Starting phenix.real_space_refine on Mon Aug 25 17:48:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iig_60594/08_2025/9iig_60594_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iig_60594/08_2025/9iig_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_60594/08_2025/9iig_60594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iig_60594/08_2025/9iig_60594.map" model { file = "/net/cci-nas-00/data/ceres_data/9iig_60594/08_2025/9iig_60594_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iig_60594/08_2025/9iig_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-2.0-5787/lib/python3.9/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, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 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: 7.20, per 1000 atoms: 0.23 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: 2.81 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.79 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: 5.77 Time building geometry restraints manager: 3.69 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: 0.10 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: 0.000 Normalize map: mean=0, sd=1: 6.040 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: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 28.530 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.150 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: 0.010 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 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 aren 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 covalent geometry : bond 0.00817 (31368) covalent geometry : angle 0.74121 (42360) hydrogen bonds : bond 0.09209 ( 2652) hydrogen bonds : angle 5.14087 ( 7956) Misc. bond : bond 0.12702 ( 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 : 1.310 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: 0.8145 time to fit residues: 1047.9435 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 : 1.287 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 GLN L 110 GLN L 115 GLN ** L 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 70 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 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: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.148765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.137599 restraints weight = 28870.132| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.07 r_work: 0.3450 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.588 31374 Z= 0.135 Angle : 0.507 13.900 42360 Z= 0.247 Chirality : 0.032 0.128 4656 Planarity : 0.004 0.039 5484 Dihedral : 6.353 86.947 4118 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.14 % Allowed : 10.65 % Favored : 87.21 % 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 aren not related in a simple way. whole: 2.84 (0.13), residues: 3696 helix: 2.37 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.91 (0.20), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 74 TYR 0.020 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 covalent geometry : bond 0.00290 (31368) covalent geometry : angle 0.50743 (42360) hydrogen bonds : bond 0.04099 ( 2652) hydrogen bonds : angle 3.89392 ( 7956) Misc. bond : bond 0.46026 ( 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 979 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 908 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7076 (mm-30) REVERT: A 115 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7243 (tm-30) REVERT: B 39 GLU cc_start: 0.7720 (tt0) cc_final: 0.7483 (tt0) REVERT: B 43 ARG cc_start: 0.7599 (tpt170) cc_final: 0.7204 (tpt170) REVERT: B 112 LYS cc_start: 0.8131 (mptt) cc_final: 0.7400 (mmmt) REVERT: C 1 MET cc_start: 0.6684 (ptm) cc_final: 0.6266 (ptm) REVERT: C 43 ARG cc_start: 0.7359 (tpt170) cc_final: 0.7120 (tpt170) REVERT: C 50 ASP cc_start: 0.7256 (m-30) cc_final: 0.6778 (t0) REVERT: C 52 LYS cc_start: 0.6789 (tptt) cc_final: 0.5914 (mtmm) REVERT: C 66 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7556 (mp0) REVERT: C 112 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7447 (mmmt) REVERT: D 1 MET cc_start: 0.7842 (ptp) cc_final: 0.7023 (ptt) REVERT: D 52 LYS cc_start: 0.6919 (tptt) cc_final: 0.5720 (mtmm) REVERT: D 66 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: D 115 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7556 (tm130) REVERT: D 117 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7780 (ttt90) REVERT: E 115 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.6442 (tm-30) REVERT: E 122 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.8027 (m) REVERT: F 22 MET cc_start: 0.7784 (ttp) cc_final: 0.7322 (ttm) REVERT: F 47 GLU cc_start: 0.7402 (tp30) cc_final: 0.6744 (tp30) REVERT: F 52 LYS cc_start: 0.6883 (tptt) cc_final: 0.6590 (tptt) REVERT: F 103 LYS cc_start: 0.7863 (mtmt) cc_final: 0.7394 (ttpt) REVERT: G 13 ARG cc_start: 0.7468 (mtm110) cc_final: 0.7208 (mtm-85) REVERT: G 66 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7870 (mp0) REVERT: G 96 LYS cc_start: 0.7896 (ttpp) cc_final: 0.7386 (tmtm) REVERT: G 100 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7192 (m-30) REVERT: G 115 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: G 125 ASP cc_start: 0.7844 (t70) cc_final: 0.7565 (t0) REVERT: H 1 MET cc_start: 0.7189 (ptp) cc_final: 0.6958 (ptt) REVERT: I 9 ASP cc_start: 0.7961 (m-30) cc_final: 0.7656 (m-30) REVERT: I 50 ASP cc_start: 0.6463 (m-30) cc_final: 0.5870 (t0) REVERT: I 75 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7429 (mm-30) REVERT: J 50 ASP cc_start: 0.7135 (m-30) cc_final: 0.6890 (m-30) REVERT: J 57 LYS cc_start: 0.7666 (mtmt) cc_final: 0.7377 (mttm) REVERT: J 96 LYS cc_start: 0.7887 (ttpp) cc_final: 0.7525 (ttpp) REVERT: J 103 LYS cc_start: 0.7883 (mtmt) cc_final: 0.7290 (mmtt) REVERT: J 110 GLN cc_start: 0.7547 (mt0) cc_final: 0.7193 (mt0) REVERT: K 1 MET cc_start: 0.6928 (ptm) cc_final: 0.6687 (ptm) REVERT: K 66 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7872 (mp0) REVERT: K 88 ARG cc_start: 0.7223 (mtm110) cc_final: 0.6790 (mmt180) REVERT: K 103 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7153 (mmtt) REVERT: L 1 MET cc_start: 0.6938 (ptm) cc_final: 0.6543 (ptp) REVERT: L 22 MET cc_start: 0.7339 (ttp) cc_final: 0.6934 (mtp) REVERT: L 112 LYS cc_start: 0.8445 (mppt) cc_final: 0.7552 (mmmt) REVERT: L 152 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8430 (tt0) REVERT: O 1 MET cc_start: 0.6821 (ttp) cc_final: 0.6231 (ptp) REVERT: O 13 ARG cc_start: 0.7355 (ttm-80) cc_final: 0.7087 (ttm110) REVERT: O 50 GLU cc_start: 0.7460 (tt0) cc_final: 0.7257 (tt0) REVERT: O 68 LEU cc_start: 0.8433 (mt) cc_final: 0.8164 (mm) REVERT: O 96 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7036 (tm-30) REVERT: O 138 ARG cc_start: 0.7488 (ttm-80) cc_final: 0.6789 (ttm-80) REVERT: P 1 MET cc_start: 0.7155 (ttp) cc_final: 0.6772 (ttp) REVERT: P 38 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8045 (mm-30) REVERT: P 57 LYS cc_start: 0.7587 (mtmt) cc_final: 0.7301 (mttt) REVERT: P 76 LYS cc_start: 0.7713 (mmtt) cc_final: 0.7260 (tmtt) REVERT: Q 57 LYS cc_start: 0.7823 (mtmt) cc_final: 0.7553 (mttt) REVERT: Q 81 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: Q 125 GLU cc_start: 0.7164 (pt0) cc_final: 0.6696 (mt-10) REVERT: R 1 MET cc_start: 0.6923 (ttp) cc_final: 0.6691 (ttp) REVERT: R 6 LYS cc_start: 0.8031 (mmtp) cc_final: 0.7752 (mttp) REVERT: R 97 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7056 (tm-30) REVERT: R 129 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6762 (mt-10) REVERT: S 6 LYS cc_start: 0.8245 (mmtp) cc_final: 0.7849 (mptt) REVERT: S 45 TYR cc_start: 0.7844 (t80) cc_final: 0.7607 (t80) REVERT: S 73 GLN cc_start: 0.6903 (mm110) cc_final: 0.6648 (tt0) REVERT: S 96 GLU cc_start: 0.7192 (tm-30) cc_final: 0.6927 (tm-30) REVERT: T 6 LYS cc_start: 0.7883 (mmtp) cc_final: 0.7347 (mtmm) REVERT: T 13 ARG cc_start: 0.7395 (ttm-80) cc_final: 0.6859 (mtm-85) REVERT: T 53 LYS cc_start: 0.7980 (mttp) cc_final: 0.7648 (mttt) REVERT: T 73 GLN cc_start: 0.7467 (mm-40) cc_final: 0.6796 (tp40) REVERT: T 75 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7606 (mm-30) REVERT: T 96 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7192 (tt0) REVERT: T 103 ASP cc_start: 0.8048 (m-30) cc_final: 0.7664 (m-30) REVERT: T 127 GLU cc_start: 0.6745 (mm-30) cc_final: 0.6321 (mm-30) REVERT: U 10 GLN cc_start: 0.8017 (mm110) cc_final: 0.7775 (mm110) REVERT: U 39 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7886 (mttm) REVERT: U 68 LEU cc_start: 0.8736 (mt) cc_final: 0.8468 (mm) REVERT: U 96 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7264 (tt0) REVERT: U 126 ASP cc_start: 0.7921 (m-30) cc_final: 0.7650 (m-30) REVERT: V 13 ARG cc_start: 0.7697 (ttm110) cc_final: 0.7266 (mtm-85) REVERT: V 33 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7673 (ttpp) REVERT: V 81 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7505 (mt-10) REVERT: V 129 GLU cc_start: 0.6624 (mt-10) cc_final: 0.6316 (tm-30) REVERT: W 6 LYS cc_start: 0.7837 (mmtp) cc_final: 0.7380 (mtmm) REVERT: W 13 ARG cc_start: 0.7861 (mtm-85) cc_final: 0.7614 (mtt90) REVERT: W 46 LYS cc_start: 0.7517 (pttt) cc_final: 0.7192 (mmmt) REVERT: W 66 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7588 (mm-30) REVERT: W 88 ASP cc_start: 0.8115 (m-30) cc_final: 0.7837 (m-30) REVERT: W 100 LEU cc_start: 0.8367 (tt) cc_final: 0.8063 (tp) REVERT: W 129 GLU cc_start: 0.6652 (mt-10) cc_final: 0.6090 (pt0) REVERT: W 135 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7912 (mt-10) REVERT: W 151 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: X 6 LYS cc_start: 0.7859 (mmtp) cc_final: 0.7191 (mmpt) REVERT: X 66 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8056 (mt-10) outliers start: 71 outliers final: 9 residues processed: 938 average time/residue: 0.7628 time to fit residues: 826.1020 Evaluate side-chains 841 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 815 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 100 ASP 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 39 LYS Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U 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 66 GLU 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: 10.0000 chunk 170 optimal weight: 8.9990 chunk 259 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 322 optimal weight: 10.0000 chunk 297 optimal weight: 0.9980 chunk 272 optimal weight: 8.9990 chunk 299 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 110 GLN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN B 115 GLN B 149 ASN C 60 GLN D 138 GLN E 149 ASN ** 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 L 149 ASN M 70 ASN N 70 ASN N 151 GLN O 148 ASN P 73 GLN P 130 HIS Q 112 GLN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 148 ASN T 41 ASN T 42 HIS V 148 ASN ** X 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.134259 restraints weight = 29311.225| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.22 r_work: 0.3400 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.573 31374 Z= 0.123 Angle : 0.487 15.420 42360 Z= 0.231 Chirality : 0.032 0.142 4656 Planarity : 0.003 0.032 5484 Dihedral : 5.963 88.896 4116 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.32 % Allowed : 12.64 % Favored : 85.05 % 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 aren not related in a simple way. whole: 