Starting phenix.real_space_refine on Wed Jun 25 18:10:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iig_60594/06_2025/9iig_60594_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iig_60594/06_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_60594/06_2025/9iig_60594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iig_60594/06_2025/9iig_60594.map" model { file = "/net/cci-nas-00/data/ceres_data/9iig_60594/06_2025/9iig_60594_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iig_60594/06_2025/9iig_60594_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.25, per 1000 atoms: 0.56 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: 7.78 Conformation dependent library (CDL) restraints added in 3.6 seconds 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7128 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 0 sheets defined 85.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 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: 10.20 Time building geometry restraints manager: 9.14 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: 0.24 Found NCS groups: ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'W' selection = chain 'V' } ncs_group { reference = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'X' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' selection = chain 'G' selection = chain 'K' } 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: 6.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.570 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 63.750 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.230 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:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.380 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (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 TRP 0.032 0.003 TRP O 35 HIS 0.008 0.002 HIS P 34 PHE 0.026 0.004 PHE B 26 TYR 0.022 0.004 TYR G 93 ARG 0.012 0.002 ARG I 117 Details of bonding type rmsd hydrogen bonds : bond 0.09209 ( 2652) hydrogen bonds : angle 5.14087 ( 7956) covalent geometry : bond 0.00817 (31368) covalent geometry : angle 0.74121 (42360) 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 : 3.464 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: 0.8108 (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: 0.7471 (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: 0.7518 (ttm) REVERT: F 52 LYS cc_start: 0.6940 (tptt) cc_final: 0.6608 (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: 0.7504 (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: 0.7544 (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: 0.7609 (mmtt) REVERT: J 110 GLN cc_start: 0.7573 (mt0) cc_final: 0.7271 (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: 0.7181 (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: 0.7216 (mtm) REVERT: L 42 GLU cc_start: 0.7594 (mt-10) cc_final: 0.6980 (tm-30) REVERT: L 52 LYS cc_start: 0.7095 (tptt) cc_final: 0.6885 (tptt) 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: 0.7164 (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: 0.7035 (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: 0.7589 (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: 0.7330 (m-30) REVERT: S 73 GLN cc_start: 0.7420 (mm110) cc_final: 0.7005 (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: 0.7926 (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: 0.7640 (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: 0.7476 (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: 1.6650 time to fit residues: 2144.4356 Evaluate side-chains 838 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 837 time to evaluate : 3.741 ------------------------------------------------------------------------------- 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 303 optimal weight: 2.9990 chunk 272 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 282 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 326 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.149423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.138261 restraints weight = 28836.658| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.07 r_work: 0.3458 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.547 31374 Z= 0.125 Angle : 0.514 15.949 42360 Z= 0.245 Chirality : 0.032 0.120 4656 Planarity : 0.003 0.043 5484 Dihedral : 6.337 86.943 4118 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.23 % Allowed : 10.50 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.13), residues: 3696 helix: 2.45 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.92 (0.20), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 35 HIS 0.006 0.001 HIS J 131 PHE 0.024 0.002 PHE U 26 TYR 0.020 0.002 TYR D 133 ARG 0.005 0.001 ARG C 74 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 2652) hydrogen bonds : angle 3.86107 ( 7956) covalent geometry : bond 0.00269 (31368) covalent geometry : angle 0.51445 (42360) Misc. bond : bond 0.45911 ( 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 991 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 917 time to evaluate : 3.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7294 (mm-30) cc_final: 0.7063 (mm-30) REVERT: A 115 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: B 39 GLU cc_start: 0.7694 (tt0) cc_final: 0.7337 (tt0) REVERT: B 43 ARG cc_start: 0.7606 (tpt170) cc_final: 0.7206 (tpt170) REVERT: B 112 LYS cc_start: 0.8136 (mptt) cc_final: 0.7408 (mmmt) REVERT: C 1 MET cc_start: 0.6687 (ptm) cc_final: 0.6295 (ptm) REVERT: C 43 ARG cc_start: 0.7359 (tpt170) cc_final: 0.7120 (tpt170) REVERT: C 50 ASP cc_start: 0.7265 (m-30) cc_final: 0.6787 (t0) REVERT: C 52 LYS cc_start: 0.6796 (tptt) cc_final: 0.5930 (mtmm) REVERT: C 66 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7573 (mp0) REVERT: C 112 LYS cc_start: 0.8057 (mmtm) cc_final: 0.7456 (mmmt) REVERT: D 1 MET cc_start: 0.7825 (ptp) cc_final: 0.7021 (ptt) REVERT: D 24 GLN cc_start: 0.8508 (tt0) cc_final: 0.8217 (tt0) REVERT: D 52 LYS cc_start: 0.6931 (tptt) cc_final: 0.5750 (mtmm) REVERT: D 66 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8086 (mp0) REVERT: D 115 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7541 (tm130) REVERT: D 117 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7798 (ttt90) REVERT: E 115 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.6423 (tm-30) REVERT: E 122 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.8032 (m) REVERT: F 22 MET cc_start: 0.7802 (ttp) cc_final: 0.7353 (ttp) REVERT: F 52 LYS cc_start: 0.6857 (tptt) cc_final: 0.6545 (tptt) REVERT: F 103 LYS cc_start: 0.7858 (mtmt) cc_final: 0.7392 (ttpt) REVERT: G 13 ARG cc_start: 0.7451 (mtm110) cc_final: 0.7191 (mtm-85) REVERT: G 66 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7872 (mp0) REVERT: G 96 LYS cc_start: 0.7894 (ttpp) cc_final: 0.7383 (tmtm) REVERT: G 100 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7219 (m-30) REVERT: G 115 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7748 (tm-30) REVERT: G 125 ASP cc_start: 0.7845 (t70) cc_final: 0.7566 (t0) REVERT: H 1 MET cc_start: 0.7166 (ptp) cc_final: 0.6950 (ptt) REVERT: I 9 ASP cc_start: 0.7956 (m-30) cc_final: 0.7655 (m-30) REVERT: I 50 ASP cc_start: 0.6455 (m-30) cc_final: 0.5892 (t0) REVERT: I 75 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7433 (mm-30) REVERT: J 50 ASP cc_start: 0.7147 (m-30) cc_final: 0.6925 (m-30) REVERT: J 57 LYS cc_start: 0.7660 (mtmt) cc_final: 0.7376 (mttm) REVERT: J 96 LYS cc_start: 0.7876 (ttpp) cc_final: 0.7516 (ttpp) REVERT: J 103 LYS cc_start: 0.7880 (mtmt) cc_final: 0.7288 (mmtt) REVERT: J 110 GLN cc_start: 0.7548 (mt0) cc_final: 0.7191 (mt0) REVERT: K 1 MET cc_start: 0.6933 (ptm) cc_final: 0.6694 (ptm) REVERT: K 66 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7874 (mp0) REVERT: K 88 ARG cc_start: 0.7209 (mtm110) cc_final: 0.6788 (mmt180) REVERT: K 103 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7151 (mmtt) REVERT: L 1 MET cc_start: 0.6954 (ptm) cc_final: 0.6568 (ptp) REVERT: L 22 MET cc_start: 0.7337 (ttp) cc_final: 0.6950 (mtp) REVERT: L 51 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7808 (mm-30) REVERT: L 112 LYS cc_start: 0.8446 (mppt) cc_final: 0.7560 (mmmt) REVERT: L 152 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8416 (tt0) REVERT: O 1 MET cc_start: 0.6790 (ttp) cc_final: 0.6236 (ptp) REVERT: O 13 ARG cc_start: 0.7352 (ttm-80) cc_final: 0.7090 (ttm110) REVERT: O 51 ASP cc_start: 0.7719 (m-30) cc_final: 0.7505 (m-30) REVERT: O 68 LEU cc_start: 0.8436 (mt) cc_final: 0.8170 (mm) REVERT: O 75 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7399 (mt-10) REVERT: O 96 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7031 (tm-30) REVERT: O 138 ARG cc_start: 0.7480 (ttm-80) cc_final: 0.6786 (ttm-80) REVERT: P 1 MET cc_start: 0.7126 (ttp) cc_final: 0.6741 (ttp) REVERT: P 38 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8053 (mm-30) REVERT: P 57 LYS cc_start: 0.7591 (mtmt) cc_final: 0.7311 (mttt) REVERT: P 76 LYS cc_start: 0.7714 (mmtt) cc_final: 0.7220 (tptt) REVERT: Q 53 LYS cc_start: 0.8088 (mttp) cc_final: 0.7741 (mttp) REVERT: Q 57 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7562 (mttt) REVERT: Q 81 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: Q 125 GLU cc_start: 0.7168 (pt0) cc_final: 0.6701 (mt-10) REVERT: R 1 MET cc_start: 0.6920 (ttp) cc_final: 0.6688 (ttp) REVERT: R 6 LYS cc_start: 0.8034 (mmtp) cc_final: 0.7762 (mttp) REVERT: R 97 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: R 129 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6775 (mt-10) REVERT: S 6 LYS cc_start: 0.8243 (mmtp) cc_final: 0.7848 (mptt) REVERT: S 45 TYR cc_start: 0.7835 (t80) cc_final: 0.7602 (t80) REVERT: S 73 GLN cc_start: 0.6892 (mm110) cc_final: 0.6647 (tt0) REVERT: S 96 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6920 (tm-30) REVERT: T 6 LYS cc_start: 0.7887 (mmtp) cc_final: 0.7355 (mtmm) REVERT: T 13 ARG cc_start: 0.7378 (ttm-80) cc_final: 0.6931 (mtm-85) REVERT: T 53 LYS cc_start: 0.7953 (mttp) cc_final: 0.7634 (mttt) REVERT: T 73 GLN cc_start: 0.7464 (mm-40) cc_final: 0.6799 (tp40) REVERT: T 75 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7596 (mm-30) REVERT: T 96 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7195 (tt0) REVERT: T 103 ASP cc_start: 0.8037 (m-30) cc_final: 0.7652 (m-30) REVERT: T 127 GLU cc_start: 0.6723 (mm-30) cc_final: 0.6282 (mm-30) REVERT: U 10 GLN cc_start: 0.8014 (mm110) cc_final: 0.7777 (mm110) REVERT: U 68 LEU cc_start: 0.8735 (mt) cc_final: 0.8471 (mm) REVERT: U 96 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: U 126 ASP cc_start: 0.7915 (m-30) cc_final: 0.7631 (m-30) REVERT: V 13 ARG cc_start: 0.7686 (ttm110) cc_final: 0.7267 (mtm-85) REVERT: V 33 LYS cc_start: 0.8268 (ttmt) cc_final: 0.7682 (ttpp) REVERT: V 81 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7474 (mt-10) REVERT: V 96 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7165 (pt0) REVERT: V 129 GLU cc_start: 0.6634 (mt-10) cc_final: 0.6345 (tm-30) REVERT: W 6 LYS cc_start: 0.7845 (mmtp) cc_final: 0.7388 (mtmm) REVERT: W 13 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7624 (mtt90) REVERT: W 46 LYS cc_start: 0.7499 (pttt) cc_final: 0.7183 (mmmt) REVERT: W 66 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7580 (mm-30) REVERT: W 88 ASP cc_start: 0.8112 (m-30) cc_final: 0.7833 (m-30) REVERT: W 100 LEU cc_start: 0.8369 (tt) cc_final: 0.8069 (tp) REVERT: W 129 GLU cc_start: 0.6650 (mt-10) cc_final: 0.6097 (pt0) REVERT: W 135 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7900 (mt-10) REVERT: W 151 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: X 6 LYS cc_start: 0.7858 (mmtp) cc_final: 0.7191 (mmpt) REVERT: X 66 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8029 (mt-10) outliers start: 74 outliers final: 10 residues processed: 947 average time/residue: 1.5988 time to fit residues: 1754.3572 Evaluate side-chains 850 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 823 time to evaluate : 3.457 ------------------------------------------------------------------------------- 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 74 LEU Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain R residue 97 GLN Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 96 GLU Chi-restraints excluded: chain V residue 96 GLU Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 151 GLN Chi-restraints excluded: chain X residue 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 62 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 169 optimal weight: 1.9990 chunk 312 optimal weight: 0.9980 chunk 197 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 346 optimal weight: 0.9990 chunk 241 optimal weight: 0.5980 chunk 214 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 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 ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 GLN L 115 GLN L 149 ASN M 70 ASN M 84 GLN N 70 ASN N 151 GLN O 148 ASN P 73 GLN ** P 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 112 GLN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 148 ASN T 41 ASN V 148 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.147269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.134998 restraints weight = 29055.605| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.22 r_work: 0.3408 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.539 31374 Z= 0.117 Angle : 0.473 14.181 42360 Z= 0.228 Chirality : 0.032 0.113 4656 Planarity : 0.003 0.030 5484 Dihedral : 5.898 88.596 4116 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.20 % Allowed : 12.85 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.13), residues: 3696 helix: 3.13 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.84 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 35 HIS 0.006 0.001 HIS T 42 PHE 0.022 0.002 PHE S 26 TYR 0.017 0.001 TYR D 133 ARG 0.004 0.001 ARG C 74 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 2652) hydrogen bonds : angle 3.60598 ( 7956) covalent geometry : bond 0.00249 (31368) covalent geometry : angle 0.47338 (42360) Misc. bond : bond 0.46221 ( 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: 73 poor density : 865 time to evaluate : 3.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7104 (mm-30) REVERT: A 115 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7292 (tm-30) REVERT: B 39 GLU cc_start: 0.7679 (tt0) cc_final: 0.7382 (tt0) REVERT: B 112 LYS cc_start: 0.8174 (mptt) cc_final: 0.7442 (mmmt) REVERT: C 1 MET cc_start: 0.6825 (ptm) cc_final: 0.6322 (ptm) REVERT: C 50 ASP cc_start: 0.7361 (m-30) cc_final: 0.6695 (t0) REVERT: C 52 LYS cc_start: 0.6828 (tptt) cc_final: 0.5958 (mtmm) REVERT: C 66 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7511 (mp0) REVERT: C 112 LYS cc_start: 0.8023 (mmtm) cc_final: 0.7426 (mmmt) REVERT: D 1 MET cc_start: 0.7872 (ptp) cc_final: 0.7173 (ptt) REVERT: D 5 LYS cc_start: 0.7359 (mppt) cc_final: 0.6444 (tttp) REVERT: D 24 GLN cc_start: 0.8564 (tt0) cc_final: 0.8258 (tt0) REVERT: D 52 LYS cc_start: 0.6980 (tptt) cc_final: 0.5744 (mtmm) REVERT: D 66 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8092 (mp0) REVERT: D 100 ASP cc_start: 0.7535 (t0) cc_final: 0.7271 (m-30) REVERT: D 118 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6481 (mt-10) REVERT: D 133 TYR cc_start: 0.7155 (t80) cc_final: 0.6954 (t80) REVERT: E 113 ASP cc_start: 0.8783 (t0) cc_final: 0.8558 (t70) REVERT: E 115 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.6319 (tm-30) REVERT: E 122 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.8004 (m) REVERT: F 103 LYS cc_start: 0.7899 (mtmt) cc_final: 0.7419 (ttmt) REVERT: G 13 ARG cc_start: 0.7531 (mtm110) cc_final: 0.7252 (mtm-85) REVERT: G 50 ASP cc_start: 0.6976 (m-30) cc_final: 0.6026 (t0) REVERT: G 66 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7861 (mp0) REVERT: G 96 LYS cc_start: 0.7932 (ttpp) cc_final: 0.7253 (tmtm) REVERT: G 100 ASP cc_start: 0.7707 (t0) cc_final: 0.7345 (m-30) REVERT: G 115 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: G 125 ASP cc_start: 0.7978 (t70) cc_final: 0.7730 (t0) REVERT: H 103 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7799 (tttm) REVERT: I 1 MET cc_start: 0.6799 (ptm) cc_final: 0.6431 (ptm) REVERT: I 9 ASP cc_start: 0.7956 (m-30) cc_final: 0.7640 (m-30) REVERT: I 50 ASP cc_start: 0.6485 (m-30) cc_final: 0.5833 (t70) REVERT: I 75 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7411 (mm-30) REVERT: I 103 LYS cc_start: 0.7998 (mtmt) cc_final: 0.7356 (mmpt) REVERT: I 112 LYS cc_start: 0.8103 (mmtm) cc_final: 0.7390 (mmmt) REVERT: J 1 MET cc_start: 0.6865 (ptm) cc_final: 0.6511 (ptt) REVERT: J 50 ASP cc_start: 0.7176 (m-30) cc_final: 0.6918 (m-30) REVERT: J 57 LYS cc_start: 0.7715 (mtmt) cc_final: 0.7429 (mttm) REVERT: J 96 LYS cc_start: 0.7950 (ttpp) cc_final: 0.7583 (ttpp) REVERT: J 103 LYS cc_start: 0.7969 (mtmt) cc_final: 0.7331 (mmtt) REVERT: J 110 GLN cc_start: 0.7533 (mt0) cc_final: 0.7203 (mt0) REVERT: K 1 MET cc_start: 0.6942 (ptm) cc_final: 0.6725 (ptm) REVERT: K 52 LYS cc_start: 0.6639 (tptt) cc_final: 0.5510 (mtmm) REVERT: K 66 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7873 (mp0) REVERT: K 88 ARG cc_start: 0.7288 (mtm110) cc_final: 0.6822 (mmt180) REVERT: K 103 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7188 (mmtt) REVERT: L 1 MET cc_start: 0.6890 (ptm) cc_final: 0.6404 (ptm) REVERT: L 52 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.5987 (mtmm) REVERT: L 112 LYS cc_start: 0.8532 (mppt) cc_final: 0.7683 (mmmt) REVERT: L 152 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8533 (tt0) REVERT: N 76 LYS cc_start: 0.8538 (tmtt) cc_final: 0.8304 (tmtt) REVERT: O 1 MET cc_start: 0.6776 (ttp) cc_final: 0.6122 (ptp) REVERT: O 13 ARG cc_start: 0.7444 (ttm-80) cc_final: 0.7023 (mtm110) REVERT: O 68 LEU cc_start: 0.8441 (mt) cc_final: 0.8163 (mm) REVERT: O 96 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7063 (tm-30) REVERT: O 138 ARG cc_start: 0.7522 (ttm-80) cc_final: 0.6768 (ttm-80) REVERT: P 1 MET cc_start: 0.7216 (ttp) cc_final: 0.6796 (ttp) REVERT: P 38 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8084 (mm-30) REVERT: P 57 LYS cc_start: 0.7613 (mtmt) cc_final: 0.7330 (mttt) REVERT: Q 57 LYS cc_start: 0.7846 (mtmt) cc_final: 0.7576 (mttt) REVERT: Q 81 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: Q 139 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: R 6 LYS cc_start: 0.8012 (mmtp) cc_final: 0.7708 (mttp) REVERT: R 85 GLU cc_start: 0.8130 (tt0) cc_final: 0.7813 (tt0) REVERT: R 97 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.7131 (tm-30) REVERT: R 129 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6986 (mt-10) REVERT: S 6 LYS cc_start: 0.8204 (mmtp) cc_final: 0.7772 (mmtm) REVERT: S 45 TYR cc_start: 0.7873 (t80) cc_final: 0.7600 (t80) REVERT: S 96 GLU cc_start: 0.7311 (tm-30) cc_final: 0.7017 (tm-30) REVERT: T 6 LYS cc_start: 0.7893 (mmtp) cc_final: 0.7413 (mttp) REVERT: T 13 ARG cc_start: 0.7420 (ttm-80) cc_final: 0.6997 (mtm-85) REVERT: T 53 LYS cc_start: 0.8052 (mttp) cc_final: 0.7729 (mttt) REVERT: T 73 GLN cc_start: 0.7443 (mm-40) cc_final: 0.6843 (tp-100) REVERT: T 96 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7180 (tt0) REVERT: T 103 ASP cc_start: 0.8169 (m-30) cc_final: 0.7794 (m-30) REVERT: U 10 GLN cc_start: 0.8081 (mm110) cc_final: 0.7834 (mm110) REVERT: U 68 LEU cc_start: 0.8736 (mt) cc_final: 0.8496 (mm) REVERT: U 126 ASP cc_start: 0.8004 (m-30) cc_final: 0.7739 (m-30) REVERT: V 33 LYS cc_start: 0.8345 (tttt) cc_final: 0.7648 (ttpp) REVERT: V 81 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7473 (mt-10) REVERT: V 96 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7164 (pt0) REVERT: V 129 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6386 (tm-30) REVERT: W 6 LYS cc_start: 0.7841 (mmtp) cc_final: 0.7345 (mtmm) REVERT: W 46 LYS cc_start: 0.7535 (pttt) cc_final: 0.7206 (mmmt) REVERT: W 66 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7633 (mm-30) REVERT: W 88 ASP cc_start: 0.8138 (m-30) cc_final: 0.7854 (m-30) REVERT: W 100 LEU cc_start: 0.8339 (tt) cc_final: 0.8056 (tp) REVERT: W 135 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7930 (mt-10) REVERT: X 6 LYS cc_start: 0.7826 (mmtp) cc_final: 0.7132 (mmpt) REVERT: X 39 LYS cc_start: 0.8323 (ttmt) cc_final: 0.8105 (mttt) outliers start: 73 outliers final: 17 residues processed: 894 average time/residue: 1.5496 time to fit residues: 1606.6872 Evaluate side-chains 835 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 806 time to evaluate : 3.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain C residue 4 ASP Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain 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 1 MET 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 U residue 84 GLN Chi-restraints excluded: chain W residue 94 VAL 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 107 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 236 optimal weight: 0.3980 chunk 153 optimal weight: 9.9990 chunk 230 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 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 W 41 ASN ** X 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 148 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.133026 restraints weight = 29359.502| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.23 r_work: 0.3385 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.568 31374 Z= 0.127 Angle : 0.489 18.194 42360 Z= 0.230 Chirality : 0.033 0.114 4656 Planarity : 0.003 0.034 5484 Dihedral : 5.725 88.028 4116 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.23 % Allowed : 13.63 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.23 (0.13), residues: 3696 helix: 3.32 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.74 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 133 HIS 0.006 0.001 HIS T 42 PHE 0.023 0.002 PHE S 26 TYR 0.019 0.002 TYR K 133 ARG 0.004 0.000 ARG D 74 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 2652) hydrogen bonds : angle 3.54019 ( 7956) covalent geometry : bond 0.00274 (31368) covalent geometry : angle 0.48920 (42360) Misc. bond : bond 0.46848 ( 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 922 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 848 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7122 (mm-30) REVERT: A 115 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: B 39 GLU cc_start: 0.7699 (tt0) cc_final: 0.7498 (tt0) REVERT: B 43 ARG cc_start: 0.7684 (tpt170) cc_final: 0.7337 (tpt170) REVERT: B 112 LYS cc_start: 0.8236 (mptt) cc_final: 0.7565 (mtmt) REVERT: C 1 MET cc_start: 0.6917 (ptm) cc_final: 0.6392 (ptm) REVERT: C 50 ASP cc_start: 0.7399 (m-30) cc_final: 0.6699 (t0) REVERT: C 52 LYS cc_start: 0.6866 (tptt) cc_final: 0.5971 (mtmm) REVERT: C 66 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7588 (mp0) REVERT: C 112 LYS cc_start: 0.8022 (mmtm) cc_final: 0.7427 (mmmt) REVERT: D 1 MET cc_start: 0.7877 (ptp) cc_final: 0.7208 (ptt) REVERT: D 5 LYS cc_start: 0.7319 (mppt) cc_final: 0.6419 (tttp) REVERT: D 24 GLN cc_start: 0.8573 (tt0) cc_final: 0.8262 (tt0) REVERT: D 52 LYS cc_start: 0.7029 (tptt) cc_final: 0.5771 (mtmm) REVERT: D 66 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: D 117 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7950 (ttt90) REVERT: D 118 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6483 (mt-10) REVERT: E 115 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.6432 (tm-30) REVERT: E 122 VAL cc_start: 0.8267 (OUTLIER) cc_final: 0.8002 (m) REVERT: F 22 MET cc_start: 0.7765 (ttp) cc_final: 0.7291 (ttm) REVERT: F 103 LYS cc_start: 0.7919 (mtmt) cc_final: 0.7441 (ttmt) REVERT: G 66 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7907 (mp0) REVERT: G 96 LYS cc_start: 0.7944 (ttpp) cc_final: 0.7284 (tmtm) REVERT: G 100 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7383 (m-30) REVERT: G 115 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: H 57 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7782 (mtpt) REVERT: H 103 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7776 (tttm) REVERT: I 1 MET cc_start: 0.6873 (ptm) cc_final: 0.6492 (ptm) REVERT: I 9 ASP cc_start: 0.8006 (m-30) cc_final: 0.7680 (m-30) REVERT: I 50 ASP cc_start: 0.6505 (m-30) cc_final: 0.5841 (t70) REVERT: I 75 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7402 (mm-30) REVERT: I 112 LYS cc_start: 0.8193 (mmtm) cc_final: 0.7500 (mmmt) REVERT: J 1 MET cc_start: 0.6917 (ptm) cc_final: 0.6588 (ptt) REVERT: J 50 ASP cc_start: 0.7193 (m-30) cc_final: 0.6956 (m-30) REVERT: J 57 LYS cc_start: 0.7717 (mtmt) cc_final: 0.7437 (mttm) REVERT: J 96 LYS cc_start: 0.7979 (ttpp) cc_final: 0.7698 (ttpp) REVERT: J 103 LYS cc_start: 0.8009 (mtmt) cc_final: 0.7374 (mmtt) REVERT: J 110 GLN cc_start: 0.7571 (mt0) cc_final: 0.7234 (mt0) REVERT: K 1 MET cc_start: 0.6990 (ptm) cc_final: 0.6718 (ptm) REVERT: K 52 LYS cc_start: 0.6652 (tptt) cc_final: 0.5548 (mtmm) REVERT: K 66 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7921 (mp0) REVERT: K 88 ARG cc_start: 0.7315 (mtm110) cc_final: 0.6891 (mmt180) REVERT: K 103 LYS cc_start: 0.8186 (mtmt) cc_final: 0.7235 (mmtt) REVERT: L 1 MET cc_start: 0.6881 (ptm) cc_final: 0.6424 (ptm) REVERT: L 42 GLU cc_start: 0.7679 (mt-10) cc_final: 0.6822 (pp20) REVERT: L 52 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6010 (mtmm) REVERT: L 112 LYS cc_start: 0.8537 (mppt) cc_final: 0.7693 (mtmt) REVERT: M 112 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8140 (mt0) REVERT: O 1 MET cc_start: 0.6840 (ttp) cc_final: 0.6105 (ptp) REVERT: O 68 LEU cc_start: 0.8446 (mt) cc_final: 0.8156 (mm) REVERT: O 138 ARG cc_start: 0.7580 (ttm-80) cc_final: 0.6786 (ttm-80) REVERT: P 1 MET cc_start: 0.7315 (ttp) cc_final: 0.6974 (ttp) REVERT: P 38 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7998 (mm-30) REVERT: P 57 LYS cc_start: 0.7659 (mtmt) cc_final: 0.7382 (mttm) REVERT: Q 39 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8217 (mtpt) REVERT: Q 53 LYS cc_start: 0.8126 (mttp) cc_final: 0.7720 (mttt) REVERT: Q 57 LYS cc_start: 0.7857 (mtmt) cc_final: 0.7584 (mttt) REVERT: Q 81 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: Q 125 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6898 (mt-10) REVERT: Q 139 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: R 6 LYS cc_start: 0.8030 (mmtp) cc_final: 0.7719 (mttp) REVERT: R 52 MET cc_start: 0.6951 (mtt) cc_final: 0.6746 (mtt) REVERT: R 85 GLU cc_start: 0.8150 (tt0) cc_final: 0.7833 (tt0) REVERT: R 97 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: R 129 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: S 1 MET cc_start: 0.6658 (ptm) cc_final: 0.6230 (ptt) REVERT: S 45 TYR cc_start: 0.7950 (t80) cc_final: 0.7685 (t80) REVERT: S 96 GLU cc_start: 0.7375 (tm-30) cc_final: 0.7052 (tm-30) REVERT: T 6 LYS cc_start: 0.7933 (mmtp) cc_final: 0.7399 (mtmm) REVERT: T 13 ARG cc_start: 0.7487 (ttm-80) cc_final: 0.7045 (mtm-85) REVERT: T 53 LYS cc_start: 0.8067 (mttp) cc_final: 0.7741 (mttt) REVERT: T 73 GLN cc_start: 0.7483 (mm-40) cc_final: 0.6890 (tp-100) REVERT: T 74 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.6975 (mp) REVERT: T 75 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7343 (mm-30) REVERT: T 96 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7253 (mt-10) REVERT: T 103 ASP cc_start: 0.8203 (m-30) cc_final: 0.7835 (m-30) REVERT: U 6 LYS cc_start: 0.8068 (mptm) cc_final: 0.7635 (mtmm) REVERT: U 10 GLN cc_start: 0.8053 (mm110) cc_final: 0.7828 (mm110) REVERT: U 68 LEU cc_start: 0.8770 (mt) cc_final: 0.8530 (mm) REVERT: U 91 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7626 (tp) REVERT: V 13 ARG cc_start: 0.7684 (ttm110) cc_final: 0.7194 (mtm-85) REVERT: V 33 LYS cc_start: 0.8378 (tttt) cc_final: 0.7704 (ttpp) REVERT: V 81 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7522 (mt-10) REVERT: V 96 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7152 (pt0) REVERT: V 129 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6424 (tm-30) REVERT: W 6 LYS cc_start: 0.7805 (mmtp) cc_final: 0.7395 (mtmm) REVERT: W 46 LYS cc_start: 0.7561 (pttt) cc_final: 0.7218 (mmmt) REVERT: W 66 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7653 (mm-30) REVERT: W 88 ASP cc_start: 0.8182 (m-30) cc_final: 0.7911 (m-30) REVERT: W 100 LEU cc_start: 0.8367 (tt) cc_final: 0.8067 (tp) REVERT: W 135 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7927 (mt-10) REVERT: W 151 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8173 (tt0) REVERT: X 6 LYS cc_start: 0.7835 (mmtp) cc_final: 0.7124 (mmpt) REVERT: X 51 ASP cc_start: 0.7559 (m-30) cc_final: 0.7331 (m-30) outliers start: 74 outliers final: 21 residues processed: 879 average time/residue: 1.5991 time to fit residues: 1629.5899 Evaluate side-chains 833 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 792 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain C residue 4 ASP Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 127 THR 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 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 96 GLU Chi-restraints excluded: chain R residue 97 GLN Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 155 SER Chi-restraints excluded: chain W residue 74 LEU Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 119 LEU Chi-restraints excluded: chain W residue 151 GLN Chi-restraints excluded: chain X residue 94 VAL Chi-restraints excluded: chain X residue 96 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 275 optimal weight: 0.0970 chunk 319 optimal weight: 0.9990 chunk 266 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** N 70 ASN O 10 GLN ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 GLN P 130 HIS R 148 ASN S 148 ASN T 42 HIS W 148 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.147515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.134881 restraints weight = 29002.095| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.25 r_work: 0.3398 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.590 31374 Z= 0.114 Angle : 0.475 15.848 42360 Z= 0.222 Chirality : 0.032 0.123 4656 Planarity : 0.002 0.029 5484 Dihedral : 5.514 88.662 4116 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.11 % Allowed : 14.50 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.41 (0.13), residues: 3696 helix: 3.44 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.68 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 133 HIS 0.008 0.001 HIS T 42 PHE 0.028 0.002 PHE U 26 TYR 0.020 0.001 TYR K 133 ARG 0.004 0.000 ARG L 74 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 2652) hydrogen bonds : angle 3.44746 ( 7956) covalent geometry : bond 0.00237 (31368) covalent geometry : angle 0.47540 (42360) Misc. bond : bond 0.48943 ( 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 915 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 845 time to evaluate : 4.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7116 (mm-30) REVERT: A 115 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7235 (tm-30) REVERT: A 126 ASP cc_start: 0.7898 (m-30) cc_final: 0.7654 (t0) REVERT: B 39 GLU cc_start: 0.7709 (tt0) cc_final: 0.7492 (tt0) REVERT: B 43 ARG cc_start: 0.7659 (tpt170) cc_final: 0.7270 (tpt170) REVERT: B 112 LYS cc_start: 0.8193 (mptt) cc_final: 0.7545 (mtmt) REVERT: C 1 MET cc_start: 0.6965 (ptm) cc_final: 0.6384 (ptm) REVERT: C 50 ASP cc_start: 0.7382 (m-30) cc_final: 0.6647 (t0) REVERT: C 52 LYS cc_start: 0.6855 (tptt) cc_final: 0.5945 (mtmm) REVERT: C 66 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7547 (mp0) REVERT: C 75 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7651 (mt-10) REVERT: C 112 LYS cc_start: 0.7921 (mmtm) cc_final: 0.7346 (mmmt) REVERT: D 1 MET cc_start: 0.7839 (ptp) cc_final: 0.7228 (ptt) REVERT: D 5 LYS cc_start: 0.7261 (mppt) cc_final: 0.6831 (mptp) REVERT: D 24 GLN cc_start: 0.8558 (tt0) cc_final: 0.8254 (tt0) REVERT: D 52 LYS cc_start: 0.7047 (tptt) cc_final: 0.5804 (mtmm) REVERT: D 66 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: D 117 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7874 (ttt90) REVERT: D 118 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6460 (mt-10) REVERT: E 113 ASP cc_start: 0.8737 (t0) cc_final: 0.8434 (t70) REVERT: E 115 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.6492 (tm-30) REVERT: E 122 VAL cc_start: 0.8265 (OUTLIER) cc_final: 0.7986 (m) REVERT: E 136 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7919 (mp0) REVERT: F 22 MET cc_start: 0.7726 (ttp) cc_final: 0.7281 (ttm) REVERT: F 52 LYS cc_start: 0.6955 (tptt) cc_final: 0.6567 (tptt) REVERT: F 103 LYS cc_start: 0.7889 (mtmt) cc_final: 0.7420 (ttmt) REVERT: G 50 ASP cc_start: 0.6924 (m-30) cc_final: 0.5983 (t0) REVERT: G 66 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7884 (mp0) REVERT: G 96 LYS cc_start: 0.7934 (ttpp) cc_final: 0.7270 (tmtm) REVERT: G 100 ASP cc_start: 0.7709 (t0) cc_final: 0.7382 (m-30) REVERT: G 112 LYS cc_start: 0.8173 (mmtm) cc_final: 0.7801 (mmmt) REVERT: G 115 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: H 66 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7966 (mt-10) REVERT: H 103 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7780 (tttm) REVERT: I 1 MET cc_start: 0.6835 (ptm) cc_final: 0.6442 (ptm) REVERT: I 9 ASP cc_start: 0.7987 (m-30) cc_final: 0.7691 (m-30) REVERT: I 42 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7051 (mt-10) REVERT: I 50 ASP cc_start: 0.6411 (m-30) cc_final: 0.5729 (t70) REVERT: I 75 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7375 (mm-30) REVERT: I 112 LYS cc_start: 0.8224 (mmtm) cc_final: 0.7454 (mtpm) REVERT: I 113 ASP cc_start: 0.8512 (t0) cc_final: 0.8300 (t0) REVERT: J 1 MET cc_start: 0.6927 (ptm) cc_final: 0.6588 (ptt) REVERT: J 50 ASP cc_start: 0.7201 (m-30) cc_final: 0.6945 (m-30) REVERT: J 57 