236 (mmtm) cc_final: 0.7842 (mmmt) REVERT: G 115 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: H 57 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7777 (mtpt) REVERT: H 96 LYS cc_start: 0.8198 (tttm) cc_final: 0.7807 (ttpt) REVERT: H 103 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7779 (tttm) REVERT: I 1 MET cc_start: 0.6796 (ptm) cc_final: 0.6468 (ptt) REVERT: I 42 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7021 (mt-10) REVERT: I 50 ASP cc_start: 0.6381 (m-30) cc_final: 0.5698 (t70) REVERT: I 75 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7453 (mm-30) REVERT: I 112 LYS cc_start: 0.8261 (mmtm) cc_final: 0.7554 (mtpm) REVERT: I 113 ASP cc_start: 0.8518 (t0) cc_final: 0.8315 (t0) REVERT: J 50 ASP cc_start: 0.7187 (m-30) cc_final: 0.6870 (m-30) REVERT: J 57 LYS cc_start: 0.7740 (mtmt) cc_final: 0.7462 (mttm) REVERT: J 103 LYS cc_start: 0.8020 (mtmt) cc_final: 0.7372 (mmtt) REVERT: J 110 GLN cc_start: 0.7527 (mt0) cc_final: 0.7265 (mt0) REVERT: K 1 MET cc_start: 0.7222 (ptm) cc_final: 0.6724 (ptt) REVERT: K 42 GLU cc_start: 0.7597 (mt-10) cc_final: 0.6651 (tm-30) REVERT: K 66 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7975 (mp0) REVERT: K 88 ARG cc_start: 0.7333 (mtm110) cc_final: 0.6951 (mmt180) REVERT: K 103 LYS cc_start: 0.8233 (mtmt) cc_final: 0.7295 (mmtt) REVERT: K 110 GLN cc_start: 0.7653 (tt0) cc_final: 0.7425 (tt0) REVERT: L 1 MET cc_start: 0.6830 (ptm) cc_final: 0.6298 (ptm) REVERT: L 42 GLU cc_start: 0.7738 (mt-10) cc_final: 0.6883 (pp20) REVERT: L 52 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.5890 (mtmm) REVERT: L 66 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7586 (mp0) REVERT: L 112 LYS cc_start: 0.8571 (mppt) cc_final: 0.7702 (mtmt) REVERT: L 125 ASP cc_start: 0.8166 (t70) cc_final: 0.7738 (t70) REVERT: N 1 MET cc_start: 0.6071 (ptt) cc_final: 0.5815 (ptt) REVERT: N 76 LYS cc_start: 0.8476 (tmtt) cc_final: 0.8097 (tptp) REVERT: O 1 MET cc_start: 0.6996 (ttp) cc_final: 0.6017 (ptp) REVERT: O 13 ARG cc_start: 0.7216 (mtm180) cc_final: 0.6892 (mtm-85) REVERT: O 68 LEU cc_start: 0.8443 (mt) cc_final: 0.8139 (mm) REVERT: O 75 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7387 (mt-10) REVERT: O 97 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7308 (tp40) REVERT: O 138 ARG cc_start: 0.7606 (ttm-80) cc_final: 0.6759 (ttm-80) REVERT: P 39 LYS cc_start: 0.7983 (ttpt) cc_final: 0.7479 (ttmt) REVERT: P 57 LYS cc_start: 0.7631 (mtmt) cc_final: 0.7339 (mttm) REVERT: P 97 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7102 (tp-100) REVERT: P 127 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7183 (mm-30) REVERT: P 138 ARG cc_start: 0.8070 (ttm170) cc_final: 0.7848 (ttp-170) REVERT: Q 38 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7701 (mm-30) REVERT: Q 39 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8243 (mtpt) REVERT: Q 57 LYS cc_start: 0.7873 (mtmt) cc_final: 0.7566 (mttt) REVERT: Q 81 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: Q 125 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6905 (mt-10) REVERT: Q 139 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.6926 (tm-30) REVERT: R 6 LYS cc_start: 0.8042 (mmtp) cc_final: 0.7725 (mttp) REVERT: R 96 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7238 (pt0) REVERT: R 129 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6729 (tm-30) REVERT: S 1 MET cc_start: 0.6660 (ptm) cc_final: 0.6383 (ptt) REVERT: S 57 LYS cc_start: 0.8108 (mttm) cc_final: 0.7850 (mttp) REVERT: S 96 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7146 (tm-30) REVERT: T 6 LYS cc_start: 0.7943 (mmtp) cc_final: 0.7376 (mtmm) REVERT: T 13 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7107 (ttp-110) REVERT: T 53 LYS cc_start: 0.8005 (mttp) cc_final: 0.7656 (mtmt) REVERT: T 57 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7681 (mmtt) REVERT: T 73 GLN cc_start: 0.7512 (mm-40) cc_final: 0.6952 (tp40) REVERT: T 75 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7277 (mm-30) REVERT: T 96 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7176 (mt-10) REVERT: T 103 ASP cc_start: 0.8231 (m-30) cc_final: 0.7860 (m-30) REVERT: U 10 GLN cc_start: 0.8048 (mm110) cc_final: 0.7794 (mm110) REVERT: U 33 LYS cc_start: 0.8288 (ttpp) cc_final: 0.7755 (ttpp) REVERT: U 45 TYR cc_start: 0.8099 (t80) cc_final: 0.7331 (t80) REVERT: U 68 LEU cc_start: 0.8764 (mt) cc_final: 0.8508 (mm) REVERT: U 91 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7607 (tt) REVERT: U 112 GLN cc_start: 0.8355 (mp10) cc_final: 0.7843 (mt0) REVERT: U 113 ASP cc_start: 0.8463 (t0) cc_final: 0.8085 (t70) REVERT: V 33 LYS cc_start: 0.8416 (tttt) cc_final: 0.7762 (ttpp) REVERT: V 76 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7618 (tmmt) REVERT: V 81 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7575 (mt-10) REVERT: V 129 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6440 (tm-30) REVERT: W 6 LYS cc_start: 0.7776 (mmtp) cc_final: 0.7370 (mtmm) REVERT: W 46 LYS cc_start: 0.7557 (pttt) cc_final: 0.7248 (mmmt) REVERT: W 75 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7342 (mt-10) REVERT: W 88 ASP cc_start: 0.8214 (m-30) cc_final: 0.7940 (m-30) REVERT: W 135 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7941 (mt-10) REVERT: W 151 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: X 1 MET cc_start: 0.6508 (ttp) cc_final: 0.6230 (ptt) outliers start: 62 outliers final: 27 residues processed: 834 average time/residue: 0.7306 time to fit residues: 708.5573 Evaluate side-chains 847 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 795 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 17 CYS Chi-restraints excluded: chain O residue 97 GLN Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 97 GLN Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 139 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 74 LEU Chi-restraints excluded: chain T residue 13 ARG Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 155 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 76 LYS Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 119 LEU Chi-restraints excluded: chain W residue 151 GLN Chi-restraints excluded: chain X residue 94 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 6 optimal weight: 0.9990 chunk 230 optimal weight: 5.9990 chunk 335 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 315 optimal weight: 8.9990 chunk 321 optimal weight: 1.9990 chunk 342 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 273 optimal weight: 0.7980 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN D 115 GLN E 70 ASN G 60 GLN G 149 ASN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 ASN J 89 ASN K 60 GLN K 89 ASN K 115 GLN L 60 GLN ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 ASN N 70 ASN O 10 GLN O 148 ASN P 73 GLN P 97 GLN P 148 ASN Q 148 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.146060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.133940 restraints weight = 29047.612| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.18 r_work: 0.3392 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.620 