3.89 (0.13), residues: 3696 helix: 3.10 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.84 (0.20), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 74 TYR 0.018 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 covalent geometry : bond 0.00262 (31368) covalent geometry : angle 0.48704 (42360) hydrogen bonds : bond 0.03977 ( 2652) hydrogen bonds : angle 3.63493 ( 7956) Misc. bond : bond 0.47215 ( 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 938 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 861 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7051 (mm-30) REVERT: A 115 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7272 (tm-30) REVERT: B 39 GLU cc_start: 0.7699 (tt0) cc_final: 0.7495 (tt0) REVERT: C 1 MET cc_start: 0.6792 (ptm) cc_final: 0.6296 (ptm) REVERT: C 50 ASP cc_start: 0.7356 (m-30) cc_final: 0.6698 (t0) REVERT: C 52 LYS cc_start: 0.6818 (tptt) cc_final: 0.5944 (mtmm) REVERT: C 66 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7513 (mp0) REVERT: C 112 LYS cc_start: 0.8010 (mmtm) cc_final: 0.7399 (mmmt) REVERT: C 118 GLU cc_start: 0.7426 (mp0) cc_final: 0.7216 (mp0) REVERT: D 1 MET cc_start: 0.7877 (ptp) cc_final: 0.7195 (ptt) REVERT: D 5 LYS cc_start: 0.7376 (mppt) cc_final: 0.6456 (tttp) REVERT: D 24 GLN cc_start: 0.8579 (tt0) cc_final: 0.8205 (tt0) REVERT: D 52 LYS cc_start: 0.6980 (tptt) cc_final: 0.5731 (mtmm) REVERT: D 66 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: D 78 ASN cc_start: 0.7109 (t0) cc_final: 0.6828 (m-40) REVERT: D 100 ASP cc_start: 0.7525 (t0) cc_final: 0.7242 (m-30) REVERT: D 118 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6481 (mt-10) REVERT: D 133 TYR cc_start: 0.7161 (t80) cc_final: 0.6914 (t80) REVERT: E 115 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.6320 (tm-30) REVERT: E 122 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.8021 (m) REVERT: F 47 GLU cc_start: 0.7434 (tp30) cc_final: 0.6885 (tp30) REVERT: F 52 LYS cc_start: 0.6916 (tptt) cc_final: 0.6693 (tptt) REVERT: F 103 LYS cc_start: 0.7885 (mtmt) cc_final: 0.7399 (ttmt) REVERT: F 115 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7720 (tm130) REVERT: G 13 ARG cc_start: 0.7532 (mtm110) cc_final: 0.7255 (mtm-85) REVERT: G 50 ASP cc_start: 0.6972 (m-30) cc_final: 0.6015 (t0) REVERT: G 66 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7858 (mp0) REVERT: G 96 LYS cc_start: 0.7942 (ttpp) cc_final: 0.7254 (tmtm) REVERT: G 100 ASP cc_start: 0.7693 (t0) cc_final: 0.7336 (m-30) REVERT: G 115 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: H 103 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7775 (tttm) REVERT: I 1 MET cc_start: 0.6818 (ptm) cc_final: 0.6442 (ptm) REVERT: I 9 ASP cc_start: 0.7969 (m-30) cc_final: 0.7674 (m-30) REVERT: I 50 ASP cc_start: 0.6470 (m-30) cc_final: 0.5813 (t70) REVERT: I 75 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7419 (mm-30) REVERT: I 112 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7380 (mmmt) REVERT: J 1 MET cc_start: 0.6876 (ptm) cc_final: 0.6502 (ptt) REVERT: J 57 LYS cc_start: 0.7707 (mtmt) cc_final: 0.7408 (mttm) REVERT: J 96 LYS cc_start: 0.7943 (ttpp) cc_final: 0.7571 (ttpp) REVERT: J 103 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7320 (mmtt) REVERT: J 110 GLN cc_start: 0.7545 (mt0) cc_final: 0.7215 (mt0) REVERT: K 1 MET cc_start: 0.6931 (ptm) cc_final: 0.6722 (ptm) REVERT: K 52 LYS cc_start: 0.6625 (tptt) cc_final: 0.5477 (mtmm) REVERT: K 66 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7880 (mp0) REVERT: K 88 ARG cc_start: 0.7279 (mtm110) cc_final: 0.6788 (mmt180) REVERT: K 103 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7175 (mmtt) REVERT: L 1 MET cc_start: 0.6888 (ptm) cc_final: 0.6394 (ptm) REVERT: L 52 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.5938 (mtmm) REVERT: L 112 LYS cc_start: 0.8510 (mppt) cc_final: 0.7646 (mmmt) REVERT: L 152 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8542 (tt0) REVERT: M 107 LEU cc_start: 0.8405 (tt) cc_final: 0.8197 (tm) REVERT: N 76 LYS cc_start: 0.8537 (tmtt) cc_final: 0.8302 (tmtt) REVERT: O 1 MET cc_start: 0.6810 (ttp) cc_final: 0.6116 (ptp) REVERT: O 13 ARG cc_start: 0.7447 (ttm-80) cc_final: 0.7031 (mtm110) REVERT: O 68 LEU cc_start: 0.8445 (mt) cc_final: 0.8158 (mm) REVERT: O 96 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7054 (tm-30) REVERT: O 138 ARG cc_start: 0.7531 (ttm-80) cc_final: 0.6768 (ttm-80) REVERT: P 1 MET cc_start: 0.7253 (ttp) cc_final: 0.6902 (ttp) REVERT: P 38 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8082 (mm-30) REVERT: P 57 LYS cc_start: 0.7611 (mtmt) cc_final: 0.7326 (mttt) REVERT: P 76 LYS cc_start: 0.7775 (mmtt) cc_final: 0.7304 (tmtt) REVERT: Q 57 LYS cc_start: 0.7842 (mtmt) cc_final: 0.7563 (mttt) REVERT: Q 81 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: Q 139 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: R 6 LYS cc_start: 0.8005 (mmtp) cc_final: 0.7694 (mttp) REVERT: R 85 GLU cc_start: 0.8151 (tt0) cc_final: 0.7838 (tt0) REVERT: R 97 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7115 (tm-30) REVERT: R 129 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6952 (mt-10) REVERT: S 6 LYS cc_start: 0.8211 (mmtp) cc_final: 0.7776 (mmtm) REVERT: S 45 TYR cc_start: 0.7885 (t80) cc_final: 0.7621 (t80) REVERT: S 96 GLU cc_start: 0.7308 (tm-30) cc_final: 0.7007 (tm-30) REVERT: T 6 LYS cc_start: 0.7888 (mmtp) cc_final: 0.7399 (mttp) REVERT: T 13 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.6990 (mtm-85) REVERT: T 53 LYS cc_start: 0.8047 (mttp) cc_final: 0.7718 (mttt) REVERT: T 73 GLN cc_start: 0.7468 (mm-40) cc_final: 0.6862 (tp-100) REVERT: T 75 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7448 (mm-30) REVERT: T 96 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7187 (tt0) REVERT: T 103 ASP cc_start: 0.8160 (m-30) cc_final: 0.7777 (m-30) REVERT: U 10 GLN cc_start: 0.8082 (mm110) cc_final: 0.7832 (mm110) REVERT: U 39 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7973 (mttm) REVERT: U 68 LEU cc_start: 0.8726 (mt) cc_final: 0.8474 (mm) REVERT: U 74 LEU cc_start: 0.7785 (mt) cc_final: 0.7575 (tp) REVERT: U 126 ASP cc_start: 0.8024 (m-30) cc_final: 0.7751 (m-30) REVERT: V 13 ARG cc_start: 0.7709 (ttm110) cc_final: 0.7309 (mtm-85) REVERT: V 33 LYS cc_start: 0.8335 (tttt) cc_final: 0.7632 (ttpp) REVERT: V 81 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7435 (mt-10) REVERT: V 85 GLU cc_start: 0.8530 (tt0) cc_final: 0.8297 (tt0) REVERT: V 96 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7154 (pt0) REVERT: V 129 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6374 (tm-30) REVERT: W 6 LYS cc_start: 0.7834 (mmtp) cc_final: 0.7335 (mtmm) REVERT: W 46 LYS cc_start: 0.7556 (pttt) cc_final: 0.7196 (mmmt) REVERT: W 66 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7632 (mm-30) REVERT: W 88 ASP cc_start: 0.8153 (m-30) cc_final: 0.7872 (m-30) REVERT: W 100 LEU cc_start: 0.8352 (tt) cc_final: 0.8055 (tp) REVERT: W 135 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7923 (mt-10) REVERT: W 151 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: X 6 LYS cc_start: 0.7820 (mmtp) cc_final: 0.7115 (mmpt) REVERT: X 39 LYS cc_start: 0.8322 (ttmt) cc_final: 0.8098 (mttt) outliers start: 77 outliers final: 18 residues processed: 891 average time/residue: 0.7830 time to fit residues: 807.1584 Evaluate side-chains 838 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 804 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN 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 5 LYS Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 152 GLN 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 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 39 LYS Chi-restraints excluded: chain U residue 84 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 34 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 297 optimal weight: 0.8980 chunk 287 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 110 GLN A 149 ASN B 110 GLN B 115 GLN B 149 ASN C 60 GLN D 115 GLN F 138 GLN G 60 GLN G 149 ASN H 115 GLN H 149 ASN H 152 GLN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN L 60 GLN L 115 GLN M 148 ASN N 70 ASN O 148 ASN P 73 GLN R 148 ASN S 148 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 = 0.3641 r_free = 0.3641 target = 0.145776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.133177 restraints weight = 29031.212| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.24 r_work: 0.3377 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.586 31374 Z= 0.131 Angle : 0.499 18.147 42360 Z= 0.233 Chirality : 0.033 0.115 4656 Planarity : 0.003 0.036 5484 Dihedral : 5.785 88.439 4116 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.32 % Allowed : 13.24 % Favored : 84.45 % 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 aren 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 0.005 0.001 ARG C 74 TYR 0.020 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 covalent geometry : bond 0.00287 (31368) covalent geometry : angle 0.49876 (42360) hydrogen bonds : bond 0.04082 ( 2652) hydrogen bonds : angle 3.56417 ( 7956) Misc. bond : bond 0.48587 ( 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 913 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 836 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7119 (mm-30) REVERT: A 115 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: B 39 GLU cc_start: 0.7727 (tt0) cc_final: 0.7471 (tt0) REVERT: B 43 ARG cc_start: 0.7685 (tpt170) cc_final: 0.7336 (tpt170) REVERT: B 112 LYS cc_start: 0.8137 (mptt) cc_final: 0.7478 (mtmt) REVERT: C 1 MET cc_start: 0.6906 (ptm) cc_final: 0.6381 (ptm) REVERT: C 50 ASP cc_start: 0.7391 (m-30) cc_final: 0.6682 (t0) REVERT: C 52 LYS cc_start: 0.6848 (tptt) cc_final: 0.5964 (mtmm) REVERT: C 66 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7588 (mp0) REVERT: C 112 LYS cc_start: 0.7982 (mmtm) cc_final: 0.7370 (mmmt) REVERT: D 1 MET cc_start: 0.7898 (ptp) cc_final: 0.7216 (ptt) REVERT: D 5 LYS cc_start: 0.7346 (mppt) cc_final: 0.6445 (tttp) REVERT: D 52 LYS cc_start: 0.7023 (tptt) cc_final: 0.5776 (mtmm) REVERT: D 66 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8101 (mp0) REVERT: D 88 ARG cc_start: 0.7881 (mtm110) cc_final: 0.7274 (mmt-90) REVERT: D 117 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7916 (ttt90) REVERT: D 118 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6488 (mt-10) REVERT: E 115 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.6418 (tm-30) REVERT: E 122 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.8014 (m) REVERT: E 152 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8334 (tt0) REVERT: F 47 GLU cc_start: 0.7479 (tp30) cc_final: 0.6924 (tp30) REVERT: F 103 LYS cc_start: 0.7905 (mtmt) cc_final: 0.7432 (ttmt) REVERT: G 50 ASP cc_start: 0.6978 (m-30) cc_final: 0.6046 (t0) REVERT: G 66 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7891 (mp0) REVERT: G 96 LYS cc_start: 0.7952 (ttpp) cc_final: 0.7295 (tmtm) REVERT: G 100 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7389 (m-30) REVERT: G 115 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: H 1 MET cc_start: 0.6424 (ptm) cc_final: 0.6149 (ptt) REVERT: H 57 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7778 (mtpt) REVERT: H 103 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7750 (tttm) REVERT: I 1 MET cc_start: 0.6878 (ptm) cc_final: 0.6494 (ptm) REVERT: I 9 ASP cc_start: 0.8000 (m-30) cc_final: 0.7660 (m-30) REVERT: I 50 ASP cc_start: 0.6486 (m-30) cc_final: 0.5822 (t70) REVERT: I 75 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7417 (mm-30) REVERT: I 112 LYS cc_start: 0.8196 (mmtm) cc_final: 0.7485 (mmmt) REVERT: J 1 MET cc_start: 0.6934 (ptm) cc_final: 0.6602 (ptt) REVERT: J 50 ASP cc_start: 0.7195 (m-30) cc_final: 0.6900 (m-30) REVERT: J 57 LYS cc_start: 0.7726 (mtmt) cc_final: 0.7438 (mttm) REVERT: J 96 LYS cc_start: 0.7980 (ttpp) cc_final: 0.7702 (ttpp) REVERT: J 103 LYS cc_start: 0.7997 (mtmt) cc_final: 0.7365 (mmtt) REVERT: J 110 GLN cc_start: 0.7556 (mt0) cc_final: 0.7219 (mt0) REVERT: K 1 MET cc_start: 0.6988 (ptm) cc_final: 0.6093 (ptp) REVERT: K 66 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7906 (mp0) REVERT: K 88 ARG cc_start: 0.7332 (mtm110) cc_final: 0.6895 (mmt180) REVERT: K 96 LYS cc_start: 0.8064 (mtpp) cc_final: 0.7454 (mtmm) REVERT: K 103 LYS cc_start: 0.8191 (mtmt) cc_final: 0.7243 (mmtt) REVERT: L 1 MET cc_start: 0.6922 (ptm) cc_final: 0.6486 (ptm) REVERT: L 42 GLU cc_start: 0.7668 (mt-10) cc_final: 0.6838 (pp20) REVERT: L 52 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.5955 (mtmm) REVERT: L 112 LYS cc_start: 0.8533 (mppt) cc_final: 0.7719 (mmmt) REVERT: O 1 MET cc_start: 0.6882 (ttp) cc_final: 0.6102 (ptp) REVERT: O 52 MET cc_start: 0.6413 (mtt) cc_final: 0.6185 (mtp) REVERT: O 68 LEU cc_start: 0.8449 (mt) cc_final: 0.8154 (mm) REVERT: O 96 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7059 (tm-30) REVERT: O 125 GLU cc_start: 0.7247 (pt0) cc_final: 0.7014 (pt0) REVERT: O 138 ARG cc_start: 0.7578 (ttm-80) cc_final: 0.6780 (ttm-80) REVERT: P 1 MET cc_start: 0.7305 (ttp) cc_final: 0.6992 (ttp) REVERT: P 38 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8093 (mm-30) REVERT: P 57 LYS cc_start: 0.7653 (mtmt) cc_final: 0.7374 (mttm) REVERT: P 76 LYS cc_start: 0.7791 (mmtt) cc_final: 0.7314 (tmtt) REVERT: Q 39 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8222 (mtpt) REVERT: Q 53 LYS cc_start: 0.8099 (mttm) cc_final: 0.7814 (mttp) REVERT: Q 57 LYS cc_start: 0.7865 (mtmt) cc_final: 0.7587 (mttt) REVERT: Q 81 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: Q 125 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6887 (mt-10) REVERT: Q 139 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7066 (tm-30) REVERT: R 6 LYS cc_start: 0.8026 (mmtp) cc_final: 0.7708 (mttp) REVERT: R 81 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: R 85 GLU cc_start: 0.8170 (tt0) cc_final: 0.7668 (tt0) REVERT: R 129 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6818 (tm-30) REVERT: S 1 MET cc_start: 0.6646 (ptm) cc_final: 0.6308 (ptt) REVERT: S 6 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7746 (mmtm) REVERT: S 45 TYR cc_start: 0.7957 (t80) cc_final: 0.7688 (t80) REVERT: S 96 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7057 (tm-30) REVERT: T 6 LYS cc_start: 0.7913 (mmtp) cc_final: 0.7374 (mtmm) REVERT: T 13 ARG cc_start: 0.7499 (ttm-80) cc_final: 0.7164 (mtm-85) REVERT: T 53 LYS cc_start: 0.8081 (mttp) cc_final: 0.7750 (mttt) REVERT: T 73 GLN cc_start: 0.7497 (mm-40) cc_final: 0.6881 (tp40) REVERT: T 74 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.6997 (mp) REVERT: T 75 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7332 (mm-30) REVERT: T 96 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7244 (mt-10) REVERT: T 103 ASP cc_start: 0.8193 (m-30) cc_final: 0.7822 (m-30) REVERT: U 10 GLN cc_start: 0.8048 (mm110) cc_final: 0.7822 (mm110) REVERT: U 68 LEU cc_start: 0.8755 (mt) cc_final: 0.8513 (mm) REVERT: U 91 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7600 (tp) REVERT: V 33 LYS cc_start: 0.8373 (tttt) cc_final: 0.7698 (ttpp) REVERT: V 81 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7512 (mt-10) REVERT: V 129 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6428 (tm-30) REVERT: W 6 LYS cc_start: 0.7816 (mmtp) cc_final: 0.7410 (mtmm) REVERT: W 46 LYS cc_start: 0.7583 (pttt) cc_final: 0.7221 (mmmt) REVERT: W 66 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7620 (mm-30) REVERT: W 88 ASP cc_start: 0.8183 (m-30) cc_final: 0.7911 (m-30) REVERT: W 100 LEU cc_start: 0.8375 (tt) cc_final: 0.8124 (tp) REVERT: W 135 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7948 (mt-10) REVERT: W 151 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: X 6 LYS cc_start: 0.7841 (mmtp) cc_final: 0.7121 (mmpt) outliers start: 77 outliers final: 25 residues processed: 870 average time/residue: 0.8099 time to fit residues: 813.3856 Evaluate side-chains 833 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 788 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain C residue 84 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 E residue 115 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 152 GLN 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 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 39 LYS 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 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: 0.0570 chunk 91 optimal weight: 7.9990 chunk 296 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 330 optimal weight: 8.9990 chunk 287 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 chunk 339 optimal weight: 0.9990 chunk 329 optimal weight: 2.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 89 ASN A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN F 115 GLN F 138 GLN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** S 148 ASN V 10 GLN W 41 ASN W 148 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.146003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.133789 restraints weight = 29232.568| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.22 r_work: 0.3393 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.604 31374 Z= 0.125 Angle : 0.487 16.083 42360 Z= 0.229 Chirality : 0.033 0.134 4656 Planarity : 0.003 0.033 5484 Dihedral : 5.620 88.440 4116 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.44 % Allowed : 14.02 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.32 (0.13), residues: 3696 helix: 3.39 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.71 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG V 13 TYR 0.020 0.001 TYR K 133 PHE 0.029 0.002 PHE U 26 TRP 0.005 0.001 TRP X 133 HIS 0.007 0.001 HIS T 42 Details of bonding type rmsd covalent geometry : bond 0.00269 (31368) covalent geometry : angle 0.48655 (42360) hydrogen bonds : bond 0.04006 ( 2652) hydrogen bonds : angle 3.50547 ( 7956) Misc. bond : bond 0.49483 ( 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 912 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 831 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7094 (mm-30) REVERT: A 115 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7212 (tm-30) REVERT: B 39 GLU cc_start: 0.7712 (tt0) cc_final: 0.7493 (tt0) REVERT: B 43 ARG cc_start: 0.7650 (tpt170) cc_final: 0.7263 (tpt170) REVERT: B 112 LYS cc_start: 0.8129 (mptt) cc_final: 0.7479 (mtmt) REVERT: C 1 MET cc_start: 0.6998 (ptm) cc_final: 0.6399 (ptm) REVERT: C 50 ASP cc_start: 0.7381 (m-30) cc_final: 0.6649 (t0) REVERT: C 52 LYS cc_start: 0.6821 (tptt) cc_final: 0.5928 (mtmm) REVERT: C 66 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7561 (mp0) REVERT: C 112 LYS cc_start: 0.7926 (mmtm) cc_final: 0.7343 (mmmt) REVERT: D 1 MET cc_start: 0.7847 (ptp) cc_final: 0.7176 (ptt) REVERT: D 5 LYS cc_start: 0.7270 (mppt) cc_final: 0.6807 (mptp) REVERT: D 24 GLN cc_start: 0.8584 (tt0) cc_final: 0.8211 (tt0) REVERT: D 52 LYS cc_start: 0.7018 (tptt) cc_final: 0.5778 (mtmm) REVERT: D 66 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: D 88 ARG cc_start: 0.7903 (mtm110) cc_final: 0.7280 (mmt-90) REVERT: D 117 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7483 (ttt180) REVERT: D 118 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6480 (mt-10) REVERT: E 113 ASP cc_start: 0.8742 (t0) cc_final: 0.8421 (t70) REVERT: E 115 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.6423 (tm-30) REVERT: E 122 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.7984 (m) REVERT: E 136 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7912 (mp0) REVERT: F 22 MET cc_start: 0.7729 (ttp) cc_final: 0.7252 (ttp) REVERT: F 47 GLU cc_start: 0.7452 (tp30) cc_final: 0.6943 (tp30) REVERT: F 103 LYS cc_start: 0.7883 (mtmt) cc_final: 0.7410 (ttmt) REVERT: F 111 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7110 (mptm) REVERT: G 50 ASP cc_start: 0.6946 (m-30) cc_final: 0.5990 (t0) REVERT: G 66 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7880 (mp0) REVERT: G 96 LYS cc_start: 0.7931 (ttpp) cc_final: 0.7270 (tmtm) REVERT: G 100 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7352 (m-30) REVERT: G 112 LYS cc_start: 0.8206 (mmtm) cc_final: 0.7808 (mmmt) REVERT: G 115 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7728 (tm-30) REVERT: H 57 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7762 (mtpt) REVERT: H 96 LYS cc_start: 0.8177 (tttm) cc_final: 0.7746 (ttpt) REVERT: H 103 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7751 (tttm) REVERT: I 1 MET cc_start: 0.6832 (ptm) cc_final: 0.6442 (ptm) REVERT: I 9 ASP cc_start: 0.7982 (m-30) cc_final: 0.7649 (m-30) REVERT: I 42 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7032 (mt-10) REVERT: I 50 ASP cc_start: 0.6431 (m-30) cc_final: 0.5748 (t70) REVERT: I 75 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7405 (mm-30) REVERT: I 112 LYS cc_start: 0.8219 (mmtm) cc_final: 0.7557 (mmmt) REVERT: J 1 MET cc_start: 0.6939 (ptm) cc_final: 0.6600 (ptt) REVERT: J 50 ASP cc_start: 0.7187 (m-30) cc_final: 0.6865 (m-30) REVERT: J 57 LYS cc_start: 0.7702 (mtmt) cc_final: 0.7415 (mttm) REVERT: J 103 LYS cc_start: 0.7985 (mtmt) cc_final: 0.7340 (mmtt) REVERT: J 110 GLN cc_start: 0.7513 (mt0) cc_final: 0.7190 (mt0) REVERT: K 1 MET cc_start: 0.6954 (ptm) cc_final: 0.6690 (ptm) REVERT: K 42 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6571 (tm-30) REVERT: K 66 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7909 (mp0) REVERT: K 88 ARG cc_start: 0.7290 (mtm110) cc_final: 0.6880 (mmt180) REVERT: K 96 LYS cc_start: 0.8048 (mtpp) cc_final: 0.7444 (mtmm) REVERT: K 103 LYS cc_start: 0.8181 (mtmt) cc_final: 0.7235 (mmtt) REVERT: L 1 MET cc_start: 0.6885 (ptm) cc_final: 0.6375 (ptt) REVERT: L 42 GLU cc_start: 0.7649 (mt-10) cc_final: 0.6809 (pp20) REVERT: L 52 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.5942 (mtmm) REVERT: L 66 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7513 (mp0) REVERT: L 112 LYS cc_start: 0.8543 (mppt) cc_final: 0.7693 (mtmt) REVERT: N 76 LYS cc_start: 0.8481 (tmtt) cc_final: 0.8153 (tptp) REVERT: O 1 MET cc_start: 0.6842 (ttp) cc_final: 0.6010 (ptp) REVERT: O 13 ARG cc_start: 0.7462 (ttm-80) cc_final: 0.7186 (mtm-85) REVERT: O 52 MET cc_start: 0.6438 (mtt) cc_final: 0.6229 (mtp) REVERT: O 68 LEU cc_start: 0.8422 (mt) cc_final: 0.8127 (mm) REVERT: O 138 ARG cc_start: 0.7553 (ttm-80) cc_final: 0.6741 (ttm-80) REVERT: P 1 MET cc_start: 0.7321 (ttp) cc_final: 0.7055 (ttp) REVERT: P 38 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7980 (mm-30) REVERT: P 39 LYS cc_start: 0.7868 (ttpt) cc_final: 0.7184 (mtmt) REVERT: P 57 LYS cc_start: 0.7625 (mtmt) cc_final: 0.7343 (mttm) REVERT: Q 39 LYS cc_start: 0.8664 (ttmm) cc_final: 0.8204 (mtpt) REVERT: Q 57 LYS cc_start: 0.7842 (mtmt) cc_final: 0.7560 (mttt) REVERT: Q 81 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: Q 98 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7521 (mp) REVERT: Q 125 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6880 (mt-10) REVERT: Q 139 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7017 (tm-30) REVERT: R 6 LYS cc_start: 0.8022 (mmtp) cc_final: 0.7702 (mttp) REVERT: R 81 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: R 129 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6764 (tm-30) REVERT: S 1 MET cc_start: 0.6604 (ptm) cc_final: 0.6264 (ptt) REVERT: S 45 TYR cc_start: 0.7929 (t80) cc_final: 0.7665 (t80) REVERT: S 96 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7034 (tm-30) REVERT: T 6 LYS cc_start: 0.7891 (mmtp) cc_final: 0.7361 (mtmm) REVERT: T 13 ARG cc_start: 0.7488 (ttm-80) cc_final: 0.6874 (mtm-85) REVERT: T 53 LYS cc_start: 0.8068 (mttp) cc_final: 0.7730 (mttt) REVERT: T 73 GLN cc_start: 0.7489 (mm-40) cc_final: 0.6888 (tp40) REVERT: T 75 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7285 (mm-30) REVERT: T 96 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7214 (mt-10) REVERT: T 103 ASP cc_start: 0.8171 (m-30) cc_final: 0.7798 (m-30) REVERT: U 6 LYS cc_start: 0.8062 (mptm) cc_final: 0.7627 (mtmm) REVERT: U 10 GLN cc_start: 0.8025 (mm110) cc_final: 0.7756 (mm110) REVERT: U 39 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7869 (mttm) REVERT: U 68 LEU cc_start: 0.8745 (mt) cc_final: 0.8493 (mm) REVERT: U 91 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7597 (tp) REVERT: U 113 ASP cc_start: 0.8386 (t70) cc_final: 0.7966 (t70) REVERT: V 33 LYS cc_start: 0.8373 (tttt) cc_final: 0.7699 (ttpp) REVERT: V 81 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7513 (mt-10) REVERT: V 129 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6407 (tm-30) REVERT: W 6 LYS cc_start: 0.7773 (mmtp) cc_final: 0.7241 (mtmm) REVERT: W 46 LYS cc_start: 0.7541 (pttt) cc_final: 0.7218 (mmmt) REVERT: W 66 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7607 (mm-30) REVERT: W 88 ASP cc_start: 0.8160 (m-30) cc_final: 0.7885 (m-30) REVERT: W 100 LEU cc_start: 0.8363 (tt) cc_final: 0.8078 (tp) REVERT: W 135 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7929 (mt-10) REVERT: W 151 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: X 66 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8056 (mt-10) outliers start: 81 outliers final: 27 residues processed: 866 average time/residue: 0.8112 time to fit residues: 811.9689 Evaluate side-chains 850 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 800 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 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 111 LYS 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 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 N residue 17 CYS Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 97 GLN 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 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 75 GLU Chi-restraints excluded: chain U residue 39 LYS 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 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 66 GLU Chi-restraints excluded: chain X residue 94 VAL Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 273 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 296 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 302 optimal weight: 9.9990 chunk 224 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN F 115 GLN F 138 GLN I 60 GLN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 148 ASN V 10 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.144190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132565 restraints weight = 29216.524| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.14 r_work: 0.3385 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.636 31374 Z= 0.145 Angle : 0.511 16.967 42360 Z= 0.241 Chirality : 0.034 0.155 4656 Planarity : 0.003 0.039 5484 Dihedral : 5.555 87.420 4116 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.65 % Allowed : 13.99 % Favored : 83.36 % 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 aren not related in a simple way. whole: 4.28 (0.13), residues: 3696 helix: 3.35 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.69 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG V 13 TYR 0.023 0.002 TYR K 133 PHE 0.027 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 covalent geometry : bond 0.00322 (31368) covalent geometry : angle 0.51067 (42360) hydrogen bonds : bond 0.04217 ( 2652) hydrogen bonds : angle 3.55155 ( 7956) Misc. bond : bond 0.49620 ( 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 918 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 830 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6944 (mm-30) REVERT: A 115 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7088 (tm-30) REVERT: B 112 LYS cc_start: 0.8079 (mptt) cc_final: 0.7398 (mtmt) REVERT: C 1 MET cc_start: 0.6951 (ptm) cc_final: 0.6317 (ptm) REVERT: C 50 ASP cc_start: 0.7244 (m-30) cc_final: 0.6511 (t0) REVERT: C 66 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7506 (mp0) REVERT: C 75 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7738 (mt-10) REVERT: C 112 LYS cc_start: 0.7888 (mmtm) cc_final: 0.7294 (mmmt) REVERT: D 1 MET cc_start: 0.7809 (ptp) cc_final: 0.7120 (ptt) REVERT: D 5 LYS cc_start: 0.7222 (mppt) cc_final: 0.6815 (mptp) REVERT: D 52 LYS cc_start: 0.6881 (tptt) cc_final: 0.5622 (mtmm) REVERT: D 66 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: D 88 ARG cc_start: 0.7786 (mtm110) cc_final: 0.7167 (mmt-90) REVERT: D 117 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7688 (ttt90) REVERT: D 118 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6295 (mt-10) REVERT: E 115 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.6381 (tm-30) REVERT: E 136 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7852 (mp0) REVERT: F 1 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6998 (ptt) REVERT: F 22 MET cc_start: 0.7667 (ttp) cc_final: 0.7217 (ttm) REVERT: F 47 GLU cc_start: 0.7397 (tp30) cc_final: 0.6833 (tp30) REVERT: F 52 LYS cc_start: 0.6854 (tptt) cc_final: 0.6357 (tptt) REVERT: F 96 LYS cc_start: 0.7870 (ttpp) cc_final: 0.7569 (tttm) REVERT: F 100 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7163 (t0) REVERT: F 103 LYS cc_start: 0.7803 (mtmt) cc_final: 0.7281 (ttmt) REVERT: F 111 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7005 (mptm) REVERT: F 115 GLN cc_start: 0.8407 (tp40) cc_final: 0.8073 (mm-40) REVERT: F 118 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.5823 (mp0) REVERT: G 50 ASP cc_start: 0.6838 (m-30) cc_final: 0.5870 (t0) REVERT: G 66 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7804 (mp0) REVERT: G 96 LYS cc_start: 0.7866 (ttpp) cc_final: 0.7174 (tmtm) REVERT: G 100 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7249 (m-30) REVERT: G 112 LYS cc_start: 0.8186 (mmtm) cc_final: 0.7747 (mmmt) REVERT: G 115 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: H 57 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7641 (mtpt) REVERT: H 96 LYS cc_start: 0.8104 (tttm) cc_final: 0.7666 (ttpt) REVERT: H 103 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7653 (tttm) REVERT: H 125 ASP cc_start: 0.8040 (t0) cc_final: 0.7693 (t70) REVERT: I 1 MET cc_start: 0.6781 (ptm) cc_final: 0.6397 (ptm) REVERT: I 9 ASP cc_start: 0.7938 (m-30) cc_final: 0.7567 (m-30) REVERT: I 42 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7009 (mt-10) REVERT: I 50 ASP cc_start: 0.6326 (m-30) cc_final: 0.5636 (t70) REVERT: I 75 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7389 (mm-30) REVERT: I 112 LYS cc_start: 0.8199 (mmtm) cc_final: 0.7356 (mtpm) REVERT: J 1 MET cc_start: 0.6947 (ptm) cc_final: 0.6639 (ptt) REVERT: J 50 ASP cc_start: 0.7091 (m-30) cc_final: 0.6749 (m-30) REVERT: J 57 LYS cc_start: 0.7602 (mtmt) cc_final: 0.7296 (mttm) REVERT: J 103 LYS cc_start: 0.7899 (mtmt) cc_final: 0.7208 (mmtt) REVERT: J 110 GLN cc_start: 0.7406 (mt0) cc_final: 0.7098 (mt0) REVERT: K 1 MET cc_start: 0.6890 (ptm) cc_final: 0.6623 (ptm) REVERT: K 42 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6519 (tm-30) REVERT: K 66 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7838 (mp0) REVERT: K 88 ARG cc_start: 0.7189 (mtm110) cc_final: 0.6757 (mmt180) REVERT: K 96 LYS cc_start: 0.7971 (mtpp) cc_final: 0.7344 (mtmm) REVERT: K 103 LYS cc_start: 0.8106 (mtmt) cc_final: 0.7138 (mmtt) REVERT: K 110 GLN cc_start: 0.7604 (tt0) cc_final: 0.7398 (tt0) REVERT: L 1 MET cc_start: 0.6809 (ptm) cc_final: 0.6292 (ptt) REVERT: L 42 GLU cc_start: 0.7624 (mt-10) cc_final: 0.6763 (pp20) REVERT: L 52 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.5803 (mtmm) REVERT: L 57 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7826 (mppt) REVERT: L 66 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7425 (mp0) REVERT: L 112 LYS cc_start: 0.8484 (mppt) cc_final: 0.7590 (mtmt) REVERT: L 125 ASP cc_start: 0.8057 (t70) cc_final: 0.7650 (t70) REVERT: N 1 MET cc_start: 0.5981 (ptt) cc_final: 0.5672 (ptt) REVERT: N 76 LYS cc_start: 0.8467 (tmtt) cc_final: 0.8103 (tptp) REVERT: O 1 MET cc_start: 0.6868 (ttp) cc_final: 0.5952 (ptp) REVERT: O 13 ARG cc_start: 0.7411 (ttm-80) cc_final: 0.7200 (mtm-85) REVERT: O 52 MET cc_start: 0.6226 (mtt) cc_final: 0.6006 (mtp) REVERT: O 68 LEU cc_start: 0.8373 (mt) cc_final: 0.8054 (mm) REVERT: O 138 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.6643 (ttm-80) REVERT: P 1 MET cc_start: 0.7332 (ttp) cc_final: 0.7055 (ttp) REVERT: P 39 LYS cc_start: 0.7823 (ttpt) cc_final: 0.7070 (mtmt) REVERT: P 57 LYS cc_start: 0.7515 (mtmt) cc_final: 0.7217 (mttm) REVERT: P 76 LYS cc_start: 0.7759 (mmtt) cc_final: 0.7246 (tmtt) REVERT: P 127 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6972 (mm-30) REVERT: Q 57 LYS cc_start: 0.7773 (mtmt) cc_final: 0.7452 (mttt) REVERT: Q 81 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: Q 98 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7453 (mp) REVERT: Q 125 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6754 (mt-10) REVERT: Q 139 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.6934 (tm-30) REVERT: R 6 LYS cc_start: 0.7949 (mmtp) cc_final: 0.7611 (mttp) REVERT: R 81 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: R 96 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7104 (pt0) REVERT: R 129 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6605 (tm-30) REVERT: S 1 MET cc_start: 0.6600 (ptm) cc_final: 0.6255 (ptt) REVERT: S 45 TYR cc_start: 0.7900 (t80) cc_final: 0.7679 (t80) REVERT: S 96 GLU cc_start: 0.7358 (tm-30) cc_final: 0.6966 (tm-30) REVERT: T 6 LYS cc_start: 0.7812 (mmtp) cc_final: 0.7272 (mtmm) REVERT: T 13 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.7052 (mtm-85) REVERT: T 53 LYS cc_start: 0.7969 (mttp) cc_final: 0.7620 (mttt) REVERT: T 73 GLN cc_start: 0.7467 (mm-40) cc_final: 0.6848 (tp40) REVERT: T 75 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7215 (mm-30) REVERT: T 96 GLU cc_start: 0.7354 (tm-30) cc_final: 0.7104 (mt-10) REVERT: T 103 ASP cc_start: 0.8122 (m-30) cc_final: 0.7718 (m-30) REVERT: U 6 LYS cc_start: 0.7992 (mptm) cc_final: 0.7529 (mtmm) REVERT: U 10 GLN cc_start: 0.7935 (mm110) cc_final: 0.7638 (mm110) REVERT: U 33 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7493 (ttpp) REVERT: U 39 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7831 (mttm) REVERT: U 68 LEU cc_start: 0.8725 (mt) cc_final: 0.8452 (mm) REVERT: U 76 