Starting phenix.real_space_refine on Tue May 27 17:30:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iig_60594/05_2025/9iig_60594_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iig_60594/05_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_60594/05_2025/9iig_60594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iig_60594/05_2025/9iig_60594.map" model { file = "/net/cci-nas-00/data/ceres_data/9iig_60594/05_2025/9iig_60594_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iig_60594/05_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-5687/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: 18.19, per 1000 atoms: 0.59 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: 8.49 Conformation dependent library (CDL) restraints added in 3.4 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: 2.24 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: 10.62 Time building geometry restraints manager: 9.56 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: 0.25 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: 5.050 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: 1.430 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 64.780 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.190 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:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.800 ------------------------------------------------------------------------------- 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 : 3.361 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: 1.5960 time to fit residues: 2060.9703 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 : 3.306 ------------------------------------------------------------------------------- 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 = 28836.659| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.07 r_work: 0.3457 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 : 3.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7069 (mm-30) REVERT: A 115 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7259 (tm-30) REVERT: B 39 GLU cc_start: 0.7694 (tt0) cc_final: 0.7338 (tt0) REVERT: B 43 ARG cc_start: 0.7606 (tpt170) cc_final: 0.7207 (tpt170) REVERT: B 112 LYS cc_start: 0.8138 (mptt) cc_final: 0.7411 (mmmt) REVERT: C 1 MET cc_start: 0.6695 (ptm) cc_final: 0.6304 (ptm) REVERT: C 43 ARG cc_start: 0.7361 (tpt170) cc_final: 0.7123 (tpt170) REVERT: C 50 ASP cc_start: 0.7267 (m-30) cc_final: 0.6790 (t0) REVERT: C 52 LYS cc_start: 0.6799 (tptt) cc_final: 0.5932 (mtmm) REVERT: C 66 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7576 (mp0) REVERT: C 112 LYS cc_start: 0.8058 (mmtm) cc_final: 0.7458 (mmmt) REVERT: D 1 MET cc_start: 0.7831 (ptp) cc_final: 0.7028 (ptt) REVERT: D 24 GLN cc_start: 0.8510 (tt0) cc_final: 0.8219 (tt0) REVERT: D 52 LYS cc_start: 0.6936 (tptt) cc_final: 0.5755 (mtmm) REVERT: D 66 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: D 115 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7545 (tm130) REVERT: D 117 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7801 (ttt90) REVERT: E 115 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.6426 (tm-30) REVERT: E 122 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.8035 (m) REVERT: F 22 MET cc_start: 0.7812 (ttp) cc_final: 0.7362 (ttp) REVERT: F 52 LYS cc_start: 0.6860 (tptt) cc_final: 0.6549 (tptt) REVERT: F 103 LYS cc_start: 0.7861 (mtmt) cc_final: 0.7396 (ttpt) REVERT: G 13 ARG cc_start: 0.7454 (mtm110) cc_final: 0.7194 (mtm-85) REVERT: G 66 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7875 (mp0) REVERT: G 96 LYS cc_start: 0.7897 (ttpp) cc_final: 0.7387 (tmtm) REVERT: G 100 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7224 (m-30) REVERT: G 115 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: G 125 ASP cc_start: 0.7848 (t70) cc_final: 0.7569 (t0) REVERT: H 1 MET cc_start: 0.7171 (ptp) cc_final: 0.6957 (ptt) REVERT: I 9 ASP cc_start: 0.7961 (m-30) cc_final: 0.7661 (m-30) REVERT: I 50 ASP cc_start: 0.6459 (m-30) cc_final: 0.5898 (t0) REVERT: I 75 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7436 (mm-30) REVERT: J 50 ASP cc_start: 0.7151 (m-30) cc_final: 0.6930 (m-30) REVERT: J 57 LYS cc_start: 0.7665 (mtmt) cc_final: 0.7381 (mttm) REVERT: J 96 LYS cc_start: 0.7880 (ttpp) cc_final: 0.7521 (ttpp) REVERT: J 103 LYS cc_start: 0.7884 (mtmt) cc_final: 0.7294 (mmtt) REVERT: J 110 GLN cc_start: 0.7551 (mt0) cc_final: 0.7195 (mt0) REVERT: K 1 MET cc_start: 0.6941 (ptm) cc_final: 0.6703 (ptm) REVERT: K 66 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7877 (mp0) REVERT: K 88 ARG cc_start: 0.7217 (mtm110) cc_final: 0.6798 (mmt180) REVERT: K 103 LYS cc_start: 0.8093 (mtmt) cc_final: 0.7156 (mmtt) REVERT: L 1 