31374 Z= 0.124 Angle : 0.504 15.733 42360 Z= 0.245 Chirality : 0.033 0.198 4656 Planarity : 0.003 0.050 5484 Dihedral : 5.266 85.337 4116 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.65 % Allowed : 16.82 % Favored : 81.53 % 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: 4.29 (0.13), residues: 3696 helix: 3.35 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.63 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG V 13 TYR 0.025 0.001 TYR K 133 PHE 0.024 0.002 PHE U 26 TRP 0.005 0.001 TRP S 133 HIS 0.009 0.001 HIS T 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (31368) covalent geometry : angle 0.50437 / 0.25 (42360) hydrogen bonds : bond 0.04021 / 2.70 ( 2652) hydrogen bonds : angle 3.50347 / 2.50 ( 7956) Misc. bond : bond 0.42474 / 21.88 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 824 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7983 (mt-10) REVERT: A 47 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7037 (mm-30) REVERT: A 115 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7112 (tm-30) REVERT: A 126 ASP cc_start: 0.7775 (m-30) cc_final: 0.7558 (t0) REVERT: B 43 ARG cc_start: 0.7569 (tpt170) cc_final: 0.7187 (tpt170) REVERT: B 112 LYS cc_start: 0.8089 (mptt) cc_final: 0.7430 (mtmt) REVERT: C 22 MET cc_start: 0.7572 (ttp) cc_final: 0.7200 (ttm) REVERT: C 50 ASP cc_start: 0.7274 (m-30) cc_final: 0.6521 (t0) REVERT: C 66 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7490 (mp0) REVERT: C 75 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7835 (mt-10) REVERT: D 1 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7087 (ptt) REVERT: D 5 LYS cc_start: 0.7216 (mppt) cc_final: 0.6893 (mptp) REVERT: D 24 GLN cc_start: 0.8543 (tt0) cc_final: 0.8174 (tt0) REVERT: D 42 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7101 (mt-10) REVERT: D 52 LYS cc_start: 0.7304 (tptp) cc_final: 0.5863 (mtmm) REVERT: D 66 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: D 88 ARG cc_start: 0.7855 (mtm110) cc_final: 0.7234 (mmt-90) REVERT: D 117 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7709 (ttt90) REVERT: D 118 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6330 (mt-10) REVERT: D 125 ASP cc_start: 0.8010 (t70) cc_final: 0.7792 (t0) REVERT: E 122 VAL cc_start: 0.8177 (OUTLIER) cc_final: 0.7906 (m) REVERT: E 136 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7878 (mp0) REVERT: F 22 MET cc_start: 0.7718 (ttp) cc_final: 0.7188 (ttp) REVERT: F 52 LYS cc_start: 0.6989 (tptt) cc_final: 0.6664 (tptt) REVERT: F 96 LYS cc_start: 0.7900 (ttpp) cc_final: 0.7607 (tttm) REVERT: F 103 LYS cc_start: 0.7756 (mtmt) cc_final: 0.7264 (ttmt) REVERT: F 118 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.6086 (mt-10) REVERT: G 50 ASP cc_start: 0.6880 (m-30) cc_final: 0.5871 (t0) REVERT: G 66 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7805 (mp0) REVERT: G 96 LYS cc_start: 0.7846 (ttpp) cc_final: 0.7124 (tmtm) REVERT: G 100 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7288 (m-30) REVERT: G 112 LYS cc_start: 0.8164 (mmtm) cc_final: 0.7757 (mmmt) REVERT: G 115 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: H 57 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7679 (mtpt) REVERT: H 66 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7860 (mt-10) REVERT: H 96 LYS cc_start: 0.8082 (tttm) cc_final: 0.7678 (ttpt) REVERT: H 103 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7662 (tttm) REVERT: H 125 ASP cc_start: 0.8088 (t0) cc_final: 0.7762 (t70) REVERT: I 1 MET cc_start: 0.6706 (ptm) cc_final: 0.6371 (ptt) REVERT: I 42 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6966 (mt-10) REVERT: I 50 ASP cc_start: 0.6258 (m-30) cc_final: 0.5552 (t70) REVERT: I 75 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7342 (mm-30) REVERT: I 112 LYS cc_start: 0.8209 (mmtm) cc_final: 0.7505 (mtpm) REVERT: I 113 ASP cc_start: 0.8472 (t0) cc_final: 0.8251 (t0) REVERT: J 57 LYS cc_start: 0.7609 (mtmt) cc_final: 0.7312 (mttm) REVERT: J 103 LYS cc_start: 0.7902 (mtmt) cc_final: 0.7190 (mmtt) REVERT: J 110 GLN cc_start: 0.7482 (mt0) cc_final: 0.7221 (mt0) REVERT: K 1 MET cc_start: 0.7164 (ptm) cc_final: 0.6676 (ptt) REVERT: K 42 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6526 (tm-30) REVERT: K 66 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7901 (mp0) REVERT: K 88 ARG cc_start: 0.7203 (mtm110) cc_final: 0.6793 (mmt180) REVERT: K 103 LYS cc_start: 0.8102 (mtmt) cc_final: 0.7132 (mmtt) REVERT: K 110 GLN cc_start: 0.7575 (tt0) cc_final: 0.7326 (tt0) REVERT: L 1 MET cc_start: 0.6763 (ptm) cc_final: 0.6230 (ptm) REVERT: L 42 GLU cc_start: 0.7623 (mt-10) cc_final: 0.6764 (pp20) REVERT: L 52 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.5724 (mtmm) REVERT: L 66 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7455 (mp0) REVERT: L 112 LYS cc_start: 0.8510 (mppt) cc_final: 0.7638 (mtmt) REVERT: N 1 MET cc_start: 0.5926 (ptt) cc_final: 0.5681 (ptt) REVERT: N 76 LYS cc_start: 0.8435 (tmtt) cc_final: 0.8050 (tptp) REVERT: O 1 MET cc_start: 0.6932 (ttp) cc_final: 0.5958 (ptp) REVERT: O 13 ARG cc_start: 0.7025 (mtm180) cc_final: 0.6700 (mtm-85) REVERT: O 68 LEU cc_start: 0.8388 (mt) cc_final: 0.8074 (mm) REVERT: O 75 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7349 (mt-10) REVERT: O 97 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7256 (tp40) REVERT: O 138 ARG cc_start: 0.7523 (ttm-80) cc_final: 0.6659 (ttm-80) REVERT: P 39 LYS cc_start: 0.7897 (ttpt) cc_final: 0.7346 (ttmt) REVERT: P 57 LYS cc_start: 0.7470 (mtmt) cc_final: 0.7163 (mttm) REVERT: P 97 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.6955 (tp-100) REVERT: Q 39 LYS cc_start: 0.8659 (ttmm) cc_final: 0.8168 (mtpt) REVERT: Q 53 LYS cc_start: 0.7940 (mttp) cc_final: 0.7550 (mttp) REVERT: Q 57 LYS cc_start: 0.7765 (mtmt) cc_final: 0.7446 (mttt) REVERT: Q 81 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: Q 139 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: R 6 LYS cc_start: 0.7964 (mmtp) cc_final: 0.7629 (mttp) REVERT: R 96 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7082 (pt0) REVERT: R 129 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6603 (tm-30) REVERT: S 1 MET cc_start: 0.6580 (ptm) cc_final: 0.6303 (ptt) REVERT: S 57 LYS cc_start: 0.8020 (mttm) cc_final: 0.7761 (mttp) REVERT: S 96 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7022 (tm-30) REVERT: T 6 LYS cc_start: 0.7809 (mmtp) cc_final: 0.7232 (mtmm) REVERT: T 53 LYS cc_start: 0.7875 (mttp) cc_final: 0.7526 (mtmt) REVERT: T 57 LYS cc_start: 0.8106 (mtmt) cc_final: 0.7538 (mmtp) REVERT: T 73 GLN cc_start: 0.7448 (mm-40) cc_final: 0.6878 (tp40) REVERT: T 75 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7262 (mm-30) REVERT: T 96 GLU cc_start: 0.7313 (tm-30) cc_final: 0.7072 (mt-10) REVERT: T 103 ASP cc_start: 0.8143 (m-30) cc_final: 0.7768 (m-30) REVERT: U 6 LYS cc_start: 0.7955 (mptm) cc_final: 0.7517 (mtmm) REVERT: U 10 GLN cc_start: 0.7936 (mm110) cc_final: 0.7680 (mm110) REVERT: U 33 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7560 (ttpp) REVERT: U 45 TYR cc_start: 0.7987 (t80) cc_final: 