LYS cc_start: 0.7727 (mtmt) cc_final: 0.7447 (mttm) REVERT: J 103 LYS cc_start: 0.8005 (mtmt) cc_final: 0.7359 (mmtt) REVERT: J 110 GLN cc_start: 0.7542 (mt0) cc_final: 0.7230 (mt0) REVERT: K 1 MET cc_start: 0.6958 (ptm) cc_final: 0.6710 (ptm) REVERT: K 52 LYS cc_start: 0.6641 (tptt) cc_final: 0.5563 (mtmm) REVERT: K 66 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7918 (mp0) REVERT: K 88 ARG cc_start: 0.7286 (mtm110) cc_final: 0.6883 (mmt180) REVERT: K 103 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7220 (mmtt) REVERT: L 1 MET cc_start: 0.6825 (ptm) cc_final: 0.6310 (ptm) REVERT: L 42 GLU cc_start: 0.7642 (mt-10) cc_final: 0.6800 (pp20) REVERT: L 52 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.5974 (mtmm) REVERT: L 66 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7499 (mp0) REVERT: L 112 LYS cc_start: 0.8541 (mppt) cc_final: 0.7710 (mtmt) REVERT: N 76 LYS cc_start: 0.8478 (tmtt) cc_final: 0.8149 (tptp) REVERT: O 1 MET cc_start: 0.6807 (ttp) cc_final: 0.6069 (ptp) REVERT: O 13 ARG cc_start: 0.7460 (ttm-80) cc_final: 0.7176 (mtm-85) REVERT: O 68 LEU cc_start: 0.8419 (mt) cc_final: 0.8122 (mm) REVERT: O 138 ARG cc_start: 0.7545 (ttm-80) cc_final: 0.6732 (ttm-80) REVERT: P 1 MET cc_start: 0.7295 (ttp) cc_final: 0.6952 (ttp) REVERT: P 38 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7977 (mm-30) REVERT: P 57 LYS cc_start: 0.7653 (mtmt) cc_final: 0.7376 (mttm) REVERT: Q 39 LYS cc_start: 0.8655 (ttmm) cc_final: 0.8201 (mtpt) REVERT: Q 52 MET cc_start: 0.8073 (mtt) cc_final: 0.7783 (ttm) REVERT: Q 57 LYS cc_start: 0.7856 (mtmt) cc_final: 0.7584 (mttt) REVERT: Q 81 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: Q 125 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6919 (mt-10) REVERT: Q 139 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7000 (tm-30) REVERT: R 6 LYS cc_start: 0.8020 (mmtp) cc_final: 0.7706 (mttp) REVERT: R 52 MET cc_start: 0.6971 (mtt) cc_final: 0.6761 (mtt) REVERT: R 97 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7137 (tm-30) REVERT: R 129 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: S 1 MET cc_start: 0.6575 (ptm) cc_final: 0.6225 (ptt) REVERT: S 45 TYR cc_start: 0.7905 (t80) cc_final: 0.7656 (t80) REVERT: S 96 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7025 (tm-30) REVERT: T 6 LYS cc_start: 0.7892 (mmtp) cc_final: 0.7367 (mtmm) REVERT: T 13 ARG cc_start: 0.7463 (ttm-80) cc_final: 0.6982 (mtt180) REVERT: T 53 LYS cc_start: 0.8046 (mttp) cc_final: 0.7711 (mttt) REVERT: T 73 GLN cc_start: 0.7419 (mm-40) cc_final: 0.6820 (tp40) REVERT: T 75 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7279 (mm-30) REVERT: T 96 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7122 (tt0) REVERT: T 103 ASP cc_start: 0.8191 (m-30) cc_final: 0.7808 (m-30) REVERT: U 6 LYS cc_start: 0.8051 (mptm) cc_final: 0.7632 (mtmm) REVERT: U 10 GLN cc_start: 0.8027 (mm110) cc_final: 0.7758 (mm110) REVERT: U 68 LEU cc_start: 0.8730 (mt) cc_final: 0.8488 (mm) REVERT: U 91 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7583 (tp) REVERT: U 113 ASP cc_start: 0.8382 (t70) cc_final: 0.7968 (t70) REVERT: V 33 LYS cc_start: 0.8363 (tttt) cc_final: 0.7686 (ttpp) REVERT: V 81 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7473 (mt-10) REVERT: V 96 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7135 (pt0) REVERT: V 129 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6439 (tm-30) REVERT: W 6 LYS cc_start: 0.7760 (mmtp) cc_final: 0.7229 (mtmm) REVERT: W 46 LYS cc_start: 0.7509 (pttt) cc_final: 0.7177 (mmmt) REVERT: W 66 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7615 (mm-30) REVERT: W 88 ASP cc_start: 0.8157 (m-30) cc_final: 0.7877 (m-30) REVERT: W 135 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7903 (mt-10) REVERT: W 151 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: X 66 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8022 (mt-10) outliers start: 70 outliers final: 25 residues processed: 875 average time/residue: 1.6526 time to fit residues: 1677.4068 Evaluate side-chains 849 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 806 time to evaluate : 3.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain C residue 4 ASP Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 10 GLN 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 Q residue 74 LEU Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 139 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain R residue 97 GLN Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 155 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 132 optimal weight: 0.9990 chunk 163 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 276 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** N 70 ASN O 10 GLN ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 GLN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 148 ASN T 42 HIS T 72 GLN V 10 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.147711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135047 restraints weight = 29197.942| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.25 r_work: 0.3402 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.593 31374 Z= 0.113 Angle : 0.475 16.830 42360 Z= 0.223 Chirality : 0.032 0.136 4656 Planarity : 0.002 0.028 5484 Dihedral : 5.363 86.047 4116 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.29 % Allowed : 15.10 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.48 (0.13), residues: 3696 helix: 3.49 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.63 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 133 HIS 0.008 0.001 HIS T 42 PHE 0.024 0.002 PHE U 26 TYR 0.021 0.001 TYR K 133 ARG 0.004 0.000 ARG M 138 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 2652) hydrogen bonds : angle 3.41412 ( 7956) covalent geometry : bond 0.00235 (31368) covalent geometry : angle 0.47478 (42360) Misc. bond : bond 0.47309 ( 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 928 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 852 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7125 (mm-30) REVERT: A 93 TYR cc_start: 0.7719 (t80) cc_final: 0.7495 (t80) REVERT: A 115 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7196 (tm-30) REVERT: A 126 ASP cc_start: 0.7889 (m-30) cc_final: 0.7680 (t0) REVERT: B 43 ARG cc_start: 0.7685 (tpt170) cc_final: 0.7246 (tpt170) REVERT: B 112 LYS cc_start: 0.8194 (mptt) cc_final: 0.7563 (mtmt) REVERT: C 22 MET cc_start: 0.7666 (ttp) cc_final: 0.7255 (ttm) REVERT: C 50 ASP cc_start: 0.7360 (m-30) cc_final: 0.6618 (t0) REVERT: C 52 LYS cc_start: 0.6838 (tptt) cc_final: 0.5877 (mtmm) REVERT: C 66 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7547 (mp0) REVERT: C 75 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7650 (mt-10) REVERT: C 112 LYS cc_start: 0.7940 (mmtm) cc_final: 0.7398 (mmmt) REVERT: D 1 MET cc_start: 0.7792 (ptp) cc_final: 0.7189 (ptt) REVERT: D 5 LYS cc_start: 0.7240 (mppt) cc_final: 0.6876 (mptp) REVERT: D 24 GLN cc_start: 0.8570 (tt0) cc_final: 0.8263 (tt0) REVERT: D 52 LYS cc_start: 0.7048 (tptt) cc_final: 0.5854 (mtmm) REVERT: D 66 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: D 117 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7930 (ttt90) REVERT: D 118 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6430 (mt-10) REVERT: E 122 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.7973 (m) REVERT: E 136 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7890 (mp0) REVERT: F 22 MET cc_start: 0.7786 (ttp) cc_final: 0.7297 (ttp) REVERT: F 52 LYS cc_start: 0.6982 (tptt) cc_final: 0.6626 (tptt) REVERT: F 103 LYS cc_start: 0.7896 (mtmt) cc_final: 0.7423 (ttmt) REVERT: F 118 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.5948 (mp0) REVERT: G 50 ASP cc_start: 0.6914 (m-30) cc_final: 0.5968 (t0) REVERT: G 66 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7868 (mp0) REVERT: G 96 LYS cc_start: 0.7939 (ttpp) cc_final: 0.7280 (tmtm) REVERT: G 100 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: G 112 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7829 (mmmt) REVERT: G 115 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: H 57 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7785 (mtpt) REVERT: H 66 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7958 (mt-10) REVERT: H 103 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7782 (tttm) REVERT: H 125 ASP cc_start: 0.8146 (t0) cc_final: 0.7836 (t70) REVERT: I 1 MET cc_start: 0.6802 (ptm) cc_final: 0.6400 (ptm) REVERT: I 9 ASP cc_start: 0.7988 (m-30) cc_final: 0.7698 (m-30) REVERT: I 42 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7059 (mt-10) REVERT: I 50 ASP cc_start: 0.6342 (m-30) cc_final: 0.5680 (t70) REVERT: I 75 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7379 (mm-30) REVERT: I 112 LYS cc_start: 0.8260 (mmtm) cc_final: 0.7515 (mtpm) REVERT: J 1 MET cc_start: 0.6916 (ptm) cc_final: 0.6597 (ptt) REVERT: J 50 ASP cc_start: 0.7185 (m-30) cc_final: 0.6900 (m-30) REVERT: J 57 LYS cc_start: 0.7715 (mtmt) cc_final: 0.7440 (mttm) REVERT: J 103 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7366 (mmtt) REVERT: J 110 GLN cc_start: 0.7565 (mt0) cc_final: 0.7243 (mt0) REVERT: K 1 MET cc_start: 0.6941 (ptm) cc_final: 0.6696 (ptm) REVERT: K 52 LYS cc_start: 0.6641 (tptt) cc_final: 0.5564 (mtmm) REVERT: K 66 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7928 (mp0) REVERT: K 88 ARG cc_start: 0.7300 (mtm110) cc_final: 0.6901 (mmt180) REVERT: K 103 LYS cc_start: 0.8186 (mtmt) cc_final: 0.7233 (mmtt) REVERT: L 1 MET cc_start: 0.6807 (ptm) cc_final: 0.6317 (ptm) REVERT: L 42 GLU cc_start: 0.7652 (mt-10) cc_final: 0.6813 (pp20) REVERT: L 52 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.5953 (mtmm) REVERT: L 66 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7523 (mp0) REVERT: L 112 LYS cc_start: 0.8541 (mppt) cc_final: 0.7759 (mtmt) REVERT: N 1 MET cc_start: 0.6043 (ptt) cc_final: 0.5743 (ptt) REVERT: N 76 LYS cc_start: 0.8470 (tmtt) cc_final: 0.8126 (tptp) REVERT: O 1 MET cc_start: 0.6821 (ttp) cc_final: 0.6021 (ptp) REVERT: O 13 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.7166 (mtm-85) REVERT: O 50 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6792 (pp20) REVERT: O 68 LEU cc_start: 0.8417 (mt) cc_final: 0.8124 (mm) REVERT: O 75 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7449 (mt-10) REVERT: O 138 ARG cc_start: 0.7536 (ttm-80) cc_final: 0.6722 (ttm-80) REVERT: P 1 MET cc_start: 0.7305 (ttp) cc_final: 0.6959 (ttp) REVERT: P 57 LYS cc_start: 0.7641 (mtmt) cc_final: 0.7356 (mttm) REVERT: Q 39 LYS cc_start: 0.8664 (ttmm) cc_final: 0.8210 (mtpt) REVERT: Q 57 LYS cc_start: 0.7841 (mtmt) cc_final: 0.7574 (mttt) REVERT: Q 81 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: Q 125 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6920 (mt-10) REVERT: Q 139 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: R 6 LYS cc_start: 0.8034 (mmtp) cc_final: 0.7722 (mttp) REVERT: R 81 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: R 85 GLU cc_start: 0.8251 (tt0) cc_final: 0.7950 (tt0) REVERT: R 97 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: R 129 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: S 1 MET cc_start: 0.6590 (ptm) cc_final: 0.6245 (ptt) REVERT: S 45 TYR cc_start: 0.7905 (t80) cc_final: 0.7668 (t80) REVERT: S 96 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7018 (tm-30) REVERT: T 6 LYS cc_start: 0.7893 (mmtp) cc_final: 0.7377 (mtmm) REVERT: T 13 ARG cc_start: 0.7481 (ttm-80) cc_final: 0.7114 (mtm-85) REVERT: T 53 LYS cc_start: 0.8044 (mttp) cc_final: 0.7736 (mttt) REVERT: T 73 GLN cc_start: 0.7391 (mm-40) cc_final: 0.6747 (tp40) REVERT: T 75 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7353 (mm-30) REVERT: T 96 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7163 (tt0) REVERT: T 103 ASP cc_start: 0.8201 (m-30) cc_final: 0.7832 (m-30) REVERT: U 6 LYS cc_start: 0.8061 (mptm) cc_final: 0.7641 (mtmm) REVERT: U 10 GLN cc_start: 0.8037 (mm110) cc_final: 0.7758 (mm110) REVERT: U 68 LEU cc_start: 0.8733 (mt) cc_final: 0.8488 (mm) REVERT: U 91 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7576 (tp) REVERT: V 33 LYS cc_start: 0.8381 (tttt) cc_final: 0.7712 (ttpp) REVERT: V 81 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7438 (mt-10) REVERT: V 85 GLU cc_start: 0.8516 (tt0) cc_final: 0.8277 (tt0) REVERT: V 93 MET cc_start: 0.8099 (ttp) cc_final: 0.7720 (ttm) REVERT: V 96 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7147 (pt0) REVERT: V 129 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6439 (tm-30) REVERT: W 6 LYS cc_start: 0.7750 (mmtp) cc_final: 0.7331 (mtmm) REVERT: W 46 LYS cc_start: 0.7500 (pttt) cc_final: 0.7189 (mmmt) REVERT: W 52 MET cc_start: 0.7365 (ttm) cc_final: 0.6960 (ttt) REVERT: W 66 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7609 (mm-30) REVERT: W 75 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7401 (mt-10) REVERT: W 88 ASP cc_start: 0.8144 (m-30) cc_final: 0.7860 (m-30) REVERT: W 135 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7923 (mt-10) REVERT: W 151 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: X 66 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8033 (mt-10) outliers start: 76 outliers final: 22 residues processed: 886 average time/residue: 1.6134 time to fit residues: 1664.1437 Evaluate side-chains 849 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 805 time to evaluate : 3.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain C residue 4 ASP Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 117 ARG 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 F residue 118 GLU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 17 CYS Chi-restraints excluded: chain O residue 50 GLU 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 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 97 GLN Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 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 Chi-restraints excluded: chain X residue 96 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 73 optimal weight: 0.9990 chunk 320 optimal weight: 5.9990 chunk 308 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 258 optimal weight: 4.9990 chunk 329 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 C 131 HIS E 115 GLN F 115 GLN I 60 GLN I 131 HIS J 149 ASN ** 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 82 HIS O 148 ASN P 73 GLN P 148 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 148 ASN T 42 HIS T 72 GLN V 10 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.144590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.132976 restraints weight = 29151.674| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.14 r_work: 0.3392 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.646 31374 Z= 0.146 Angle : 0.520 17.516 42360 Z= 0.244 Chirality : 0.034 0.181 4656 Planarity : 0.003 0.037 5484 Dihedral : 5.352 83.623 4116 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.23 % Allowed : 15.28 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.36 (0.13), residues: 3696 helix: 3.40 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.63 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 35 HIS 0.009 0.001 HIS T 42 PHE 0.026 0.002 PHE U 26 TYR 0.023 0.002 TYR K 133 ARG 0.004 0.000 ARG U 30 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 2652) hydrogen bonds : angle 3.52214 ( 7956) covalent geometry : bond 0.00325 (31368) covalent geometry : angle 0.51954 (42360) Misc. bond : bond 0.49147 ( 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 917 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 843 time to evaluate : 3.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7004 (mm-30) REVERT: A 93 TYR cc_start: 0.7666 (t80) cc_final: 0.7434 (t80) REVERT: A 115 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: A 126 ASP cc_start: 0.7818 (m-30) cc_final: 0.7571 (t0) REVERT: B 112 LYS cc_start: 0.8140 (mptt) cc_final: 0.7462 (mtmt) REVERT: C 22 MET cc_start: 0.7513 (ttp) cc_final: 0.7176 (ttm) REVERT: C 50 ASP cc_start: 0.7301 (m-30) cc_final: 0.6564 (t0) REVERT: C 66 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7485 (mp0) REVERT: C 75 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7584 (mt-10) REVERT: C 112 LYS cc_start: 0.7880 (mmtm) cc_final: 0.7354 (mtmt) REVERT: D 1 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7104 (ptt) REVERT: D 5 LYS cc_start: 0.7212 (mppt) cc_final: 0.6869 (mptp) REVERT: D 24 GLN cc_start: 0.8483 (tt0) cc_final: 0.8151 (tt0) REVERT: D 52 LYS cc_start: 0.6916 (tptt) cc_final: 0.5696 (mtmm) REVERT: D 66 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: D 88 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7182 (mmt-90) REVERT: D 117 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7704 (ttt90) REVERT: D 118 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6285 (mt-10) REVERT: E 113 ASP cc_start: 0.8704 (t0) cc_final: 0.8360 (t70) REVERT: E 136 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7840 (mp0) REVERT: F 22 MET cc_start: 0.7739 (ttp) cc_final: 0.7220 (ttp) REVERT: F 52 LYS cc_start: 0.6931 (tptt) cc_final: 0.6500 (tptt) REVERT: F 96 LYS cc_start: 0.7872 (ttpp) cc_final: 0.7565 (tttm) REVERT: F 103 LYS cc_start: 0.7801 (mtmt) cc_final: 0.7303 (ttmt) REVERT: F 118 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5851 (mp0) REVERT: G 50 ASP cc_start: 0.6855 (m-30) cc_final: 0.5880 (t0) REVERT: G 66 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7811 (mp0) REVERT: G 96 LYS cc_start: 0.7865 (ttpp) cc_final: 0.7389 (tmtm) REVERT: G 112 LYS cc_start: 0.8135 (mmtm) cc_final: 0.7749 (mmmt) REVERT: G 115 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7614 (tm-30) REVERT: H 57 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7654 (mtpt) REVERT: H 66 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7933 (mt-10) REVERT: H 103 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7667 (tttm) REVERT: I 1 MET cc_start: 0.6787 (ptm) cc_final: 0.6406 (ptm) REVERT: I 9 ASP cc_start: 0.7936 (m-30) cc_final: 0.7570 (m-30) REVERT: I 42 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7007 (mt-10) REVERT: I 50 ASP cc_start: 0.6218 (m-30) cc_final: 0.5582 (t70) REVERT: I 75 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7349 (mm-30) REVERT: I 112 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7431 (mtpm) REVERT: J 1 MET cc_start: 0.6946 (ptm) cc_final: 0.6639 (ptt) REVERT: J 50 ASP cc_start: 0.7114 (m-30) cc_final: 0.6823 (m-30) REVERT: J 57 LYS cc_start: 0.7598 (mtmt) cc_final: 0.7299 (mttm) REVERT: J 103 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7240 (mmtt) REVERT: J 110 GLN cc_start: 0.7448 (mt0) cc_final: 0.7151 (mt0) REVERT: K 1 MET cc_start: 0.6910 (ptm) cc_final: 0.6607 (ptm) REVERT: K 42 GLU cc_start: 0.7510 (mt-10) cc_final: 0.6520 (tm-30) REVERT: K 66 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7831 (mp0) REVERT: K 88 ARG cc_start: 0.7224 (mtm110) cc_final: 0.6782 (mmt180) REVERT: K 96 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7367 (mtmm) REVERT: K 103 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7139 (mmtt) REVERT: K 110 GLN cc_start: 0.7609 (tt0) cc_final: 0.7403 (tt0) REVERT: L 1 MET cc_start: 0.6724 (ptm) cc_final: 0.6178 (ptt) REVERT: L 42 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6770 (pp20) REVERT: L 52 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.5794 (mtmm) REVERT: L 57 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7822 (mppt) REVERT: L 66 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7408 (mp0) REVERT: L 112 LYS cc_start: 0.8475 (mppt) cc_final: 0.7605 (mtmt) REVERT: N 1 MET cc_start: 0.5961 (ptt) cc_final: 0.5666 (ptt) REVERT: N 76 LYS cc_start: 0.8481 (tmtt) cc_final: 0.8108 (tptp) REVERT: O 1 MET cc_start: 0.6812 (ttp) cc_final: 0.5938 (ptp) REVERT: O 13 ARG cc_start: 0.7385 (ttm-80) cc_final: 0.7177 (mtm-85) REVERT: O 68 LEU cc_start: 0.8367 (mt) cc_final: 0.8051 (mm) REVERT: O 75 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7366 (mt-10) REVERT: O 97 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7227 (tp40) REVERT: O 138 ARG cc_start: 0.7483 (ttm-80) cc_final: 0.6623 (ttm-80) REVERT: P 57 LYS cc_start: 0.7521 (mtmt) cc_final: 0.7224 (mttm) REVERT: Q 53 LYS cc_start: 0.8016 (mttm) cc_final: 0.7686 (mttt) REVERT: Q 57 LYS cc_start: 0.7767 (mtmt) cc_final: 0.7454 (mttt) REVERT: Q 81 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: Q 98 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7422 (mp) REVERT: Q 125 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6767 (mt-10) REVERT: Q 139 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.6932 (tm-30) REVERT: R 6 LYS cc_start: 0.7939 (mmtp) cc_final: 0.7610 (mttp) REVERT: R 81 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: R 85 GLU cc_start: 0.8211 (tt0) cc_final: 0.7871 (tt0) REVERT: R 97 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: R 129 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6629 (tm-30) REVERT: S 1 MET cc_start: 0.6579 (ptm) cc_final: 0.6243 (ptt) REVERT: S 57 LYS cc_start: 0.8035 (mttt) cc_final: 0.7782 (mttp) REVERT: S 96 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6964 (tm-30) REVERT: T 6 LYS cc_start: 0.7823 (mmtp) cc_final: 0.7307 (mtmm) REVERT: T 13 ARG cc_start: 0.7442 (ttm-80) cc_final: 0.6870 (mtm-85) REVERT: T 53 LYS cc_start: 0.7908 (mttp) cc_final: 0.7597 (mttt) REVERT: T 73 GLN cc_start: 0.7449 (mm-40) cc_final: 0.6795 (tp40) REVERT: T 74 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6904 (mp) REVERT: T 75 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7385 (mm-30) REVERT: T 96 GLU cc_start: 0.7301 (tm-30) cc_final: 0.7008 (tt0) REVERT: T 103 ASP cc_start: 0.8123 (m-30) cc_final: 0.7726 (m-30) REVERT: U 6 LYS cc_start: 0.7993 (mptm) cc_final: 0.7546 (mtmm) REVERT: U 10 GLN cc_start: 0.7923 (mm110) cc_final: 0.7633 (mm110) REVERT: U 68 LEU cc_start: 0.8716 (mt) cc_final: 0.8447 (mm) REVERT: U 76 LYS cc_start: 0.8492 (tmtt) cc_final: 0.8283 (tmtm) REVERT: U 91 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7448 (tt) REVERT: U 113 ASP cc_start: 0.8322 (t70) cc_final: 0.7907 (t70) REVERT: V 33 LYS cc_start: 0.8323 (tttt) cc_final: 0.7620 (ttpp) REVERT: V 81 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7516 (mt-10) REVERT: V 129 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6270 (tm-30) REVERT: W 6 LYS cc_start: 0.7663 (mmtp) cc_final: 0.7227 (mtmm) REVERT: W 46 LYS cc_start: 0.7456 (pttt) cc_final: 0.7103 (mmmt) REVERT: W 66 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7533 (mm-30) REVERT: W 75 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7339 (mt-10) REVERT: W 88 ASP cc_start: 0.8068 (m-30) cc_final: 0.7790 (m-30) REVERT: W 135 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7864 (mt-10) REVERT: W 151 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: X 1 MET cc_start: 0.6397 (ttp) cc_final: 0.6090 (ptt) REVERT: X 6 LYS cc_start: 0.7763 (mmtp) cc_final: 0.7081 (mmpt) REVERT: X 119 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7873 (tp) outliers start: 74 outliers final: 26 residues processed: 875 average time/residue: 1.6357 time to fit residues: 1652.1646 Evaluate side-chains 853 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 803 time to evaluate : 4.