LYS cc_start: 0.8499 (tmtt) cc_final: 0.8291 (tmtm) REVERT: U 91 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7545 (tp) REVERT: V 33 LYS cc_start: 0.8322 (tttt) cc_final: 0.7619 (ttpp) REVERT: V 81 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7516 (mt-10) REVERT: V 129 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6256 (tm-30) REVERT: W 6 LYS cc_start: 0.7699 (mmtp) cc_final: 0.7294 (mtmm) REVERT: W 46 LYS cc_start: 0.7487 (pttt) cc_final: 0.7126 (mmmt) REVERT: W 52 MET cc_start: 0.7398 (ttm) cc_final: 0.6970 (ttt) REVERT: W 66 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7520 (mm-30) REVERT: W 88 ASP cc_start: 0.8089 (m-30) cc_final: 0.7813 (m-30) REVERT: W 100 LEU cc_start: 0.8313 (tt) cc_final: 0.8014 (tp) REVERT: W 135 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7884 (mt-10) REVERT: W 151 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: X 1 MET cc_start: 0.6333 (ttp) cc_final: 0.6029 (ptt) REVERT: X 6 LYS cc_start: 0.7754 (mmtp) cc_final: 0.7068 (mmpt) REVERT: X 66 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8031 (mt-10) outliers start: 88 outliers final: 31 residues processed: 868 average time/residue: 0.8015 time to fit residues: 801.4989 Evaluate side-chains 860 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 802 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain C residue 2 LYS 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 115 GLN Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 127 THR 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 68 VAL 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 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 98 LEU Chi-restraints excluded: chain Q residue 74 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 S residue 73 GLN Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 39 LYS 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 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 66 GLU Chi-restraints excluded: chain X residue 94 VAL Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 100 LEU Chi-restraints excluded: chain X residue 106 THR 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: 20.0000 chunk 159 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 342 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 358 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 247 optimal weight: 8.9990 chunk 142 optimal weight: 0.3980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 89 ASN A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN F 138 GLN J 89 ASN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 N 151 GLN O 10 GLN O 148 ASN P 73 GLN R 148 ASN T 42 HIS V 10 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.145341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.133712 restraints weight = 29115.177| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.14 r_work: 0.3401 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.622 31374 Z= 0.128 Angle : 0.498 16.995 42360 Z= 0.234 Chirality : 0.033 0.142 4656 Planarity : 0.003 0.034 5484 Dihedral : 5.386 81.983 4116 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.41 % Allowed : 14.74 % Favored : 82.85 % 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 aren not related in a simple way. whole: 4.36 (0.13), residues: 3696 helix: 3.40 (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 0.006 0.000 ARG V 13 TYR 0.023 0.001 TYR K 133 PHE 0.024 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 covalent geometry : bond 0.00276 (31368) covalent geometry : angle 0.49812 (42360) hydrogen bonds : bond 0.04054 ( 2652) hydrogen bonds : angle 3.49217 ( 7956) Misc. bond : bond 0.48282 ( 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 922 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 842 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6998 (mm-30) REVERT: A 115 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7089 (tm-30) REVERT: B 43 ARG cc_start: 0.7561 (tpt170) cc_final: 0.7240 (tpt170) REVERT: B 112 LYS cc_start: 0.8063 (mptt) cc_final: 0.7392 (mtmt) REVERT: C 1 MET cc_start: 0.6932 (ptm) cc_final: 0.6301 (ptm) REVERT: C 22 MET cc_start: 0.7512 (ttp) cc_final: 0.7134 (ttm) REVERT: C 50 ASP cc_start: 0.7219 (m-30) cc_final: 0.6471 (t0) REVERT: C 57 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7776 (mtpt) REVERT: C 66 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7473 (mp0) REVERT: C 75 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7746 (mt-10) REVERT: C 112 LYS cc_start: 0.7830 (mmtm) cc_final: 0.7290 (mtmt) REVERT: D 1 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7132 (ptt) REVERT: D 5 LYS cc_start: 0.7221 (mppt) cc_final: 0.6859 (mptp) REVERT: D 24 GLN cc_start: 0.8512 (tt0) cc_final: 0.8125 (tt0) REVERT: D 42 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7078 (mt-10) REVERT: D 52 LYS cc_start: 0.6880 (tptt) cc_final: 0.5656 (mtmm) REVERT: D 66 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: D 88 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7175 (mmt-90) REVERT: D 117 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7496 (ttt90) REVERT: D 118 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6307 (mt-10) REVERT: D 125 ASP cc_start: 0.7999 (t70) cc_final: 0.7770 (t0) REVERT: E 113 ASP cc_start: 0.8688 (t0) cc_final: 0.8363 (t70) REVERT: E 115 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.6390 (tm-30) REVERT: E 122 VAL cc_start: 0.8174 (p) cc_final: 0.7904 (m) REVERT: E 136 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7832 (mp0) REVERT: F 1 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6965 (ptt) REVERT: F 22 MET cc_start: 0.7665 (ttp) cc_final: 0.7191 (ttm) REVERT: F 47 GLU cc_start: 0.7350 (tp30) cc_final: 0.6829 (tp30) REVERT: F 52 LYS cc_start: 0.6939 (tptt) cc_final: 0.6545 (tptt) REVERT: F 96 LYS cc_start: 0.7856 (ttpp) cc_final: 0.7550 (tttm) REVERT: F 103 LYS cc_start: 0.7765 (mtmt) cc_final: 0.7281 (ttmt) REVERT: F 111 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7027 (mptm) REVERT: F 118 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.5802 (mp0) REVERT: G 50 ASP cc_start: 0.6822 (m-30) cc_final: 0.5846 (t0) REVERT: G 66 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7777 (mp0) REVERT: G 96 LYS cc_start: 0.7859 (ttpp) cc_final: 0.7166 (tmtm) REVERT: G 100 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7262 (m-30) REVERT: G 112 LYS cc_start: 0.8157 (mmtm) cc_final: 0.7738 (mmmt) REVERT: G 115 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: H 57 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7646 (mtpt) REVERT: H 96 LYS cc_start: 0.8089 (tttm) cc_final: 0.7671 (ttpt) REVERT: H 103 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7648 (tttm) REVERT: I 1 MET cc_start: 0.6778 (ptm) cc_final: 0.6373 (ptm) REVERT: I 9 ASP cc_start: 0.7909 (m-30) cc_final: 0.7565 (m-30) REVERT: I 42 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6960 (mt-10) REVERT: I 50 ASP cc_start: 0.6271 (m-30) cc_final: 0.5606 (t70) REVERT: I 75 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7332 (mm-30) REVERT: I 112 LYS cc_start: 0.8180 (mmtm) cc_final: 0.7351 (mtpm) REVERT: J 1 MET cc_start: 0.6927 (ptm) cc_final: 0.6680 (ptt) REVERT: J 57 LYS cc_start: 0.7569 (mtmt) cc_final: 0.7258 (mttm) REVERT: J 96 LYS cc_start: 0.7811 (ttpp) cc_final: 0.7605 (ttpp) REVERT: J 103 LYS cc_start: 0.7883 (mtmt) cc_final: 0.7185 (mmtt) REVERT: J 110 GLN cc_start: 0.7432 (mt0) cc_final: 0.7126 (mt0) REVERT: K 1 MET cc_start: 0.6863 (ptm) cc_final: 0.6620 (ptm) REVERT: K 42 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6505 (tm-30) REVERT: K 66 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7831 (mp0) REVERT: K 88 ARG cc_start: 0.7180 (mtm110) cc_final: 0.6756 (mmt180) REVERT: K 96 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7346 (mtmm) REVERT: K 103 LYS cc_start: 0.8086 (mtmt) cc_final: 0.7108 (mmtt) REVERT: K 110 GLN cc_start: 0.7579 (tt0) cc_final: 0.7364 (tt0) REVERT: L 1 MET cc_start: 0.6775 (ptm) cc_final: 0.6241 (ptt) REVERT: L 42 GLU cc_start: 0.7602 (mt-10) cc_final: 0.6742 (pp20) REVERT: L 52 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.5784 (mtmm) REVERT: L 57 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7789 (mppt) REVERT: L 66 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7459 (mp0) REVERT: L 112 LYS cc_start: 0.8453 (mppt) cc_final: 0.7561 (mtmt) REVERT: N 1 MET cc_start: 0.5927 (ptt) cc_final: 0.5656 (ptt) REVERT: N 76 LYS cc_start: 0.8447 (tmtt) cc_final: 0.8070 (tptp) REVERT: O 1 MET cc_start: 0.6818 (ttp) cc_final: 0.5872 (ptp) REVERT: O 13 ARG cc_start: 0.7390 (ttm-80) cc_final: 0.7093 (mtm-85) REVERT: O 68 LEU cc_start: 0.8351 (mt) cc_final: 0.8032 (mm) REVERT: O 138 ARG cc_start: 0.7487 (ttm-80) cc_final: 0.6618 (ttm-80) REVERT: P 1 MET cc_start: 0.7322 (ttp) cc_final: 0.7048 (ttp) REVERT: P 39 LYS cc_start: 0.7821 (ttpt) cc_final: 0.7070 (mtmt) REVERT: P 57 LYS cc_start: 0.7464 (mtmt) cc_final: 0.7164 (mttm) REVERT: Q 39 LYS cc_start: 0.8611 (ttmm) cc_final: 0.8149 (mtpt) REVERT: Q 53 LYS cc_start: 0.7967 (mttp) cc_final: 0.7594 (mttp) REVERT: Q 57 LYS cc_start: 0.7744 (mtmt) cc_final: 0.7428 (mttt) REVERT: Q 81 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: Q 98 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7428 (mp) REVERT: Q 125 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6730 (mt-10) REVERT: Q 139 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.6890 (tm-30) REVERT: R 6 LYS cc_start: 0.7929 (mmtp) cc_final: 0.7593 (mttp) REVERT: R 96 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7087 (pt0) REVERT: R 129 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6610 (tm-30) REVERT: S 1 MET cc_start: 0.6554 (ptm) cc_final: 0.6215 (ptt) REVERT: S 45 TYR cc_start: 0.7884 (t80) cc_final: 0.7670 (t80) REVERT: S 96 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6919 (tm-30) REVERT: T 6 LYS cc_start: 0.7792 (mmtp) cc_final: 0.7261 (mtmm) REVERT: T 13 ARG cc_start: 0.7379 (ttm-80) cc_final: 0.7027 (mtm-85) REVERT: T 53 LYS cc_start: 0.7924 (mttp) cc_final: 0.7522 (mtmt) REVERT: T 57 LYS cc_start: 0.8103 (mtmt) cc_final: 0.7525 (mmtt) REVERT: T 73 GLN cc_start: 0.7442 (mm-40) cc_final: 0.6843 (tp40) REVERT: T 75 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7213 (mm-30) REVERT: T 96 GLU cc_start: 0.7309 (tm-30) cc_final: 0.7081 (mt-10) REVERT: T 103 ASP cc_start: 0.8090 (m-30) cc_final: 0.7700 (m-30) REVERT: U 10 GLN cc_start: 0.7918 (mm110) cc_final: 0.7645 (mm110) REVERT: U 33 LYS cc_start: 0.8174 (ttpp) cc_final: 0.7466 (ttpp) REVERT: U 39 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7835 (mttm) REVERT: U 68 LEU cc_start: 0.8714 (mt) cc_final: 0.8447 (mm) REVERT: U 76 LYS cc_start: 0.8497 (tmtt) cc_final: 0.8296 (tmtm) REVERT: U 91 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7522 (tp) REVERT: U 113 ASP cc_start: 0.8312 (t70) cc_final: 0.7913 (t70) REVERT: V 33 LYS cc_start: 0.8316 (tttt) cc_final: 0.7616 (ttpp) REVERT: V 81 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7489 (mt-10) REVERT: V 129 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6249 (tm-30) REVERT: W 6 LYS cc_start: 0.7671 (mmtp) cc_final: 0.7241 (mtmm) REVERT: W 46 LYS cc_start: 0.7451 (pttt) cc_final: 0.7097 (mmmt) REVERT: W 66 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7499 (mm-30) REVERT: W 88 ASP cc_start: 0.8074 (m-30) cc_final: 0.7788 (m-30) REVERT: W 135 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7880 (mt-10) REVERT: W 151 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: X 1 MET cc_start: 0.6265 (ttp) cc_final: 0.6019 (ptt) REVERT: X 66 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8007 (mt-10) outliers start: 80 outliers final: 27 residues processed: 877 average time/residue: 0.8004 time to fit residues: 811.1047 Evaluate side-chains 863 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 808 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C 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 117 ARG Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 111 LYS 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 68 VAL 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 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 74 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 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 T residue 75 GLU Chi-restraints excluded: chain U residue 39 LYS 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 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: 1.9990 chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 190 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN F 115 GLN F 138 GLN H 149 ASN J 89 ASN J 149 ASN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 73 GLN R 148 ASN S 148 ASN T 42 HIS V 10 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.144217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.132621 restraints weight = 29305.437| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.14 r_work: 0.3386 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.643 31374 Z= 0.145 Angle : 0.524 17.165 42360 Z= 0.248 Chirality : 0.034 0.147 4656 Planarity : 0.003 0.038 5484 Dihedral : 5.337 80.635 4116 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.41 % Allowed : 15.31 % Favored : 82.28 % 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 aren not related in a simple way. whole: 4.28 (0.13), residues: 3696 helix: 3.35 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.65 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG V 13 TYR 0.024 0.002 TYR K 133 PHE 0.025 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 covalent geometry : bond 0.00320 (31368) covalent geometry : angle 0.52372 (42360) hydrogen bonds : bond 0.04218 ( 2652) hydrogen bonds : angle 3.54689 ( 7956) Misc. bond : bond 0.48931 ( 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 905 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 825 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6999 (mm-30) REVERT: A 115 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7121 (tm-30) REVERT: B 43 ARG cc_start: 0.7582 (tpt170) cc_final: 0.7241 (tpt170) REVERT: B 112 LYS cc_start: 0.8084 (mptt) cc_final: 0.7400 (mtmt) REVERT: C 1 MET cc_start: 0.6932 (ptm) cc_final: 0.6251 (ptm) REVERT: C 22 MET cc_start: 0.7526 (ttp) cc_final: 0.7194 (ttm) REVERT: C 50 ASP cc_start: 0.7245 (m-30) cc_final: 0.6500 (t0) REVERT: C 66 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7491 (mp0) REVERT: C 75 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7767 (mt-10) REVERT: D 1 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7119 (ptt) REVERT: D 5 LYS cc_start: 0.7249 (mppt) cc_final: 0.6910 (mptp) REVERT: D 24 GLN cc_start: 0.8509 (tt0) cc_final: 0.8112 (tt0) REVERT: D 42 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7075 (mt-10) REVERT: D 52 LYS cc_start: 0.6888 (tptt) cc_final: 0.5648 (mtmm) REVERT: D 66 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8041 (mp0) REVERT: D 88 ARG cc_start: 0.7804 (mtm110) cc_final: 0.7203 (mmt-90) REVERT: D 117 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7755 (ttt90) REVERT: D 118 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6290 (mt-10) REVERT: D 125 ASP cc_start: 0.8030 (t70) cc_final: 0.7783 (t0) REVERT: E 115 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.6363 (tm-30) REVERT: E 122 VAL cc_start: 0.8196 (p) cc_final: 0.7923 (m) REVERT: E 136 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7776 (mp0) REVERT: F 22 MET cc_start: 0.7708 (ttp) cc_final: 0.7214 (ttp) REVERT: F 47 GLU cc_start: 0.7372 (tp30) cc_final: 0.6879 (tp30) REVERT: F 52 LYS cc_start: 0.6949 (tptt) cc_final: 0.6504 (tptt) REVERT: F 96 LYS cc_start: 0.7858 (ttpp) cc_final: 0.7560 (tttm) REVERT: F 103 LYS cc_start: 0.7791 (mtmt) cc_final: 0.7300 (ttmt) REVERT: F 111 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7046 (mptm) REVERT: F 115 GLN cc_start: 0.8423 (tp40) cc_final: 0.8141 (mm-40) REVERT: F 118 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.5826 (mp0) REVERT: G 50 ASP cc_start: 0.6844 (m-30) cc_final: 0.5863 (t0) REVERT: G 66 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7749 (mp0) REVERT: G 96 LYS cc_start: 0.7866 (ttpp) cc_final: 0.7180 (tmtm) REVERT: G 100 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7252 (m-30) REVERT: G 112 LYS cc_start: 0.8165 (mmtm) cc_final: 0.7752 (mmmt) REVERT: G 115 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: H 57 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7635 (mtpt) REVERT: H 96 LYS cc_start: 0.8101 (tttm) cc_final: 0.7679 (ttpt) REVERT: H 103 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7662 (tttm) REVERT: H 125 ASP cc_start: 0.8060 (t0) cc_final: 0.7713 (t70) REVERT: I 1 MET cc_start: 0.6748 (ptm) cc_final: 0.6366 (ptm) REVERT: I 9 ASP cc_start: 0.7938 (m-30) cc_final: 0.7571 (m-30) REVERT: I 42 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6997 (mt-10) REVERT: I 50 ASP cc_start: 0.6178 (m-30) cc_final: 0.5555 (t70) REVERT: I 75 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7342 (mm-30) REVERT: I 112 LYS cc_start: 0.8187 (mmtm) cc_final: 0.7356 (mtpm) REVERT: J 1 MET cc_start: 0.6916 (ptm) cc_final: 0.6663 (ptt) REVERT: J 57 LYS cc_start: 0.7591 (mtmt) cc_final: 0.7287 (mttm) REVERT: J 103 LYS cc_start: 0.7896 (mtmt) cc_final: 0.7197 (mmtt) REVERT: J 110 GLN cc_start: 0.7449 (mt0) cc_final: 0.7130 (mt0) REVERT: K 1 MET cc_start: 0.6908 (ptm) cc_final: 0.6662 (ptm) REVERT: K 42 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6541 (tm-30) REVERT: K 66 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7843 (mp0) REVERT: K 88 ARG cc_start: 0.7200 (mtm110) cc_final: 0.6789 (mmt180) REVERT: K 96 LYS cc_start: 0.7978 (mtpp) cc_final: 0.7353 (mtmm) REVERT: K 103 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7140 (mmtt) REVERT: K 110 GLN cc_start: 0.7596 (tt0) cc_final: 0.7376 (tt0) REVERT: L 1 MET cc_start: 0.6775 (ptm) cc_final: 0.6236 (ptt) REVERT: L 42 GLU cc_start: 0.7641 (mt-10) cc_final: 0.6775 (pp20) REVERT: L 52 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.5758 (mtmm) REVERT: L 57 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7800 (mppt) REVERT: L 66 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7411 (mp0) REVERT: L 112 LYS cc_start: 0.8459 (mppt) cc_final: 0.7564 (mtmt) REVERT: L 125 ASP cc_start: 0.8017 (t0) cc_final: 0.7653 (t70) REVERT: M 112 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7335 (mp10) REVERT: N 1 MET cc_start: 0.5975 (ptt) cc_final: 0.5698 (ptt) REVERT: N 76 LYS cc_start: 0.8449 (tmtt) cc_final: 0.8097 (tptp) REVERT: O 1 MET cc_start: 0.6840 (ttp) cc_final: 0.5855 (ptp) REVERT: O 13 ARG cc_start: 0.7406 (ttm-80) cc_final: 0.7205 (mtm-85) REVERT: O 50 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6865 (pp20) REVERT: O 68 LEU cc_start: 0.8359 (mt) cc_final: 0.8040 (mm) REVERT: O 97 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7233 (tp40) REVERT: O 138 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.6622 (ttm-80) REVERT: P 39 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7345 (ttmt) REVERT: P 57 LYS cc_start: 0.7493 (mtmt) cc_final: 0.7196 (mttm) REVERT: P 127 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7104 (mm-30) REVERT: Q 39 LYS cc_start: 0.8649 (ttmm) cc_final: 0.8177 (mtpt) REVERT: Q 57 LYS cc_start: 0.7764 (mtmt) cc_final: 0.7438 (mttt) REVERT: Q 81 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: Q 98 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7459 (mp) REVERT: Q 125 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6761 (mt-10) REVERT: Q 139 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: R 6 LYS cc_start: 0.7928 (mmtp) cc_final: 0.7590 (mttp) REVERT: R 13 ARG cc_start: 0.7567 (ttm-80) cc_final: 0.7320 (mtp85) REVERT: R 81 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: R 96 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7101 (pt0) REVERT: R 129 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6579 (tm-30) REVERT: S 1 MET cc_start: 0.6615 (ptm) cc_final: 0.6262 (ptt) REVERT: S 45 TYR cc_start: 0.7907 (t80) cc_final: 0.7698 (t80) REVERT: S 57 LYS cc_start: 0.7959 (mttm) cc_final: 0.7688 (mttp) REVERT: S 96 GLU cc_start: 0.7354 (tm-30) cc_final: 0.6949 (tm-30) REVERT: T 6 LYS cc_start: 0.7813 (mmtp) cc_final: 0.7272 (mtmm) REVERT: T 13 ARG cc_start: 0.7409 (ttm-80) cc_final: 0.7043 (mtm-85) REVERT: T 53 LYS cc_start: 0.7921 (mttp) cc_final: 0.7542 (mtmt) REVERT: T 57 LYS cc_start: 0.8109 (mtmt) cc_final: 0.7528 (mmtt) REVERT: T 73 GLN cc_start: 0.7456 (mm-40) cc_final: 0.6868 (tp40) REVERT: T 74 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.6900 (mp) REVERT: T 75 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7189 (mm-30) REVERT: T 96 GLU cc_start: 0.7349 (tm-30) cc_final: 0.7109 (mt-10) REVERT: T 103 ASP cc_start: 0.8127 (m-30) cc_final: 0.7737 (m-30) REVERT: U 6 LYS cc_start: 0.7976 (mptm) cc_final: 0.7515 (mtmm) REVERT: U 10 GLN cc_start: 0.7911 (mm110) cc_final: 0.7630 (mm110) REVERT: U 33 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7609 (ttpp) REVERT: U 39 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7857 (mttm) REVERT: U 45 TYR cc_start: 0.8025 (t80) cc_final: 0.7208 (t80) REVERT: U 68 LEU cc_start: 0.8728 (mt) cc_final: 0.8457 (mm) REVERT: U 76 LYS cc_start: 0.8511 (tmtt) cc_final: 0.8309 (tmtm) REVERT: U 91 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7534 (tp) REVERT: V 33 LYS cc_start: 0.8341 (tttt) cc_final: 0.7644 (ttpp) REVERT: V 81 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7532 (mt-10) REVERT: V 129 GLU cc_start: 0.6681 (mt-10) cc_final: 0.6261 (tm-30) REVERT: W 6 LYS cc_start: 0.7697 (mmtp) cc_final: 0.7271 (mtmm) REVERT: W 46 LYS cc_start: 0.7477 (pttt) cc_final: 0.7112 (mmmt) REVERT: W 52 MET cc_start: 0.7352 (ttm) cc_final: 0.6984 (ttt) REVERT: W 88 ASP cc_start: 0.8084 (m-30) cc_final: 0.7801 (m-30) REVERT: W 135 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7897 (mt-10) REVERT: W 151 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: X 1 MET cc_start: 0.6358 (ttp) cc_final: 0.6108 (ptt) REVERT: X 6 LYS cc_start: 0.7736 (mmtp) cc_final: 0.7059 (mmpt) REVERT: X 66 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8028 (mt-10) outliers start: 80 outliers final: 29 residues processed: 862 average time/residue: 0.8322 time to fit residues: 826.9185 Evaluate side-chains 850 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 790 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN 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 129 SER Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 111 LYS 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 68 VAL Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 112 GLN Chi-restraints excluded: chain N residue 17 CYS Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 50 GLU 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 