0.7186 (t80) REVERT: U 68 LEU cc_start: 0.8714 (mt) cc_final: 0.8456 (mm) REVERT: U 91 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7441 (tt) REVERT: U 113 ASP cc_start: 0.8412 (t0) cc_final: 0.8013 (t70) REVERT: V 33 LYS cc_start: 0.8326 (tttt) cc_final: 0.7647 (ttpp) REVERT: V 76 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7603 (tmmt) REVERT: V 81 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7522 (mt-10) REVERT: V 129 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6293 (tm-30) REVERT: W 6 LYS cc_start: 0.7721 (mmtp) cc_final: 0.7294 (mtmm) REVERT: W 46 LYS cc_start: 0.7450 (pttt) cc_final: 0.7120 (mmmt) REVERT: W 52 MET cc_start: 0.7240 (ttm) cc_final: 0.6896 (ttt) REVERT: W 75 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7240 (mt-10) REVERT: W 88 ASP cc_start: 0.8109 (m-30) cc_final: 0.7806 (m-30) REVERT: W 135 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7875 (mt-10) REVERT: W 151 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: X 1 MET cc_start: 0.6458 (ttp) cc_final: 0.6183 (ptt) outliers start: 55 outliers final: 28 residues processed: 846 average time/residue: 0.7416 time to fit residues: 729.1743 Evaluate side-chains 855 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 804 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 17 CYS Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 97 GLN Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 97 GLN Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 139 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 74 LEU Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 76 LYS Chi-restraints excluded: chain W residue 74 LEU Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 119 LEU Chi-restraints excluded: chain W residue 151 GLN Chi-restraints excluded: chain X residue 94 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 128 optimal weight: 0.9990 chunk 288 optimal weight: 0.7980 chunk 307 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 177 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 168 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN C 78 ASN D 115 GLN E 115 GLN F 115 GLN G 149 ASN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 HIS I 149 ASN J 89 ASN K 60 GLN K 115 GLN L 60 GLN ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 ASN N 70 ASN O 10 GLN O 148 ASN P 148 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.147187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.135003 restraints weight = 29331.097| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.19 r_work: 0.3412 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.682 31374 Z= 0.119 Angle : 0.527 22.898 42360 Z= 0.247 Chirality : 0.033 0.214 4656 Planarity : 0.002 0.030 5484 Dihedral : 5.206 83.801 4116 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.62 % Allowed : 17.27 % Favored : 81.11 % 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: 4.33 (0.13), residues: 3696 helix: 3.38 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.60 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 74 TYR 0.025 0.001 TYR K 133 PHE 0.025 0.002 PHE S 26 TRP 0.006 0.001 TRP N 133 HIS 0.009 0.001 HIS T 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (31368) covalent geometry : angle 0.52689 / 0.25 (42360) hydrogen bonds : bond 0.03935 / 2.64 ( 2652) hydrogen bonds : angle 3.48003 / 2.49 ( 7956) Misc. bond : bond 0.46804 / 23.45 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15093.84 seconds wall clock time: 256 minutes 59.95 seconds (15419.95 seconds total)