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain C residue 4 ASP Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 57 LYS Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 57 LYS 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 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 97 GLN Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 155 SER Chi-restraints excluded: chain 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 94 VAL Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 119 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 271 optimal weight: 5.9990 chunk 213 optimal weight: 0.0000 chunk 305 optimal weight: 0.1980 chunk 192 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 281 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 chunk 322 optimal weight: 10.0000 chunk 309 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.2388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN E 115 GLN F 115 GLN I 131 HIS 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 ** M 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 70 ASN N 151 GLN O 10 GLN O 82 HIS ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 ASN T 42 HIS T 72 GLN V 10 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.146362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133721 restraints weight = 29289.782| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.25 r_work: 0.3382 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.616 31374 Z= 0.122 Angle : 0.505 16.949 42360 Z= 0.236 Chirality : 0.033 0.145 4656 Planarity : 0.002 0.031 5484 Dihedral : 5.248 83.598 4116 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.02 % Allowed : 15.85 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.42 (0.13), residues: 3696 helix: 3.44 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.62 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 133 HIS 0.009 0.001 HIS T 42 PHE 0.023 0.002 PHE U 26 TYR 0.022 0.001 TYR K 133 ARG 0.004 0.000 ARG M 138 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 2652) hydrogen bonds : angle 3.45565 ( 7956) covalent geometry : bond 0.00259 (31368) covalent geometry : angle 0.50524 (42360) Misc. bond : bond 0.46667 ( 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 910 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 843 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7139 (mm-30) REVERT: A 115 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: B 43 ARG cc_start: 0.7676 (tpt170) cc_final: 0.7391 (tpt170) REVERT: B 112 LYS cc_start: 0.8251 (mptt) cc_final: 0.7624 (mtmt) REVERT: C 22 MET cc_start: 0.7710 (ttp) cc_final: 0.7408 (ttm) REVERT: C 50 ASP cc_start: 0.7402 (m-30) cc_final: 0.6682 (t0) REVERT: C 66 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7525 (mp0) REVERT: C 75 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7729 (mt-10) REVERT: D 1 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7206 (ptt) REVERT: D 5 LYS cc_start: 0.7260 (mppt) cc_final: 0.6965 (mptp) REVERT: D 52 LYS cc_start: 0.7067 (tptt) cc_final: 0.5888 (mtmm) REVERT: D 66 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: D 88 ARG cc_start: 0.7952 (mtm110) cc_final: 0.7375 (mmt-90) REVERT: D 117 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7800 (ttt90) REVERT: D 118 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6427 (mt-10) REVERT: D 125 ASP cc_start: 0.8103 (t70) cc_final: 0.7869 (t0) REVERT: E 122 VAL cc_start: 0.8279 (p) cc_final: 0.7997 (m) REVERT: E 136 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7903 (mp0) REVERT: F 22 MET cc_start: 0.7830 (ttp) cc_final: 0.7333 (ttp) REVERT: F 52 LYS cc_start: 0.7076 (tptt) cc_final: 0.6752 (tptt) REVERT: F 96 LYS cc_start: 0.7995 (ttpp) cc_final: 0.7702 (tttm) REVERT: F 103 LYS cc_start: 0.7894 (mtmt) cc_final: 0.7434 (ttmt) REVERT: F 118 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.6000 (mp0) REVERT: G 50 ASP cc_start: 0.6946 (m-30) cc_final: 0.5992 (t0) REVERT: G 66 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7882 (mp0) REVERT: G 75 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8075 (mt-10) REVERT: G 96 LYS cc_start: 0.7958 (ttpp) cc_final: 0.7504 (tmtm) REVERT: G 112 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7822 (mmmt) REVERT: G 115 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: H 1 MET cc_start: 0.6427 (OUTLIER) cc_final: 0.6195 (mtm) REVERT: H 57 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7808 (mtpt) REVERT: H 66 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7947 (mt-10) REVERT: H 96 LYS cc_start: 0.8261 (tttm) cc_final: 0.7633 (mttp) REVERT: H 103 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7788 (tttm) REVERT: H 125 ASP cc_start: 0.8178 (t0) cc_final: 0.7851 (t70) REVERT: I 1 MET cc_start: 0.6843 (ptm) cc_final: 0.6434 (ptm) REVERT: I 9 ASP cc_start: 0.8009 (m-30) cc_final: 0.7707 (m-30) REVERT: I 42 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7038 (mt-10) REVERT: I 50 ASP cc_start: 0.6337 (m-30) cc_final: 0.5695 (t70) REVERT: I 75 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7384 (mm-30) REVERT: I 112 LYS cc_start: 0.8251 (mmtm) cc_final: 0.7536 (mtpm) REVERT: J 1 MET cc_start: 0.6972 (ptm) cc_final: 0.6755 (ptt) REVERT: J 50 ASP cc_start: 0.7202 (m-30) cc_final: 0.6905 (m-30) REVERT: J 57 LYS cc_start: 0.7724 (mtmt) cc_final: 0.7446 (mttm) REVERT: J 103 LYS cc_start: 0.8033 (mtmt) cc_final: 0.7394 (mmtt) REVERT: J 110 GLN cc_start: 0.7555 (mt0) cc_final: 0.7276 (mt0) REVERT: K 1 MET cc_start: 0.6972 (ptm) cc_final: 0.6695 (ptm) REVERT: K 42 GLU cc_start: 0.7569 (mt-10) cc_final: 0.6620 (tm-30) REVERT: K 66 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7956 (mp0) REVERT: K 88 ARG cc_start: 0.7349 (mtm110) cc_final: 0.6954 (mmt180) REVERT: K 103 LYS cc_start: 0.8198 (mtmt) cc_final: 0.7251 (mmtt) REVERT: K 110 GLN cc_start: 0.7680 (tt0) cc_final: 0.7475 (tt0) REVERT: L 1 MET cc_start: 0.6799 (ptm) cc_final: 0.6265 (ptt) REVERT: L 42 GLU cc_start: 0.7694 (mt-10) cc_final: 0.6855 (pp20) REVERT: L 52 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.5947 (mtmm) REVERT: L 66 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7495 (mp0) REVERT: L 112 LYS cc_start: 0.8553 (mppt) cc_final: 0.7754 (mtmt) REVERT: N 1 MET cc_start: 0.6051 (ptt) cc_final: 0.5803 (ptt) REVERT: N 76 LYS cc_start: 0.8524 (tmtt) cc_final: 0.8158 (tptp) REVERT: O 1 MET cc_start: 0.6877 (ttp) cc_final: 0.6017 (ptp) REVERT: O 50 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6931 (pp20) REVERT: O 68 LEU cc_start: 0.8410 (mt) cc_final: 0.8117 (mm) REVERT: O 75 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7408 (mt-10) REVERT: O 97 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7380 (tp40) REVERT: O 138 ARG cc_start: 0.7566 (ttm-80) cc_final: 0.6744 (ttm-80) REVERT: P 57 LYS cc_start: 0.7638 (mtmt) cc_final: 0.7358 (mttm) REVERT: Q 39 LYS cc_start: 0.8662 (ttmm) cc_final: 0.8224 (mtpt) REVERT: Q 57 LYS cc_start: 0.7848 (mtmt) cc_final: 0.7566 (mttt) REVERT: Q 81 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: Q 98 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7564 (mp) REVERT: Q 125 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6924 (mt-10) REVERT: Q 139 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7014 (tm-30) REVERT: R 6 LYS cc_start: 0.8049 (mmtp) cc_final: 0.7738 (mttp) REVERT: R 81 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: R 85 GLU cc_start: 0.8266 (tt0) cc_final: 0.7960 (tt0) REVERT: R 97 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7123 (tm-30) REVERT: R 129 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: S 1 MET cc_start: 0.6607 (ptm) cc_final: 0.6380 (ptt) REVERT: S 57 LYS cc_start: 0.8151 (mttt) cc_final: 0.7909 (mttp) REVERT: S 96 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7088 (tm-30) REVERT: T 6 LYS cc_start: 0.7911 (mmtp) cc_final: 0.7379 (mtmm) REVERT: T 13 ARG cc_start: 0.7556 (ttm-80) cc_final: 0.7085 (mtt180) REVERT: T 53 LYS cc_start: 0.8028 (mttp) cc_final: 0.7681 (mtmt) REVERT: T 57 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7672 (mmtt) REVERT: T 73 GLN cc_start: 0.7486 (mm-40) cc_final: 0.6799 (tp40) REVERT: T 74 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.6986 (mp) REVERT: T 75 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7408 (mm-30) REVERT: T 96 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7202 (mt-10) REVERT: T 103 ASP cc_start: 0.8197 (m-30) cc_final: 0.7832 (m-30) REVERT: U 6 LYS cc_start: 0.8067 (mptm) cc_final: 0.7644 (mtmm) REVERT: U 10 GLN cc_start: 0.8027 (mm110) cc_final: 0.7768 (mm110) REVERT: U 68 LEU cc_start: 0.8753 (mt) cc_final: 0.8507 (mm) REVERT: U 91 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7627 (tp) REVERT: U 113 ASP cc_start: 0.8359 (t70) cc_final: 0.7960 (t70) REVERT: V 33 LYS cc_start: 0.8402 (tttt) cc_final: 0.7743 (ttpp) REVERT: V 81 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7530 (mt-10) REVERT: V 129 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6455 (tm-30) REVERT: W 6 LYS cc_start: 0.7773 (mmtp) cc_final: 0.7359 (mtmm) REVERT: W 46 LYS cc_start: 0.7534 (pttt) cc_final: 0.7229 (mmmt) REVERT: W 52 MET cc_start: 0.7381 (ttm) cc_final: 0.6996 (ttt) REVERT: W 66 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7603 (mm-30) REVERT: W 75 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7378 (mt-10) REVERT: W 88 ASP cc_start: 0.8191 (m-30) cc_final: 0.7909 (m-30) REVERT: W 135 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7896 (mt-10) REVERT: W 151 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: X 1 MET cc_start: 0.6418 (ttp) cc_final: 0.6144 (ptt) REVERT: X 66 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8075 (mt-10) outliers start: 67 outliers final: 24 residues processed: 874 average time/residue: 1.8607 time to fit residues: 1882.3471 Evaluate side-chains 861 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 812 time to evaluate : 6.299 ------------------------------------------------------------------------------- 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 1 MET 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 129 SER Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 17 CYS Chi-restraints excluded: chain O residue 10 GLN 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 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 97 GLN Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 155 SER Chi-restraints excluded: chain 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 179 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 299 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 212 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 C 78 ASN E 115 GLN F 115 GLN I 131 HIS ** 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 70 ASN M 148 ASN N 70 ASN N 151 GLN O 82 HIS O 148 ASN P 97 GLN P 148 ASN R 148 ASN S 148 ASN T 42 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.133301 restraints weight = 29181.429| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.16 r_work: 0.3393 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.625 31374 Z= 0.134 Angle : 0.519 16.071 42360 Z= 0.248 Chirality : 0.034 0.186 4656 Planarity : 0.003 0.033 5484 Dihedral : 5.174 79.426 4116 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.93 % Allowed : 16.58 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.32 (0.13), residues: 3696 helix: 3.37 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.62 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 133 HIS 0.009 0.001 HIS T 42 PHE 0.027 0.002 PHE S 26 TYR 0.023 0.002 TYR K 133 ARG 0.004 0.000 ARG L 88 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 2652) hydrogen bonds : angle 3.50684 ( 7956) covalent geometry : bond 0.00294 (31368) covalent geometry : angle 0.51937 (42360) Misc. bond : bond 0.42160 ( 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 884 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 820 time to evaluate : 3.