MET cc_start: 0.6960 (ptm) cc_final: 0.6577 (ptp) REVERT: L 22 MET cc_start: 0.7344 (ttp) cc_final: 0.6955 (mtp) REVERT: L 51 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7810 (mm-30) REVERT: L 112 LYS cc_start: 0.8447 (mppt) cc_final: 0.7562 (mmmt) REVERT: L 152 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8417 (tt0) REVERT: O 1 MET cc_start: 0.6792 (ttp) cc_final: 0.6241 (ptp) REVERT: O 13 ARG cc_start: 0.7358 (ttm-80) cc_final: 0.7096 (ttm110) REVERT: O 51 ASP cc_start: 0.7721 (m-30) cc_final: 0.7508 (m-30) REVERT: O 68 LEU cc_start: 0.8438 (mt) cc_final: 0.8173 (mm) REVERT: O 75 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7408 (mt-10) REVERT: O 96 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7037 (tm-30) REVERT: O 138 ARG cc_start: 0.7479 (ttm-80) cc_final: 0.6787 (ttm-80) REVERT: P 1 MET cc_start: 0.7131 (ttp) cc_final: 0.6747 (ttp) REVERT: P 38 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8057 (mm-30) REVERT: P 57 LYS cc_start: 0.7595 (mtmt) cc_final: 0.7315 (mttt) REVERT: P 76 LYS cc_start: 0.7719 (mmtt) cc_final: 0.7231 (tptt) REVERT: Q 53 LYS cc_start: 0.8091 (mttp) cc_final: 0.7745 (mttp) REVERT: Q 57 LYS cc_start: 0.7830 (mtmt) cc_final: 0.7565 (mttt) REVERT: Q 81 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: Q 125 GLU cc_start: 0.7170 (pt0) cc_final: 0.6704 (mt-10) REVERT: R 1 MET cc_start: 0.6927 (ttp) cc_final: 0.6696 (ttp) REVERT: R 6 LYS cc_start: 0.8038 (mmtp) cc_final: 0.7769 (mttp) REVERT: R 97 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7080 (tm-30) REVERT: R 129 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6776 (mt-10) REVERT: S 6 LYS cc_start: 0.8246 (mmtp) cc_final: 0.7853 (mptt) REVERT: S 45 TYR cc_start: 0.7837 (t80) cc_final: 0.7605 (t80) REVERT: S 73 GLN cc_start: 0.6895 (mm110) cc_final: 0.6656 (tt0) REVERT: S 96 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6922 (tm-30) REVERT: T 6 LYS cc_start: 0.7894 (mmtp) cc_final: 0.7365 (mtmm) REVERT: T 13 ARG cc_start: 0.7384 (ttm-80) cc_final: 0.6937 (mtm-85) REVERT: T 53 LYS cc_start: 0.7955 (mttp) cc_final: 0.7638 (mttt) REVERT: T 73 GLN cc_start: 0.7466 (mm-40) cc_final: 0.6804 (tp40) REVERT: T 75 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7601 (mm-30) REVERT: T 96 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7201 (tt0) REVERT: T 103 ASP cc_start: 0.8038 (m-30) cc_final: 0.7654 (m-30) REVERT: T 127 GLU cc_start: 0.6727 (mm-30) cc_final: 0.6284 (mm-30) REVERT: U 10 GLN cc_start: 0.8018 (mm110) cc_final: 0.7781 (mm110) REVERT: U 68 LEU cc_start: 0.8737 (mt) cc_final: 0.8474 (mm) REVERT: U 96 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: U 126 ASP cc_start: 0.7918 (m-30) cc_final: 0.7634 (m-30) REVERT: V 13 ARG cc_start: 0.7691 (ttm110) cc_final: 0.7272 (mtm-85) REVERT: V 33 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7687 (ttpp) REVERT: V 81 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7477 (mt-10) REVERT: V 96 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7167 (pt0) REVERT: V 129 GLU cc_start: 0.6638 (mt-10) cc_final: 0.6349 (tm-30) REVERT: W 6 LYS cc_start: 0.7848 (mmtp) cc_final: 0.7393 (mtmm) REVERT: W 13 ARG cc_start: 0.7867 (mtm-85) cc_final: 0.7629 (mtt90) REVERT: W 46 LYS cc_start: 0.7504 (pttt) cc_final: 0.7190 (mmmt) REVERT: W 66 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7583 (mm-30) REVERT: W 88 ASP cc_start: 0.8116 (m-30) cc_final: 0.7838 (m-30) REVERT: W 100 LEU cc_start: 0.8371 (tt) cc_final: 0.8072 (tp) REVERT: W 129 GLU cc_start: 0.6651 (mt-10) cc_final: 0.6098 (pt0) REVERT: W 135 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7903 (mt-10) REVERT: W 151 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8017 (tt0) REVERT: X 6 LYS cc_start: 0.7862 (mmtp) cc_final: 0.7197 (mmpt) REVERT: X 66 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8031 (mt-10) outliers start: 74 outliers final: 10 residues processed: 947 average time/residue: 1.5496 time to fit residues: 1705.2370 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 : 3.377 ------------------------------------------------------------------------------- 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: 3.9990 chunk 312 optimal weight: 0.9980 chunk 197 optimal weight: 0.7980 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: 1.2784 ------------------------------------------------------------------------------- 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 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.146374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.134106 restraints weight = 29048.983| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.22 r_work: 0.3397 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.553 31374 Z= 