98 LEU Chi-restraints excluded: chain Q residue 74 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 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 39 LYS 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 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: 0.6980 chunk 15 optimal weight: 10.0000 chunk 281 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 349 optimal weight: 5.9990 chunk 327 optimal weight: 1.9990 chunk 282 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN F 131 HIS F 138 GLN I 60 GLN J 89 ASN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 N 151 GLN O 10 GLN O 148 ASN P 97 GLN R 148 ASN T 42 HIS V 10 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132992 restraints weight = 29227.337| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.14 r_work: 0.3392 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.631 31374 Z= 0.139 Angle : 0.521 19.305 42360 Z= 0.248 Chirality : 0.034 0.183 4656 Planarity : 0.003 0.040 5484 Dihedral : 5.251 78.414 4116 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.17 % Allowed : 16.19 % Favored : 81.65 % 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 aren not related in a simple way. whole: 4.26 (0.13), residues: 3696 helix: 3.34 (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 0.010 0.000 ARG V 13 TYR 0.024 0.002 TYR K 133 PHE 0.024 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 covalent geometry : bond 0.00308 (31368) covalent geometry : angle 0.52133 (42360) hydrogen bonds : bond 0.04164 ( 2652) hydrogen bonds : angle 3.53382 ( 7956) Misc. bond : bond 0.46763 ( 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 890 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 818 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6999 (mm-30) REVERT: A 115 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7092 (tm-30) REVERT: B 43 ARG cc_start: 0.7559 (tpt170) cc_final: 0.7205 (tpt170) REVERT: B 112 LYS cc_start: 0.8085 (mptt) cc_final: 0.7395 (mtmt) REVERT: C 1 MET cc_start: 0.6913 (ptm) cc_final: 0.6235 (ptm) REVERT: C 22 MET cc_start: 0.7511 (ttp) cc_final: 0.7173 (ttm) REVERT: C 50 ASP cc_start: 0.7221 (m-30) cc_final: 0.6465 (t0) REVERT: C 66 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7478 (mp0) REVERT: C 75 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7807 (mt-10) REVERT: D 1 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7100 (ptt) REVERT: D 5 LYS cc_start: 0.7228 (mppt) cc_final: 0.6914 (mptp) REVERT: D 42 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7058 (mt-10) REVERT: D 52 LYS cc_start: 0.6873 (tptt) cc_final: 0.5644 (mtmm) REVERT: D 66 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: D 88 ARG cc_start: 0.7813 (mtm110) cc_final: 0.7209 (mmt-90) REVERT: D 117 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7555 (ttt90) REVERT: D 118 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6270 (mt-10) REVERT: D 125 ASP cc_start: 0.8009 (t70) cc_final: 0.7757 (t0) REVERT: E 115 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.6319 (tm-30) REVERT: E 122 VAL cc_start: 0.8181 (p) cc_final: 0.7909 (m) REVERT: E 136 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7770 (mp0) REVERT: F 22 MET cc_start: 0.7708 (ttp) cc_final: 0.7198 (ttp) REVERT: F 52 LYS cc_start: 0.6930 (tptt) cc_final: 0.6503 (tptt) REVERT: F 96 LYS cc_start: 0.7853 (ttpp) cc_final: 0.7554 (tttm) REVERT: F 103 LYS cc_start: 0.7771 (mtmt) cc_final: 0.7274 (ttmt) REVERT: F 115 GLN cc_start: 0.8418 (tp40) cc_final: 0.8200 (tp-100) REVERT: F 118 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.6025 (mt-10) REVERT: G 50 ASP cc_start: 0.6841 (m-30) cc_final: 0.5860 (t0) REVERT: G 66 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7741 (mp0) REVERT: G 96 LYS cc_start: 0.7872 (ttpp) cc_final: 0.7192 (tmtm) REVERT: G 100 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7218 (m-30) REVERT: G 112 LYS cc_start: 0.8156 (mmtm) cc_final: 0.7737 (mmmt) REVERT: G 115 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: H 1 MET cc_start: 0.6266 (ptt) cc_final: 0.5774 (mtm) REVERT: H 57 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7655 (mtpt) REVERT: H 66 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7833 (mt-10) REVERT: H 96 LYS cc_start: 0.8085 (tttm) cc_final: 0.7674 (ttpt) REVERT: H 103 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7657 (tttm) REVERT: H 125 ASP cc_start: 0.8037 (t0) cc_final: 0.7696 (t70) REVERT: I 1 MET cc_start: 0.6757 (ptm) cc_final: 0.6382 (ptm) REVERT: I 9 ASP cc_start: 0.7938 (m-30) cc_final: 0.7580 (m-30) REVERT: I 42 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6980 (mt-10) REVERT: I 50 ASP cc_start: 0.6240 (m-30) cc_final: 0.5548 (t70) REVERT: I 75 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7358 (mm-30) REVERT: I 112 LYS cc_start: 0.8192 (mmtm) cc_final: 0.7367 (mtpm) REVERT: J 1 MET cc_start: 0.6883 (ptm) cc_final: 0.6617 (ptt) REVERT: J 50 ASP cc_start: 0.7072 (m-30) cc_final: 0.6743 (m-30) REVERT: J 57 LYS cc_start: 0.7587 (mtmt) cc_final: 0.7275 (mttm) REVERT: J 103 LYS cc_start: 0.7888 (mtmt) cc_final: 0.7183 (mmtt) REVERT: J 110 GLN cc_start: 0.7425 (mt0) cc_final: 0.7106 (mt0) REVERT: K 1 MET cc_start: 0.6925 (ptm) cc_final: 0.6474 (ptt) REVERT: K 42 GLU cc_start: 0.7523 (mt-10) cc_final: 0.6551 (tm-30) REVERT: K 66 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7873 (mp0) REVERT: K 88 ARG cc_start: 0.7191 (mtm110) cc_final: 0.6778 (mmt180) REVERT: K 96 LYS cc_start: 0.7974 (mtpp) cc_final: 0.7348 (mtmm) REVERT: K 103 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7122 (mmtt) REVERT: K 110 GLN cc_start: 0.7591 (tt0) cc_final: 0.7365 (tt0) REVERT: L 1 MET cc_start: 0.6771 (ptm) cc_final: 0.6234 (ptt) REVERT: L 42 GLU cc_start: 0.7625 (mt-10) cc_final: 0.6768 (pp20) REVERT: L 52 LYS cc_start: 0.7171 (OUTLIER) cc_final: 0.5749 (mtmm) REVERT: L 57 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7789 (mppt) REVERT: L 66 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7398 (mp0) REVERT: L 112 LYS cc_start: 0.8466 (mppt) cc_final: 0.7562 (mtmt) REVERT: L 125 ASP cc_start: 0.8038 (t0) cc_final: 0.7741 (t70) REVERT: M 112 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7285 (mp10) REVERT: N 1 MET cc_start: 0.5961 (ptt) cc_final: 0.5687 (ptt) REVERT: N 76 LYS cc_start: 0.8439 (tmtt) cc_final: 0.8079 (tptp) REVERT: O 1 MET cc_start: 0.6832 (ttp) cc_final: 0.5838 (ptp) REVERT: O 13 ARG cc_start: 0.7391 (ttm-80) cc_final: 0.7092 (mtm-85) REVERT: O 50 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6822 (pp20) REVERT: O 68 LEU cc_start: 0.8348 (mt) cc_final: 0.8030 (mm) REVERT: O 97 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7238 (tp40) REVERT: O 138 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.6609 (ttm-80) REVERT: P 39 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7327 (ttmt) REVERT: P 57 LYS cc_start: 0.7476 (mtmt) cc_final: 0.7173 (mttm) REVERT: P 97 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7078 (tp-100) REVERT: P 127 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7032 (mm-30) REVERT: Q 39 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8181 (mtpt) REVERT: Q 53 LYS cc_start: 0.7946 (mttp) cc_final: 0.7544 (mttp) REVERT: Q 57 LYS cc_start: 0.7737 (mtmt) cc_final: 0.7418 (mttt) REVERT: Q 81 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: Q 98 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7460 (mp) REVERT: Q 125 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6757 (mt-10) REVERT: Q 139 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.6892 (tm-30) REVERT: R 6 LYS cc_start: 0.7934 (mmtp) cc_final: 0.7596 (mttp) REVERT: R 13 ARG cc_start: 0.7550 (ttm-80) cc_final: 0.7310 (mtp85) REVERT: R 96 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7056 (pt0) REVERT: R 129 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6583 (tm-30) REVERT: S 1 MET cc_start: 0.6605 (ptm) cc_final: 0.6288 (ptt) REVERT: S 45 TYR cc_start: 0.7905 (t80) cc_final: 0.7700 (t80) REVERT: S 57 LYS cc_start: 0.7961 (mttm) cc_final: 0.7692 (mttp) REVERT: S 96 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7006 (tm-30) REVERT: T 6 LYS cc_start: 0.7810 (mmtp) cc_final: 0.7252 (mtmm) REVERT: T 13 ARG cc_start: 0.7406 (ttm-80) cc_final: 0.7043 (mtm-85) REVERT: T 53 LYS cc_start: 0.7891 (mttp) cc_final: 0.7524 (mtmt) REVERT: T 57 LYS cc_start: 0.8076 (mtmt) cc_final: 0.7497 (mmtt) REVERT: T 73 GLN cc_start: 0.7447 (mm-40) cc_final: 0.6866 (tp40) REVERT: T 74 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6903 (mp) REVERT: T 75 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7196 (mm-30) REVERT: T 96 GLU cc_start: 0.7323 (tm-30) cc_final: 0.7082 (mt-10) REVERT: T 103 ASP cc_start: 0.8134 (m-30) cc_final: 0.7733 (m-30) REVERT: U 6 LYS cc_start: 0.7962 (mptm) cc_final: 0.7503 (mtmm) REVERT: U 10 GLN cc_start: 0.7912 (mm110) cc_final: 0.7640 (mm110) REVERT: U 33 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7601 (ttpp) REVERT: U 39 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7856 (mttm) REVERT: U 45 TYR cc_start: 0.8005 (t80) cc_final: 0.7199 (t80) REVERT: U 68 LEU cc_start: 0.8716 (mt) cc_final: 0.8445 (mm) REVERT: U 76 LYS cc_start: 0.8506 (tmtt) cc_final: 0.8305 (tmtm) REVERT: U 91 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7522 (tp) REVERT: U 113 ASP cc_start: 0.8331 (t70) cc_final: 0.7917 (t70) REVERT: V 33 LYS cc_start: 0.8335 (tttt) cc_final: 0.7635 (ttpp) REVERT: V 81 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7526 (mt-10) REVERT: V 129 GLU cc_start: 0.6676 (mt-10) cc_final: 0.6258 (tm-30) REVERT: W 6 LYS cc_start: 0.7685 (mmtp) cc_final: 0.7259 (mtmm) REVERT: W 46 LYS cc_start: 0.7464 (pttt) cc_final: 0.7103 (mmmt) REVERT: W 52 MET cc_start: 0.7352 (ttm) cc_final: 0.6982 (ttt) REVERT: W 88 ASP cc_start: 0.8080 (m-30) cc_final: 0.7797 (m-30) REVERT: W 135 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7885 (mt-10) REVERT: W 151 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: X 1 MET cc_start: 0.6330 (ttp) cc_final: 0.6050 (ptt) REVERT: X 6 LYS cc_start: 0.7740 (mmtp) cc_final: 0.7060 (mmpt) REVERT: X 66 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8019 (mt-10) outliers start: 72 outliers final: 29 residues processed: 853 average time/residue: 0.8312 time to fit residues: 817.5044 Evaluate side-chains 851 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 792 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN 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 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 K residue 81 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 57 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 112 GLN Chi-restraints excluded: chain N residue 17 CYS Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 50 GLU 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 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 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 39 LYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 6 optimal weight: 0.8980 chunk 230 optimal weight: 5.9990 chunk 335 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 315 optimal weight: 4.9990 chunk 321 optimal weight: 3.9990 chunk 342 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 273 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN F 138 GLN J 89 ASN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 R 148 ASN S 148 ASN T 42 HIS V 10 