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7014 (mm-30) REVERT: A 115 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: B 43 ARG cc_start: 0.7559 (tpt170) cc_final: 0.7249 (tpt170) REVERT: B 112 LYS cc_start: 0.8193 (mptt) cc_final: 0.7554 (mtmt) REVERT: C 22 MET cc_start: 0.7586 (ttp) cc_final: 0.7266 (ttm) REVERT: C 50 ASP cc_start: 0.7308 (m-30) cc_final: 0.6547 (t0) REVERT: C 66 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7438 (mp0) REVERT: C 75 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7716 (mt-10) REVERT: D 1 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7158 (ptt) REVERT: D 5 LYS cc_start: 0.7187 (mppt) cc_final: 0.6895 (mptp) REVERT: D 24 GLN cc_start: 0.8487 (tt0) cc_final: 0.8112 (tt0) REVERT: D 42 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: D 52 LYS cc_start: 0.6907 (tptt) cc_final: 0.5690 (mtmm) REVERT: D 66 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8042 (mp0) REVERT: D 88 ARG cc_start: 0.7815 (mtm110) cc_final: 0.7211 (mmt-90) REVERT: D 117 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7708 (ttt90) REVERT: D 118 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6248 (mt-10) REVERT: D 125 ASP cc_start: 0.8056 (t70) cc_final: 0.7798 (t0) REVERT: E 122 VAL cc_start: 0.8187 (p) cc_final: 0.7905 (m) REVERT: E 136 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7807 (mp0) REVERT: F 22 MET cc_start: 0.7722 (ttp) cc_final: 0.7194 (ttp) REVERT: F 52 LYS cc_start: 0.6948 (tptt) cc_final: 0.6585 (tptt) REVERT: F 96 LYS cc_start: 0.7879 (ttpp) cc_final: 0.7576 (tttm) REVERT: F 103 LYS cc_start: 0.7804 (mtmt) cc_final: 0.7310 (ttmt) REVERT: F 118 GLU cc_start: 0.6323 (OUTLIER) cc_final: 0.5872 (mp0) REVERT: G 50 ASP cc_start: 0.6848 (m-30) cc_final: 0.5865 (t0) REVERT: G 66 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7790 (mp0) REVERT: G 75 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8056 (mt-10) REVERT: G 96 LYS cc_start: 0.7866 (ttpp) cc_final: 0.7170 (tmtm) REVERT: G 100 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7277 (m-30) REVERT: G 112 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7721 (mmmt) REVERT: G 115 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7656 (tm-30) REVERT: H 1 MET cc_start: 0.6310 (OUTLIER) cc_final: 0.6069 (mtm) REVERT: H 57 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7692 (mtpt) REVERT: H 66 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7871 (mt-10) REVERT: H 96 LYS cc_start: 0.8184 (tttm) cc_final: 0.7538 (mttp) REVERT: H 103 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7677 (tttm) REVERT: H 125 ASP cc_start: 0.8072 (t0) cc_final: 0.7733 (t70) REVERT: I 1 MET cc_start: 0.6748 (ptm) cc_final: 0.6352 (ptm) REVERT: I 9 ASP cc_start: 0.7928 (m-30) cc_final: 0.7589 (m-30) REVERT: I 42 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6982 (mt-10) REVERT: I 50 ASP cc_start: 0.6203 (m-30) cc_final: 0.5539 (t70) REVERT: I 75 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7346 (mm-30) REVERT: I 112 LYS cc_start: 0.8186 (mmtm) cc_final: 0.7466 (mtpm) REVERT: J 50 ASP cc_start: 0.7099 (m-30) cc_final: 0.6790 (m-30) REVERT: J 57 LYS cc_start: 0.7616 (mtmt) cc_final: 0.7312 (mttm) REVERT: J 103 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7253 (mmtt) REVERT: J 110 GLN cc_start: 0.7463 (mt0) cc_final: 0.7163 (mt0) REVERT: K 1 MET cc_start: 0.6929 (ptm) cc_final: 0.6642 (ptm) REVERT: K 42 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6551 (tm-30) REVERT: K 66 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7850 (mp0) REVERT: K 88 ARG cc_start: 0.7219 (mtm110) cc_final: 0.6796 (mmt180) REVERT: K 103 LYS cc_start: 0.8102 (mtmt) cc_final: 0.7120 (mmtt) REVERT: K 110 GLN cc_start: 0.7610 (tt0) cc_final: 0.7389 (tt0) REVERT: L 1 MET cc_start: 0.6711 (ptm) cc_final: 0.6174 (ptt) REVERT: L 42 GLU cc_start: 0.7614 (mt-10) cc_final: 0.6767 (pp20) REVERT: L 52 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.5800 (mtmm) REVERT: L 66 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7410 (mp0) REVERT: L 112 LYS cc_start: 0.8476 (mppt) cc_final: 0.7604 (mtmt) REVERT: L 125 ASP cc_start: 0.7926 (t0) cc_final: 0.7591 (t70) REVERT: N 1 MET cc_start: 0.5945 (ptt) cc_final: 0.5679 (ptt) REVERT: N 76 LYS cc_start: 0.8468 (tmtt) cc_final: 0.8116 (tptp) REVERT: N 81 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7447 (mm-30) REVERT: O 1 MET cc_start: 0.6809 (ttp) cc_final: 0.5890 (ptp) REVERT: O 50 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6978 (pp20) REVERT: O 51 ASP cc_start: 0.7686 (m-30) cc_final: 0.7474 (t0) REVERT: O 68 LEU cc_start: 0.8373 (mt) cc_final: 0.8063 (mm) REVERT: O 75 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7340 (mt-10) REVERT: O 97 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7290 (tp40) REVERT: O 138 ARG cc_start: 0.7479 (ttm-80) cc_final: 0.6610 (ttm-80) REVERT: P 57 LYS cc_start: 0.7506 (mtmt) cc_final: 0.7205 (mttm) REVERT: P 97 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6979 (tp-100) REVERT: Q 39 LYS cc_start: 0.8644 (ttmm) cc_final: 0.8154 (mtpt) REVERT: Q 53 LYS cc_start: 0.7980 (mttp) cc_final: 0.7592 (mttp) REVERT: Q 57 LYS cc_start: 0.7759 (mtmt) cc_final: 0.7452 (mttt) REVERT: Q 81 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: Q 98 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7463 (mp) REVERT: Q 125 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6771 (mt-10) REVERT: Q 139 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.6903 (tm-30) REVERT: R 6 LYS cc_start: 0.7941 (mmtp) cc_final: 0.7616 (mttp) REVERT: R 81 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: R 85 GLU cc_start: 0.8205 (tt0) cc_final: 0.7867 (tt0) REVERT: R 97 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7010 (tm-30) REVERT: R 129 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: S 1 MET cc_start: 0.6591 (ptm) cc_final: 0.6280 (ptt) REVERT: S 57 LYS cc_start: 0.8028 (mttt) cc_final: 0.7771 (mttp) REVERT: S 96 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6968 (tm-30) REVERT: T 6 LYS cc_start: 0.7812 (mmtp) cc_final: 0.7272 (mtmm) REVERT: T 13 ARG cc_start: 0.7440 (ttm-80) cc_final: 0.6873 (mtm-85) REVERT: T 53 LYS cc_start: 0.7890 (mttp) cc_final: 0.7540 (mtmt) REVERT: T 57 LYS cc_start: 0.8078 (mtmt) cc_final: 0.7509 (mmtt) REVERT: T 73 GLN cc_start: 0.7445 (mm-40) cc_final: 0.6766 (tp40) REVERT: T 74 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6911 (mp) REVERT: T 75 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7375 (mm-30) REVERT: T 96 GLU cc_start: 0.7313 (tm-30) cc_final: 0.7074 (mt-10) REVERT: T 103 ASP cc_start: 0.8132 (m-30) cc_final: 0.7742 (m-30) REVERT: U 6 LYS cc_start: 0.7986 (mptm) cc_final: 0.7540 (mtmm) REVERT: U 10 GLN cc_start: 0.7933 (mm110) cc_final: 0.7653 (mm110) REVERT: U 68 LEU cc_start: 0.8720 (mt) cc_final: 0.8457 (mm) REVERT: U 91 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7531 (tp) REVERT: V 33 LYS cc_start: 0.8337 (tttt) cc_final: 0.7644 (ttpp) REVERT: V 81 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7509 (mt-10) REVERT: V 129 GLU cc_start: 0.6706 (mt-10) cc_final: 0.6286 (tm-30) REVERT: W 6 LYS cc_start: 0.7668 (mmtp) cc_final: 0.7242 (mtmm) REVERT: W 46 LYS cc_start: 0.7448 (pttt) cc_final: 0.7109 (mmmt) REVERT: W 52 MET cc_start: 0.7352 (ttm) cc_final: 0.6934 (ttt) REVERT: W 66 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7530 (mm-30) REVERT: W 75 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7339 (mt-10) REVERT: W 88 ASP cc_start: 0.8099 (m-30) cc_final: 0.7811 (m-30) REVERT: W 135 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7842 (mt-10) REVERT: W 151 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: X 1 MET cc_start: 0.6382 (ttp) cc_final: 0.6112 (ptt) REVERT: X 66 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: X 125 GLU cc_start: 0.6854 (pt0) cc_final: 0.6650 (tt0) outliers start: 64 outliers final: 23 residues processed: 850 average time/residue: 1.7607 time to fit residues: 1732.4270 Evaluate side-chains 852 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 800 time to evaluate : 3.586 ------------------------------------------------------------------------------- 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 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 129 SER Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 1 MET 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 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 N residue 17 CYS Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain O residue 50 GLU Chi-restraints excluded: chain O residue 97 GLN 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 81 GLU Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain R residue 97 GLN Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain S residue 74 LEU Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 155 SER Chi-restraints excluded: chain 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 231 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 296 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 351 optimal weight: 0.7980 chunk 228 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 263 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 E 115 GLN F 115 GLN F 131 HIS I 60 GLN I 131 HIS J 89 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 N 151 GLN O 10 GLN O 82 HIS O 148 ASN P 73 GLN P 97 GLN R 148 ASN T 42 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.143835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.131910 restraints weight = 29307.687| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.16 r_work: 0.3370 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2793 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= 0.155 Angle : 0.543 15.762 42360 Z= 0.261 Chirality : 0.035 0.224 4656 Planarity : 0.003 0.039 5484 Dihedral : 5.192 78.803 4116 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.93 % Allowed : 16.70 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.21 (0.13), residues: 3696 helix: 3.30 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.62 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 35 HIS 0.009 0.001 HIS T 42 PHE 0.027 0.002 PHE S 26 TYR 0.024 0.002 TYR K 133 ARG 0.004 0.001 ARG W 102 Details of bonding type rmsd hydrogen bonds : bond 0.04285 ( 2652) hydrogen bonds : angle 3.56994 ( 7956) covalent geometry : bond 0.00349 (31368) covalent geometry : angle 0.54343 (42360) Misc. bond : bond 0.43042 ( 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 885 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 821 time to evaluate : 3.913 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: 0.7396 (mm-30) cc_final: 0.7024 (mm-30) REVERT: A 115 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7092 (tm-30) REVERT: B 43 ARG cc_start: 0.7574 (tpt170) cc_final: 0.7250 (tpt170) REVERT: B 112 LYS cc_start: 0.8167 (mptt) cc_final: 0.7511 (mtmt) REVERT: C 22 MET cc_start: 0.7621 (ttp) cc_final: 0.7291 (ttm) REVERT: C 50 ASP cc_start: 0.7303 (m-30) cc_final: 0.6545 (t0) REVERT: C 66 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7428 (mp0) REVERT: C 75 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7712 (mt-10) REVERT: D 1 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7129 (ptt) REVERT: D 5 LYS cc_start: 0.7184 (mppt) cc_final: 0.6906 (mptp) REVERT: D 24 GLN cc_start: 0.8484 (tt0) cc_final: 0.8095 (tt0) REVERT: D 42 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7077 (mt-10) REVERT: D 52 LYS cc_start: 0.6865 (tptt) cc_final: 0.5648 (mtmm) REVERT: D 66 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: D 88 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7202 (mmt-90) REVERT: D 117 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7639 (ttt90) REVERT: D 118 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6244 (mt-10) REVERT: E 122 VAL cc_start: 0.8195 (p) cc_final: 0.7906 (m) REVERT: E 136 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7840 (mp0) REVERT: F 22 MET cc_start: 0.7745 (ttp) cc_final: 0.7219 (ttp) REVERT: F 52 LYS cc_start: 0.6947 (tptt) cc_final: 0.6580 (tptt) REVERT: F 96 LYS cc_start: 0.7883 (ttpp) cc_final: 0.7579 (tttm) REVERT: F 103 LYS cc_start: 0.7803 (mtmt) cc_final: 0.7303 (ttmt) REVERT: F 118 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5911 (mp0) REVERT: G 50 ASP cc_start: 0.6846 (m-30) cc_final: 0.5856 (t0) REVERT: G 66 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7802 (mp0) REVERT: G 75 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8116 (mt-10) REVERT: G 96 LYS cc_start: 0.7869 (ttpp) cc_final: 0.7176 (tmtm) REVERT: G 100 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7273 (m-30) REVERT: G 112 LYS cc_start: 0.8120 (mmtm) cc_final: 0.7729 (mmmt) REVERT: G 115 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: H 1 MET cc_start: 0.6336 (OUTLIER) cc_final: 0.6123 (mtm) REVERT: H 57 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7700 (mtpt) REVERT: H 66 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7948 (mt-10) REVERT: H 96 LYS cc_start: 0.8184 (tttm) cc_final: 0.7571 (mtmt) REVERT: H 103 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7660 (tttm) REVERT: H 125 ASP cc_start: 0.8048 (t0) cc_final: 0.7710 (t70) REVERT: I 1 MET cc_start: 0.6732 (ptm) cc_final: 0.6338 (ptm) REVERT: I 9 ASP cc_start: 0.7939 (m-30) cc_final: 0.7713 (m-30) REVERT: I 42 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7008 (mt-10) REVERT: I 50 ASP cc_start: 0.6258 (m-30) cc_final: 0.5559 (t70) REVERT: I 75 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7366 (mm-30) REVERT: I 112 LYS cc_start: 0.8189 (mmtm) cc_final: 0.7465 (mtpm) REVERT: J 50 ASP cc_start: 0.7090 (m-30) cc_final: 0.6769 (m-30) REVERT: J 57 LYS cc_start: 0.7614 (mtmt) cc_final: 0.7302 (mttm) REVERT: J 103 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7241 (mmtt) REVERT: J 110 GLN cc_start: 0.7463 (mt0) cc_final: 0.7149 (mt0) REVERT: K 1 MET cc_start: 0.6953 (ptm) cc_final: 0.6689 (ptm) REVERT: K 42 GLU cc_start: 0.7552 (mt-10) cc_final: 0.6578 (tm-30) REVERT: K 66 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7850 (mp0) REVERT: K 88 ARG cc_start: 0.7204 (mtm110) cc_final: 0.6763 (mmt180) REVERT: K 103 LYS cc_start: 0.8095 (mtmt) cc_final: 0.7116 (mmtt) REVERT: K 110 GLN cc_start: 0.7597 (tt0) cc_final: 0.7374 (tt0) REVERT: L 1 MET cc_start: 0.6717 (ptm) cc_final: 0.6172 (ptt) REVERT: L 42 GLU cc_start: 0.7638 (mt-10) cc_final: 0.6776 (pp20) REVERT: L 52 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.5776 (mtmm) REVERT: L 66 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7381 (mp0) REVERT: L 112 LYS cc_start: 0.8461 (mppt) cc_final: 0.7562 (mtmt) REVERT: N 1 MET cc_start: 0.5963 (ptt) cc_final: 0.5686 (ptt) REVERT: N 76 LYS cc_start: 0.8466 (tmtt) cc_final: 0.8109 (tptp) REVERT: O 1 MET cc_start: 0.6839 (ttp) cc_final: 0.5866 (ptp) REVERT: O 50 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6997 (pp20) REVERT: O 51 ASP cc_start: 0.7714 (m-30) cc_final: 0.7471 (t0) REVERT: O 68 LEU cc_start: 0.8364 (mt) cc_final: 0.8046 (mm) REVERT: O 75 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7310 (mt-10) REVERT: O 138 ARG cc_start: 0.7516 (ttm-80) cc_final: 0.6628 (ttm-80) REVERT: P 57 LYS cc_start: 0.7491 (mtmt) cc_final: 0.7187 (mttm) REVERT: P 97 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6988 (tp-100) REVERT: Q 39 LYS cc_start: 0.8660 (ttmm) cc_final: 0.8181 (mtpt) REVERT: Q 53 LYS cc_start: 0.7944 (mttp) cc_final: 0.7546 (mttp) REVERT: Q 57 LYS cc_start: 0.7757 (mtmt) cc_final: 0.7434 (mttt) REVERT: Q 81 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: Q 98 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7455 (mp) REVERT: Q 125 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6770 (mt-10) REVERT: Q 139 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.6917 (tm-30) REVERT: R 6 LYS cc_start: 0.7936 (mmtp) cc_final: 0.7603 (mttp) REVERT: R 52 MET cc_start: 0.6902 (mtt) cc_final: 0.6628 (mtt) REVERT: R 81 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: R 85 GLU cc_start: 0.8201 (tt0) cc_final: 0.7914 (tt0) REVERT: R 97 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.7017 (tm-30) REVERT: R 129 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6624 (tm-30) REVERT: S 1 MET cc_start: 0.6638 (ptm) cc_final: 0.6350 (ptt) REVERT: S 57 LYS cc_start: 0.8041 (mttt) cc_final: 0.7780 (mttp) REVERT: S 96 GLU cc_start: 0.7396 (tm-30) cc_final: 0.7032 (tm-30) REVERT: S 97 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7036 (mt0) REVERT: T 6 LYS cc_start: 0.7821 (mmtp) cc_final: 0.7269 (mtmm) REVERT: T 53 LYS cc_start: 0.7863 (mttp) cc_final: 0.7510 (mtmt) REVERT: T 57 LYS cc_start: 0.8080 (mtmt) cc_final: 0.7506 (mmtt) REVERT: T 73 GLN cc_start: 0.7446 (mm-40) cc_final: 0.6774 (tp40) REVERT: T 74 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.6962 (mp) REVERT: T 75 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7353 (mm-30) REVERT: T 96 GLU cc_start: 0.7314 (tm-30) cc_final: 0.7088 (mt-10) REVERT: T 103 ASP cc_start: 0.8128 (m-30) cc_final: 0.7732 (m-30) REVERT: U 6 LYS cc_start: 0.7966 (mptm) cc_final: 0.7504 (mtmm) REVERT: U 10 GLN cc_start: 0.7922 (mm110) cc_final: 0.7641 (mm110) REVERT: U 45 TYR cc_start: 0.8021 (t80) cc_final: 0.7210 (t80) REVERT: U 68 LEU cc_start: 0.8722 (mt) cc_final: 0.8449 (mm) REVERT: U 91 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7455 (tt) REVERT: U 113 ASP cc_start: 0.8346 (t70) cc_final: 0.7932 (t70) REVERT: V 33 LYS cc_start: 0.8337 (tttt) cc_final: 0.7622 (ttpp) REVERT: V 81 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7522 (mt-10) REVERT: V 129 GLU cc_start: 0.6686 (mt-10) cc_final: 0.6247 (tm-30) REVERT: W 6 LYS cc_start: 0.7692 (mmtp) cc_final: 0.7259 (mtmm) REVERT: W 46 LYS cc_start: 0.7454 (pttt) cc_final: 0.7090 (mmmt) REVERT: W 52 MET cc_start: 0.7396 (ttm) cc_final: 0.6955 (ttt) REVERT: W 75 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7359 (mt-10) REVERT: W 88 ASP cc_start: 0.8106 (m-30) cc_final: 0.7825 (m-30) REVERT: W 135 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7855 (mt-10) REVERT: W 151 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: X 1 MET cc_start: 0.6411 (ttp) cc_final: 0.6141 (ptt) REVERT: X 6 LYS cc_start: 0.7726 (mmtp) cc_final: 0.7048 (mmpt) REVERT: X 66 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: X 125 GLU cc_start: 0.6849 (pt0) cc_final: 0.6642 (tt0) outliers start: 64 outliers final: 27 residues processed: 852 average time/residue: 1.9897 time to fit residues: 1962.1990 Evaluate side-chains 856 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 801 time to evaluate : 7.498 ------------------------------------------------------------------------------- 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 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 103 LYS 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 1 MET 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 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 N residue 17 CYS Chi-restraints excluded: chain O residue 50 GLU 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 81 GLU Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain R residue 97 GLN Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain S residue 74 LEU Chi-restraints excluded: chain S residue 97 GLN Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 155 SER Chi-restraints excluded: chain 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 142 optimal weight: 0.0010 chunk 204 optimal weight: 2.9990 chunk 305 optimal weight: 0.0980 chunk 8 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 200 optimal weight: 0.2980 chunk 53 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 296 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN E 115 GLN F 115 GLN I 131 HIS J 89 ASN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 GLN K 89 ASN L 60 GLN L 115 GLN ** M 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 70 ASN O 82 HIS ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 ASN S 148 ASN T 42 HIS V 10 GLN ** X 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.149735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.137214 restraints weight = 29154.879| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.25 r_work: 0.3426 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.532 31374 Z= 0.107 Angle : 0.484 13.446 42360 Z= 0.237 Chirality : 0.033 0.197 4656 Planarity : 0.002 0.025 5484 Dihedral : 4.990 77.697 4116 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.38 % Allowed : 17.57 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.41 (0.13), residues: 3696 helix: 3.43 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.57 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 133 HIS 0.009 0.001 HIS T 42 PHE 0.021 0.002 PHE U 26 TYR 0.023 0.001 TYR K 133 ARG 0.005 0.000 ARG M 138 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 2652) hydrogen bonds : angle 3.39586 ( 7956) covalent geometry : bond 0.00214 (31368) covalent geometry : angle 0.48384 (42360) Misc. bond : bond 0.36292 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33448.91 seconds wall clock time: 576 minutes 43.80 seconds (34603.80 seconds total)