0.124 Angle : 0.485 14.833 42360 Z= 0.232 Chirality : 0.032 0.114 4656 Planarity : 0.003 0.033 5484 Dihedral : 5.927 87.804 4116 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.26 % Allowed : 12.70 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.91 (0.13), residues: 3696 helix: 3.11 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.85 (0.20), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 35 HIS 0.006 0.001 HIS T 42 PHE 0.023 0.002 PHE S 26 TYR 0.017 0.002 TYR D 133 ARG 0.004 0.000 ARG L 74 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 2652) hydrogen bonds : angle 3.63039 ( 7956) covalent geometry : bond 0.00266 (31368) covalent geometry : angle 0.48515 (42360) Misc. bond : bond 0.47513 ( 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 939 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 864 time to evaluate : 3.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7075 (mm-30) REVERT: A 115 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: B 39 GLU cc_start: 0.7708 (tt0) cc_final: 0.7408 (tt0) REVERT: C 50 ASP cc_start: 0.7367 (m-30) cc_final: 0.6697 (t0) REVERT: C 52 LYS cc_start: 0.6826 (tptt) cc_final: 0.5955 (mtmm) REVERT: C 66 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7511 (mp0) REVERT: C 112 LYS cc_start: 0.8019 (mmtm) cc_final: 0.7413 (mmmt) REVERT: D 1 MET cc_start: 0.7880 (ptp) cc_final: 0.7213 (ptt) REVERT: D 5 LYS cc_start: 0.7370 (mppt) cc_final: 0.6488 (tttp) REVERT: D 24 GLN cc_start: 0.8559 (tt0) cc_final: 0.8249 (tt0) REVERT: D 52 LYS cc_start: 0.6979 (tptt) cc_final: 0.5736 (mtmm) REVERT: D 66 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: D 100 ASP cc_start: 0.7570 (t0) cc_final: 0.7292 (m-30) REVERT: D 118 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6492 (mt-10) REVERT: D 133 TYR cc_start: 0.7175 (t80) cc_final: 0.6963 (t80) REVERT: E 113 ASP cc_start: 0.8791 (t0) cc_final: 0.8555 (t70) REVERT: E 115 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.6325 (tm-30) REVERT: E 122 VAL cc_start: 0.8271 (OUTLIER) cc_final: 0.8038 (m) REVERT: F 103 LYS cc_start: 0.7901 (mtmt) cc_final: 0.7421 (ttmt) REVERT: G 13 ARG cc_start: 0.7547 (mtm110) cc_final: 0.7269 (mtm-85) REVERT: G 50 ASP cc_start: 0.6989 (m-30) cc_final: 0.6039 (t0) REVERT: G 66 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7863 (mp0) REVERT: G 96 LYS cc_start: 0.7938 (ttpp) cc_final: 0.7265 (tmtm) REVERT: G 100 ASP cc_start: 0.7723 (t0) cc_final: 0.7347 (m-30) REVERT: G 115 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7687 (tm-30) REVERT: H 103 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7800 (tttm) REVERT: I 1 MET cc_start: 0.6806 (ptm) cc_final: 0.6435 (ptm) REVERT: I 9 ASP cc_start: 0.7973 (m-30) cc_final: 0.7657 (m-30) REVERT: I 50 ASP cc_start: 0.6493 (m-30) cc_final: 0.5834 (t70) REVERT: I 75 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7415 (mm-30) REVERT: I 103 LYS cc_start: 0.7998 (mtmt) cc_final: 0.7354 (mmpt) REVERT: I 112 LYS cc_start: 0.8119 (mmtm) cc_final: 0.7393 (mmmt) REVERT: J 1 MET cc_start: 0.6890 (ptm) cc_final: 0.6538 (ptt) REVERT: J 50 ASP cc_start: 0.7182 (m-30) cc_final: 0.6925 (m-30) REVERT: J 57 LYS cc_start: 0.7725 (mtmt) cc_final: 0.7433 (mttm) REVERT: J 96 LYS cc_start: 0.7963 (ttpp) cc_final: 0.7590 (ttpp) REVERT: J 103 LYS cc_start: 0.7972 (mtmt) cc_final: 0.7338 (mmtt) REVERT: J 110 GLN cc_start: 0.7554 (mt0) cc_final: 0.7228 (mt0) REVERT: K 1 MET cc_start: 0.6934 (ptm) cc_final: 0.6723 (ptm) REVERT: K 66 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7886 (mp0) REVERT: K 88 ARG cc_start: 0.7304 (mtm110) cc_final: 0.6827 (mmt180) REVERT: K 103 LYS cc_start: 0.8153 (mtmt) cc_final: 0.7201 (mmtt) REVERT: L 1 MET cc_start: 0.6900 (ptm) cc_final: 0.6394 (ptm) REVERT: L 52 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.5951 (mtmm) REVERT: L 112 LYS cc_start: 0.8538 (mppt) cc_final: 0.7682 (mmmt) REVERT: L 152 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8550 (tt0) REVERT: N 76 LYS cc_start: 0.8548 (tmtt) cc_final: 0.8313 (tmtt) REVERT: O 1 MET cc_start: 0.6802 (ttp) cc_final: 0.6109 (ptp) REVERT: O 13 ARG cc_start: 0.7450 (ttm-80) cc_final: 0.7041 (mtm110) REVERT: O 68 LEU cc_start: 0.8453 (mt) cc_final: 0.8167 (mm) REVERT: O 75 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7499 (mt-10) REVERT: O 96 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7051 (tm-30) REVERT: O 138 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.6777 (ttm-80) REVERT: P 1 MET cc_start: 0.7245 (ttp) cc_final: 0.6888 (ttp) REVERT: P 38 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8093 (mm-30) REVERT: P 57 LYS cc_start: 0.7623 (mtmt) cc_final: 0.7342 (mttt) REVERT: Q 57 LYS cc_start: 0.7854 (mtmt) cc_final: 0.7580 (mttt) REVERT: Q 81 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: Q 139 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7065 (tm-30) REVERT: R 6 LYS cc_start: 0.8008 (mmtp) cc_final: 0.7701 (mttp) REVERT: R 85 GLU cc_start: 0.8147 (tt0) cc_final: 0.7839 (tt0) REVERT: R 97 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7127 (tm-30) REVERT: R 129 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6975 (mt-10) REVERT: S 6 LYS cc_start: 0.8207 (mmtp) cc_final: 0.7775 (mmtm) REVERT: S 45 TYR cc_start: 0.7894 (t80) cc_final: 0.7677 (t80) REVERT: S 96 GLU cc_start: 0.7312 (tm-30) cc_final: 0.7013 (tm-30) REVERT: T 6 LYS cc_start: 0.7898 (mmtp) cc_final: 0.7413 (mttp) REVERT: T 13 ARG cc_start: 0.7451 (ttm-80) cc_final: 0.7014 (mtm-85) REVERT: T 53 LYS cc_start: 0.8049 (mttp) cc_final: 0.7725 (mttt) REVERT: T 73 GLN cc_start: 0.7467 (mm-40) cc_final: 0.6865 (tp-100) REVERT: T 75 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7443 (mm-30) REVERT: T 96 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7198 (tt0) REVERT: T 103 ASP cc_start: 0.8180 (m-30) cc_final: 0.7804 (m-30) REVERT: U 10 GLN cc_start: 0.8092 (mm110) cc_final: 0.7844 (mm110) REVERT: U 68 LEU cc_start: 0.8738 (mt) cc_final: 0.8491 (mm) REVERT: U 126 ASP cc_start: 0.8023 (m-30) cc_final: 0.7756 (m-30) REVERT: V 33 LYS cc_start: 0.8348 (tttt) cc_final: 0.7658 (ttpp) REVERT: V 81 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7481 (mt-10) REVERT: V 96 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7165 (pt0) REVERT: V 129 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6389 (tm-30) REVERT: W 6 LYS cc_start: 0.7843 (mmtp) cc_final: 0.7350 (mtmm) REVERT: W 46 LYS cc_start: 0.7551 (pttt) cc_final: 0.7208 (mmmt) REVERT: W 66 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7652 (mm-30) REVERT: W 88 ASP cc_start: 0.8164 (m-30) cc_final: 0.7886 (m-30) REVERT: W 100 LEU cc_start: 0.8352 (tt) cc_final: 0.8071 (tp) REVERT: W 135 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7929 (mt-10) REVERT: X 6 LYS cc_start: 0.7826 (mmtp) cc_final: 0.7130 (mmpt) REVERT: X 39 LYS cc_start: 0.8332 (ttmt) cc_final: 0.8116 (mttt) outliers start: 75 outliers final: 17 residues processed: 894 average time/residue: 1.5113 time to fit residues: 1568.6847 Evaluate side-chains 834 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 804 time to evaluate : 3.527 ------------------------------------------------------------------------------- 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 T residue 75 GLU Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain X residue 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: 0.9980 chunk 89 optimal weight: 7.9990 chunk 181 optimal weight: 0.9990 chunk 195 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 230 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 115 GLN F 138 GLN G 60 GLN H 115 GLN H 149 ASN H 152 GLN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN L 60 GLN L 115 GLN M 148 ASN N 70 ASN O 10 GLN O 148 ASN P 73 GLN R 148 ASN S 148 ASN ** X 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.142580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.129982 restraints weight = 29309.981| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.24 r_work: 0.3342 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.611 31374 Z= 0.170 Angle : 0.538 18.493 42360 Z= 0.254 Chirality : 0.035 0.134 4656 Planarity : 0.003 0.046 5484 Dihedral : 5.897 82.720 4116 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 2.50 % Allowed : 13.09 % Favored : 84.42 % 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: 4.02 (0.13), residues: 3696 helix: 3.19 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.80 (0.20), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 35 HIS 0.007 0.001 HIS T 42 PHE 0.027 0.002 PHE S 26 TYR 0.021 0.002 TYR F 93 ARG 0.004 0.001 ARG U 30 Details of bonding type rmsd hydrogen bonds : bond 0.04451 ( 2652) hydrogen bonds : angle 3.67306 ( 7956) covalent geometry : bond 0.00387 (31368) covalent geometry : angle 0.53802 (42360) Misc. bond : bond 0.49149 ( 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 924 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 841 time to evaluate : 3.