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.131573 restraints weight = 29202.889| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.22 r_work: 0.3374 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.642 31374 Z= 0.136 Angle : 0.522 20.055 42360 Z= 0.250 Chirality : 0.034 0.201 4656 Planarity : 0.003 0.052 5484 Dihedral : 5.194 77.968 4116 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.93 % Allowed : 16.55 % 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 aren not related in a simple way. whole: 4.26 (0.13), residues: 3696 helix: 3.33 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.62 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG V 13 TYR 0.025 0.002 TYR K 133 PHE 0.024 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 covalent geometry : bond 0.00298 (31368) covalent geometry : angle 0.52231 (42360) hydrogen bonds : bond 0.04137 ( 2652) hydrogen bonds : angle 3.53327 ( 7956) Misc. bond : bond 0.43786 ( 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 867 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 803 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7161 (mm-30) REVERT: A 115 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: B 43 ARG cc_start: 0.7664 (tpt170) cc_final: 0.7311 (tpt170) REVERT: B 112 LYS cc_start: 0.8194 (mptt) cc_final: 0.7534 (mtmt) REVERT: C 1 MET cc_start: 0.6967 (ptm) cc_final: 0.6304 (ptm) REVERT: C 22 MET cc_start: 0.7637 (ttp) cc_final: 0.7304 (ttm) REVERT: C 50 ASP cc_start: 0.7364 (m-30) cc_final: 0.6636 (t0) REVERT: C 66 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7581 (mp0) REVERT: C 75 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7827 (mt-10) REVERT: D 1 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7195 (ptt) REVERT: D 5 LYS cc_start: 0.7286 (mppt) cc_final: 0.6994 (mptp) REVERT: D 42 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7147 (mt-10) REVERT: D 52 LYS cc_start: 0.7049 (tptt) cc_final: 0.5852 (mtmm) REVERT: D 66 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: D 88 ARG cc_start: 0.7954 (mtm110) cc_final: 0.7368 (mmt-90) REVERT: D 117 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7736 (ttt90) REVERT: D 118 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6427 (mt-10) REVERT: D 125 ASP cc_start: 0.8113 (t70) cc_final: 0.7871 (t0) REVERT: E 115 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.6470 (tm-30) REVERT: E 122 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.8048 (m) REVERT: E 136 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7871 (mp0) REVERT: F 22 MET cc_start: 0.7832 (ttp) cc_final: 0.7343 (ttp) REVERT: F 52 LYS cc_start: 0.7027 (tptt) cc_final: 0.6609 (tptt) REVERT: F 96 LYS cc_start: 0.7978 (ttpp) cc_final: 0.7691 (tttm) REVERT: F 103 LYS cc_start: 0.7887 (mtmt) cc_final: 0.7418 (ttmt) REVERT: F 118 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.6206 (mt-10) REVERT: G 50 ASP cc_start: 0.6957 (m-30) cc_final: 0.6004 (t0) REVERT: G 66 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7873 (mp0) REVERT: G 96 LYS cc_start: 0.7983 (ttpp) cc_final: 0.7327 (tmtm) REVERT: G 100 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7353 (m-30) REVERT: G 112 LYS cc_start: 0.8220 (mmtm) cc_final: 0.7850 (mmmt) REVERT: G 115 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: H 1 MET cc_start: 0.6388 (ptt) cc_final: 0.6027 (mtm) REVERT: H 57 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7754 (mtpt) REVERT: H 66 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7907 (mt-10) REVERT: H 96 LYS cc_start: 0.8198 (tttm) cc_final: 0.7807 (ttpt) REVERT: H 103 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7793 (tttm) REVERT: H 125 ASP cc_start: 0.8144 (t0) cc_final: 0.7821 (t70) REVERT: I 1 MET cc_start: 0.6824 (ptm) cc_final: 0.6451 (ptm) REVERT: I 9 ASP cc_start: 0.8066 (m-30) cc_final: 0.7765 (m-30) REVERT: I 42 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7051 (mt-10) REVERT: I 50 ASP cc_start: 0.6360 (m-30) cc_final: 0.5701 (t70) REVERT: I 75 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7417 (mm-30) REVERT: I 112 LYS cc_start: 0.8264 (mmtm) cc_final: 0.7480 (mtpm) REVERT: J 1 MET cc_start: 0.6971 (ptm) cc_final: 0.6716 (ptt) REVERT: J 57 LYS cc_start: 0.7720 (mtmt) cc_final: 0.7433 (mttm) REVERT: J 103 LYS cc_start: 0.7989 (mtmt) cc_final: 0.7346 (mmtt) REVERT: J 110 GLN cc_start: 0.7558 (mt0) cc_final: 0.7256 (mt0) REVERT: K 1 MET cc_start: 0.7016 (ptm) cc_final: 0.6768 (ptm) REVERT: K 42 GLU cc_start: 0.7606 (mt-10) cc_final: 0.6657 (tm-30) REVERT: K 66 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7971 (mp0) REVERT: K 88 ARG cc_start: 0.7345 (mtm110) cc_final: 0.6967 (mmt180) REVERT: K 96 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7464 (mtmm) REVERT: K 103 LYS cc_start: 0.8202 (mtmt) cc_final: 0.7261 (mmtt) REVERT: K 110 GLN cc_start: 0.7645 (tt0) cc_final: 0.7423 (tt0) REVERT: L 1 MET cc_start: 0.6835 (ptm) cc_final: 0.6300 (ptt) REVERT: L 42 GLU cc_start: 0.7695 (mt-10) cc_final: 0.6864 (pp20) REVERT: L 51 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7708 (mm-30) REVERT: L 52 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.5886 (mtmm) REVERT: L 57 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7901 (mppt) REVERT: L 66 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7497 (mp0) REVERT: L 112 LYS cc_start: 0.8550 (mppt) cc_final: 0.7695 (mtmt) REVERT: L 125 ASP cc_start: 0.8150 (t0) cc_final: 0.7867 (t70) REVERT: M 112 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7467 (mp10) REVERT: N 1 MET cc_start: 0.6081 (ptt) cc_final: 0.5818 (ptt) REVERT: N 76 LYS cc_start: 0.8489 (tmtt) cc_final: 0.8143 (tptp) REVERT: O 1 MET cc_start: 0.6989 (ttp) cc_final: 0.6016 (ptp) REVERT: O 50 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6940 (pp20) REVERT: O 68 LEU cc_start: 0.8425 (mt) cc_final: 0.8118 (mm) REVERT: O 94 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.8097 (p) REVERT: O 97 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7351 (tp40) REVERT: O 138 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.6745 (ttm-80) REVERT: P 39 LYS cc_start: 0.7965 (ttpt) cc_final: 0.7480 (ttmt) REVERT: P 57 LYS cc_start: 0.7637 (mtmt) cc_final: 0.7344 (mttm) REVERT: Q 39 LYS cc_start: 0.8711 (ttmm) cc_final: 0.8251 (mtpt) REVERT: Q 53 LYS cc_start: 0.8077 (mttp) cc_final: 0.7679 (mttp) REVERT: Q 57 LYS cc_start: 0.7873 (mtmt) cc_final: 0.7573 (mttt) REVERT: Q 81 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: Q 125 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6904 (mt-10) REVERT: Q 139 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.6977 (tm-30) REVERT: R 6 LYS cc_start: 0.8046 (mmtp) cc_final: 0.7725 (mttp) REVERT: R 13 ARG cc_start: 0.7661 (ttm-80) cc_final: 0.7446 (mtp85) REVERT: R 96 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7213 (pt0) REVERT: R 129 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6743 (tm-30) REVERT: S 1 MET cc_start: 0.6657 (ptm) cc_final: 0.6367 (ptt) REVERT: S 45 TYR cc_start: 0.7985 (t80) cc_final: 0.7739 (t80) REVERT: S 57 LYS cc_start: 0.8112 (mttm) cc_final: 0.7849 (mttp) REVERT: S 96 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7144 (tm-30) REVERT: T 6 LYS cc_start: 0.7933 (mmtp) cc_final: 0.7387 (mtmm) REVERT: T 13 ARG cc_start: 0.7550 (ttm-80) cc_final: 0.7204 (mtm-85) REVERT: T 53 LYS cc_start: 0.7990 (mttp) cc_final: 0.7659 (mtmt) REVERT: T 57 LYS cc_start: 0.8219 (mtmt) cc_final: 0.7676 (mmtt) REVERT: T 73 GLN cc_start: 0.7502 (mm-40) cc_final: 0.6954 (tp40) REVERT: T 75 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7254 (mm-30) REVERT: T 96 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7189 (mt-10) REVERT: T 103 ASP cc_start: 0.8237 (m-30) cc_final: 0.7883 (m-30) REVERT: U 10 GLN cc_start: 0.8038 (mm110) cc_final: 0.7782 (mm110) REVERT: U 33 LYS cc_start: 0.8280 (ttpp) cc_final: 0.7706 (ttpp) REVERT: U 39 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7965 (mttm) REVERT: U 45 TYR cc_start: 0.8086 (t80) cc_final: 0.7309 (t80) REVERT: U 68 LEU cc_start: 0.8757 (mt) cc_final: 0.8499 (mm) REVERT: U 91 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7604 (tp) REVERT: U 113 ASP cc_start: 0.8422 (t70) cc_final: 0.8048 (t70) REVERT: V 33 LYS cc_start: 0.8413 (tttt) cc_final: 0.7753 (ttpp) REVERT: V 81 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7576 (mt-10) REVERT: V 129 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6428 (tm-30) REVERT: W 6 LYS cc_start: 0.7779 (mmtp) cc_final: 0.7365 (mtmm) REVERT: W 46 LYS cc_start: 0.7571 (pttt) cc_final: 0.7241 (mmmt) REVERT: W 52 MET cc_start: 0.7420 (ttm) cc_final: 0.7077 (ttt) REVERT: W 88 ASP cc_start: 0.8217 (m-30) cc_final: 0.7944 (m-30) REVERT: W 135 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7932 (mt-10) REVERT: W 151 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: X 1 MET cc_start: 0.6392 (ttp) cc_final: 0.6136 (ptt) REVERT: X 6 LYS cc_start: 0.7853 (mmtp) cc_final: 0.7191 (mmpt) REVERT: X 66 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8110 (mt-10) outliers start: 64 outliers final: 30 residues processed: 838 average time/residue: 0.8446 time to fit residues: 814.6566 Evaluate side-chains 856 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 797 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN 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 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 K residue 81 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 57 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 112 GLN Chi-restraints excluded: chain N residue 17 CYS Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 50 GLU 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 98 LEU 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 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 39 LYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 128 optimal weight: 0.9980 chunk 288 optimal weight: 0.7980 chunk 307 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 177 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN F 115 GLN I 131 HIS J 89 ASN J 149 ASN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 GLN K 89 ASN L 60 GLN ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 ASN N 70 ASN N 151 GLN O 148 ASN R 148 ASN T 42 HIS V 10 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.146713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.134490 restraints weight = 29366.793| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.19 r_work: 0.3397 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.557 31374 Z= 0.122 Angle : 0.502 16.341 42360 Z= 0.244 Chirality : 0.033 0.199 4656 Planarity : 0.002 0.041 5484 Dihedral : 5.092 77.405 4116 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.65 % Allowed : 17.09 % Favored : 81.26 % 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 aren not related in a simple way. whole: 4.32 (0.13), residues: 3696 helix: 3.37 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.59 (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 S 26 TRP 0.005 0.001 TRP X 133 HIS 0.009 0.001 HIS T 42 Details of bonding type rmsd covalent geometry : bond 0.00263 (31368) covalent geometry : angle 0.50223 (42360) hydrogen bonds : bond 0.03985 ( 2652) hydrogen bonds : angle 3.48477 ( 7956) Misc. bond : bond 0.39200 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16237.18 seconds wall clock time: 276 minutes 41.15 seconds (16601.15 seconds total)