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7091 (mm-30) REVERT: A 115 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7189 (tm-30) REVERT: B 43 ARG cc_start: 0.7698 (tpt170) cc_final: 0.7351 (tpt170) REVERT: C 50 ASP cc_start: 0.7398 (m-30) cc_final: 0.6696 (t0) REVERT: C 52 LYS cc_start: 0.6878 (tptt) cc_final: 0.6003 (mtmm) REVERT: C 66 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7540 (mp0) REVERT: C 75 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7865 (mt-10) REVERT: C 112 LYS cc_start: 0.8025 (mmtm) cc_final: 0.7445 (mmmt) REVERT: C 118 GLU cc_start: 0.7428 (mp0) cc_final: 0.7225 (mp0) REVERT: D 1 MET cc_start: 0.7915 (ptp) cc_final: 0.7257 (ptt) REVERT: D 5 LYS cc_start: 0.7336 (mppt) cc_final: 0.6434 (tttp) REVERT: D 66 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: D 88 ARG cc_start: 0.7909 (mtm110) cc_final: 0.7323 (mmt-90) REVERT: D 100 ASP cc_start: 0.7831 (t0) cc_final: 0.7610 (m-30) REVERT: D 115 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8221 (mm-40) REVERT: D 117 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7923 (ttt90) REVERT: D 118 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6514 (mt-10) REVERT: D 133 TYR cc_start: 0.7218 (t80) cc_final: 0.7012 (t80) REVERT: E 115 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.6064 (tm-30) REVERT: E 152 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: F 96 LYS cc_start: 0.8033 (ttpp) cc_final: 0.7727 (tttm) REVERT: F 103 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7469 (ttmt) REVERT: F 115 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.7748 (tm130) REVERT: G 13 ARG cc_start: 0.7647 (mtm110) cc_final: 0.7353 (mtm-85) REVERT: G 66 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7921 (mp0) REVERT: G 96 LYS cc_start: 0.7987 (ttpp) cc_final: 0.7531 (tmtm) REVERT: G 112 LYS cc_start: 0.8273 (mmtm) cc_final: 0.7820 (mmmt) REVERT: G 115 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: H 57 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7786 (mtpt) REVERT: H 103 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7778 (tttm) REVERT: I 1 MET cc_start: 0.6876 (ptm) cc_final: 0.6480 (ptm) REVERT: I 9 ASP cc_start: 0.8042 (m-30) cc_final: 0.7841 (m-30) REVERT: I 42 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7078 (mt-10) REVERT: I 50 ASP cc_start: 0.6528 (m-30) cc_final: 0.5857 (t0) REVERT: I 75 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7465 (mm-30) REVERT: I 112 LYS cc_start: 0.8230 (mmtm) cc_final: 0.7486 (mmmt) REVERT: I 149 ASN cc_start: 0.8657 (m-40) cc_final: 0.8406 (m110) REVERT: J 1 MET cc_start: 0.7019 (ptm) cc_final: 0.6705 (ptt) REVERT: J 50 ASP cc_start: 0.7188 (m-30) cc_final: 0.6945 (m-30) REVERT: J 57 LYS cc_start: 0.7769 (mtmt) cc_final: 0.7475 (mttm) REVERT: J 103 LYS cc_start: 0.8016 (mtmt) cc_final: 0.7371 (mmtt) REVERT: J 110 GLN cc_start: 0.7532 (mt0) cc_final: 0.7178 (mt0) REVERT: K 1 MET cc_start: 0.6973 (ptm) cc_final: 0.6646 (ptm) REVERT: K 42 GLU cc_start: 0.7578 (mt-10) cc_final: 0.6638 (tm-30) REVERT: K 66 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7944 (mp0) REVERT: K 88 ARG cc_start: 0.7382 (mtm110) cc_final: 0.6960 (mmt180) REVERT: K 96 LYS cc_start: 0.8089 (mtpp) cc_final: 0.7486 (mtmm) REVERT: K 103 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7287 (mmtt) REVERT: L 1 MET cc_start: 0.6940 (ptm) cc_final: 0.6574 (ptm) REVERT: L 42 GLU cc_start: 0.7771 (mt-10) cc_final: 0.6905 (pp20) REVERT: L 52 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.5951 (mtmm) REVERT: L 112 LYS cc_start: 0.8554 (mppt) cc_final: 0.7722 (mmmt) REVERT: L 125 ASP cc_start: 0.8237 (t0) cc_final: 0.7923 (t70) REVERT: N 76 LYS cc_start: 0.8521 (tmtt) cc_final: 0.8133 (tptp) REVERT: O 1 MET cc_start: 0.6945 (ttp) cc_final: 0.6073 (ptp) REVERT: O 68 LEU cc_start: 0.8458 (mt) cc_final: 0.8145 (mm) REVERT: O 96 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7012 (tm-30) REVERT: O 138 ARG cc_start: 0.7611 (ttm-80) cc_final: 0.6784 (ttm-80) REVERT: P 38 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8136 (mm-30) REVERT: P 39 LYS cc_start: 0.7920 (ttpt) cc_final: 0.7217 (mtmt) REVERT: P 57 LYS cc_start: 0.7675 (mtmt) cc_final: 0.7395 (mttm) REVERT: P 76 LYS cc_start: 0.7808 (mmtt) cc_final: 0.7316 (tmtt) REVERT: P 127 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7092 (mm-30) REVERT: Q 39 LYS cc_start: 0.8712 (ttmm) cc_final: 0.8249 (mtpt) REVERT: Q 57 LYS cc_start: 0.7882 (mtmt) cc_final: 0.7578 (mttt) REVERT: Q 81 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: Q 125 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6918 (mt-10) REVERT: Q 139 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7067 (tm-30) REVERT: R 6 LYS cc_start: 0.8023 (mmtp) cc_final: 0.7703 (mttp) REVERT: R 81 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: R 85 GLU cc_start: 0.8229 (tt0) cc_final: 0.7735 (tt0) REVERT: R 97 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7130 (tm-30) REVERT: R 129 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6902 (mt-10) REVERT: S 1 MET cc_start: 0.6742 (ptm) cc_final: 0.6334 (ptt) REVERT: S 6 LYS cc_start: 0.8205 (mmtp) cc_final: 0.7811 (mptt) REVERT: S 96 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7080 (tm-30) REVERT: T 6 LYS cc_start: 0.7916 (mmtp) cc_final: 0.7370 (mtmm) REVERT: T 13 ARG cc_start: 0.7594 (ttm-80) cc_final: 0.7229 (mtm-85) REVERT: T 53 LYS cc_start: 0.8105 (mttp) cc_final: 0.7784 (mttt) REVERT: T 73 GLN cc_start: 0.7561 (mm-40) cc_final: 0.6949 (tp40) REVERT: T 74 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7116 (mp) REVERT: T 75 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7331 (mm-30) REVERT: T 96 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7270 (mt-10) REVERT: T 103 ASP cc_start: 0.8249 (m-30) cc_final: 0.7882 (m-30) REVERT: U 10 GLN cc_start: 0.8018 (mm110) cc_final: 0.7795 (mm110) REVERT: U 68 LEU cc_start: 0.8785 (mt) cc_final: 0.8533 (mm) REVERT: U 91 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7587 (tt) REVERT: V 33 LYS cc_start: 0.8415 (tttt) cc_final: 0.7744 (ttpp) REVERT: V 81 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7603 (mt-10) REVERT: V 129 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6426 (tm-30) REVERT: W 6 LYS cc_start: 0.7812 (mmtp) cc_final: 0.7409 (mtmm) REVERT: W 46 LYS cc_start: 0.7639 (pttt) cc_final: 0.7261 (mmmt) REVERT: W 66 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7622 (mm-30) REVERT: W 88 ASP cc_start: 0.8191 (m-30) cc_final: 0.7943 (m-30) REVERT: W 100 LEU cc_start: 0.8410 (tt) cc_final: 0.8164 (tp) REVERT: W 135 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7976 (mt-10) REVERT: W 151 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: X 6 LYS cc_start: 0.7833 (mmtp) cc_final: 0.7128 (mmpt) REVERT: X 51 ASP cc_start: 0.7704 (m-30) cc_final: 0.7478 (m-30) outliers start: 83 outliers final: 25 residues processed: 878 average time/residue: 1.5593 time to fit residues: 1587.1447 Evaluate side-chains 851 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 804 time to evaluate : 3.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 4 ASP Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 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 68 VAL Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 127 THR 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 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 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 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 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 256 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 275 optimal weight: 0.0980 chunk 319 optimal weight: 5.9990 chunk 266 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 201 optimal weight: 0.8980 chunk 212 optimal weight: 10.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 89 ASN A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN F 115 GLN F 138 GLN G 60 GLN J 89 ASN J 131 HIS ** 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 N 70 ASN O 10 GLN O 148 ASN P 73 GLN Q 148 ASN R 148 ASN T 42 HIS V 10 GLN W 148 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.143667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.132496 restraints weight = 29123.548| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.09 r_work: 0.3396 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.626 31374 Z= 0.133 Angle : 0.498 16.687 42360 Z= 0.234 Chirality : 0.033 0.139 4656 Planarity : 0.003 0.036 5484 Dihedral : 5.690 82.684 4116 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.59 % Allowed : 14.02 % 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: 4.23 (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 0.005 0.001 TRP X 133 HIS 0.009 0.001 HIS T 42 PHE 0.020 0.002 PHE S 26 TYR 0.021 0.002 TYR K 133 ARG 0.004 0.000 ARG L 74 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 2652) hydrogen bonds : angle 3.55608 ( 7956) covalent geometry : bond 0.00290 (31368) covalent geometry : angle 0.49833 (42360) Misc. bond : bond 0.48641 ( 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 920 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 834 time to evaluate : 3.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6900 (mm-30) REVERT: A 115 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: B 43 ARG cc_start: 0.7526 (tpt170) cc_final: 0.7114 (tpt170) REVERT: B 112 LYS cc_start: 0.8067 (mptt) cc_final: 0.7356 (mtmt) REVERT: C 50 ASP cc_start: 0.7232 (m-30) cc_final: 0.6494 (t0) REVERT: C 52 LYS cc_start: 0.6702 (tptt) cc_final: 0.5776 (mtmm) REVERT: C 66 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7440 (mp0) REVERT: C 112 LYS cc_start: 0.7885 (mmtm) cc_final: 0.7303 (mmmt) REVERT: C 118 GLU cc_start: 0.7303 (mp0) cc_final: 0.7094 (mp0) REVERT: D 1 MET cc_start: 0.7800 (ptp) cc_final: 0.7108 (ptt) REVERT: D 5 LYS cc_start: 0.7238 (mppt) cc_final: 0.6344 (tttp) REVERT: D 24 GLN cc_start: 0.8500 (tt0) cc_final: 0.8099 (tt0) REVERT: D 52 LYS cc_start: 0.7333 (tptp) cc_final: 0.5794 (mtmm) REVERT: D 66 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: D 88 ARG cc_start: 0.7752 (mtm110) cc_final: 0.7106 (mmt-90) REVERT: D 100 ASP cc_start: 0.7657 (t0) cc_final: 0.7386 (m-30) REVERT: D 117 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7402 (ttt180) REVERT: D 118 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6329 (mt-10) REVERT: E 113 ASP cc_start: 0.8728 (t0) cc_final: 0.8358 (t70) REVERT: E 115 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.6220 (tm-30) REVERT: E 122 VAL cc_start: 0.8151 (p) cc_final: 0.7886 (m) REVERT: E 136 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7789 (mp0) REVERT: E 152 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: F 22 MET cc_start: 0.7644 (ttp) cc_final: 0.7133 (ttp) REVERT: F 52 LYS cc_start: 0.6824 (tptt) cc_final: 0.6329 (tptt) REVERT: F 96 LYS cc_start: 0.7853 (ttpp) cc_final: 0.7548 (tttm) REVERT: F 100 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7092 (t0) REVERT: F 103 LYS cc_start: 0.7745 (mtmt) cc_final: 0.7213 (ttmt) REVERT: F 115 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7550 (tm130) REVERT: G 4 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7438 (t70) REVERT: G 13 ARG cc_start: 0.7486 (mtm110) cc_final: 0.7197 (mtm-85) REVERT: G 50 ASP cc_start: 0.6806 (m-30) cc_final: 0.5831 (t0) REVERT: G 66 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7767 (mp0) REVERT: G 96 LYS cc_start: 0.7847 (ttpp) cc_final: 0.7359 (tmtm) REVERT: G 112 LYS cc_start: 0.8170 (mmtm) cc_final: 0.7707 (mmmt) REVERT: G 115 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: H 57 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7618 (mtpt) REVERT: H 96 LYS cc_start: 0.8075 (tttm) cc_final: 0.7630 (ttpt) REVERT: H 103 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7633 (tttm) REVERT: I 1 MET cc_start: 0.6772 (ptm) cc_final: 0.6394 (ptm) REVERT: I 9 ASP cc_start: 0.7901 (m-30) cc_final: 0.7530 (m-30) REVERT: I 50 ASP cc_start: 0.6322 (m-30) cc_final: 0.5625 (t70) REVERT: I 75 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7355 (mm-30) REVERT: I 112 LYS cc_start: 0.8166 (mmtm) cc_final: 0.7310 (mtpm) REVERT: J 1 MET cc_start: 0.6934 (ptm) cc_final: 0.6602 (ptt) REVERT: J 50 ASP cc_start: 0.7054 (m-30) cc_final: 0.6776 (m-30) REVERT: J 57 LYS cc_start: 0.7542 (mtmt) cc_final: 0.7223 (mttm) REVERT: J 103 LYS cc_start: 0.7854 (mtmt) cc_final: 0.7149 (mmtt) REVERT: J 110 GLN cc_start: 0.7379 (mt0) cc_final: 0.7032 (mt0) REVERT: K 1 MET cc_start: 0.6868 (ptm) cc_final: 0.5765 (ptp) REVERT: K 42 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6479 (tm-30) REVERT: K 66 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7816 (mp0) REVERT: K 88 ARG cc_start: 0.7153 (mtm110) cc_final: 0.6711 (mmt180) REVERT: K 96 LYS cc_start: 0.7962 (mtpp) cc_final: 0.7332 (mtmm) REVERT: K 103 LYS cc_start: 0.8071 (mtmt) cc_final: 0.7088 (mmtt) REVERT: L 1 MET cc_start: 0.6800 (ptm) cc_final: 0.6296 (ptt) REVERT: L 42 GLU cc_start: 0.7588 (mt-10) cc_final: 0.6717 (pp20) REVERT: L 52 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.5772 (mtmm) REVERT: L 66 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7456 (mp0) REVERT: L 112 LYS cc_start: 0.8477 (mppt) cc_final: 0.7628 (mmmt) REVERT: M 46 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7409 (ptpt) REVERT: N 76 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8192 (tmtt) REVERT: O 1 MET cc_start: 0.6850 (ttp) cc_final: 0.5942 (ptp) REVERT: O 68 LEU cc_start: 0.8369 (mt) cc_final: 0.8049 (mm) REVERT: O 96 GLU cc_start: 0.7339 (tm-30) cc_final: 0.6859 (tm-30) REVERT: O 138 ARG cc_start: 0.7478 (ttm-80) cc_final: 0.6623 (ttm-80) REVERT: P 39 LYS cc_start: 0.7814 (ttpt) cc_final: 0.7046 (mtmt) REVERT: P 57 LYS cc_start: 0.7467 (mtmt) cc_final: 0.7164 (mttm) REVERT: P 76 LYS cc_start: 0.7739 (mmtt) cc_final: 0.7223 (tmtt) REVERT: P 127 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6896 (mm-30) REVERT: Q 39 LYS cc_start: 0.8633 (ttmm) cc_final: 0.8160 (mtpt) REVERT: Q 57 LYS cc_start: 0.7731 (mtmt) cc_final: 0.7412 (mttt) REVERT: Q 81 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: Q 98 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7398 (mp) REVERT: Q 125 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6743 (mt-10) REVERT: Q 139 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: R 6 LYS cc_start: 0.7926 (mmtp) cc_final: 0.7618 (mttp) REVERT: R 85 GLU cc_start: 0.8096 (tt0) cc_final: 0.7745 (tt0) REVERT: R 97 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: R 129 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6600 (tm-30) REVERT: S 1 MET cc_start: 0.6490 (ptm) cc_final: 0.6124 (ptt) REVERT: S 96 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6922 (tm-30) REVERT: T 6 LYS cc_start: 0.7773 (mmtp) cc_final: 0.7219 (mtmm) REVERT: T 13 ARG cc_start: 0.7366 (ttm-80) cc_final: 0.7004 (mtm-85) REVERT: T 53 LYS cc_start: 0.7903 (mttp) cc_final: 0.7564 (mttt) REVERT: T 73 GLN cc_start: 0.7438 (mm-40) cc_final: 0.6809 (tp40) REVERT: T 74 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6938 (mp) REVERT: T 75 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7244 (mm-30) REVERT: T 96 GLU cc_start: 0.7304 (tm-30) cc_final: 0.7073 (mt-10) REVERT: T 103 ASP cc_start: 0.8083 (m-30) cc_final: 0.7683 (m-30) REVERT: U 6 LYS cc_start: 0.7941 (mptm) cc_final: 0.7489 (mtmm) REVERT: U 10 GLN cc_start: 0.7888 (mm110) cc_final: 0.7601 (mm110) REVERT: U 33 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7457 (ttpp) REVERT: U 68 LEU cc_start: 0.8715 (mt) cc_final: 0.8453 (mm) REVERT: U 91 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7421 (tt) REVERT: V 13 ARG cc_start: 0.7584 (ttm110) cc_final: 0.7124 (mtm-85) REVERT: V 33 LYS cc_start: 0.8299 (tttt) cc_final: 0.7591 (ttpp) REVERT: V 81 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7517 (mt-10) REVERT: V 129 GLU cc_start: 0.6632 (mt-10) cc_final: 0.6218 (tm-30) REVERT: W 6 LYS cc_start: 0.7665 (mmtp) cc_final: 0.7257 (mtmm) REVERT: W 46 LYS cc_start: 0.7463 (pttt) cc_final: 0.7086 (mmmt) REVERT: W 66 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7495 (mm-30) REVERT: W 88 ASP cc_start: 0.8063 (m-30) cc_final: 0.7782 (m-30) REVERT: W 135 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7852 (mt-10) REVERT: W 151 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: X 1 MET cc_start: 0.6423 (ttp) cc_final: 0.6096 (ptt) REVERT: X 6 LYS cc_start: 0.7698 (mmtp) cc_final: 0.7019 (mmpt) REVERT: X 51 ASP cc_start: 0.7585 (m-30) cc_final: 0.7376 (m-30) outliers start: 86 outliers final: 23 residues processed: 871 average time/residue: 1.5431 time to fit residues: 1557.8790 Evaluate side-chains 855 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 808 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain G residue 4 ASP 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 99 ASP Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 46 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 76 LYS 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 98 LEU Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 139 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain R residue 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 106 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 132 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 171 optimal weight: 0.2980 chunk 205 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 F 115 GLN F 138 GLN H 149 ASN 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 O 10 GLN ** O 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 GLN R 148 ASN S 148 ASN T 42 HIS W 41 ASN W 148 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.147638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.135268 restraints weight = 29179.411| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.26 r_work: 0.3407 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.597 31374 Z= 0.109 Angle : 0.473 16.762 42360 Z= 0.221 Chirality : 0.032 0.127 4656 Planarity : 0.002 0.028 5484 Dihedral : 5.459 84.089 4116 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.32 % Allowed : 14.71 % Favored : 82.97 % 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: 3.45 (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 S 133 HIS 0.009 0.001 HIS T 42 PHE 0.026 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 0.03820 ( 2652) hydrogen bonds : angle 3.42125 ( 7956) covalent geometry : bond 0.00223 (31368) covalent geometry : angle 0.47254 (42360) Misc. bond : bond 0.47858 ( 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 947 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 870 time to evaluate : 3.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7106 (mm-30) REVERT: A 115 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: A 126 ASP cc_start: 0.7864 (m-30) cc_final: 0.7638 (t0) REVERT: B 39 GLU cc_start: 0.7700 (tt0) cc_final: 0.7434 (tt0) REVERT: B 43 ARG cc_start: 0.7673 (tpt170) cc_final: 0.7235 (tpt170) REVERT: B 112 LYS cc_start: 0.8153 (mptt) cc_final: 0.7524 (mtmt) REVERT: C 22 MET cc_start: 0.7672 (ttp) cc_final: 0.7327 (ttm) REVERT: C 50 ASP cc_start: 0.7329 (m-30) cc_final: 0.6605 (t0) REVERT: C 66 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7510 (mp0) REVERT: C 75 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7752 (mt-10) REVERT: C 100 ASP cc_start: 0.8332 (t0) cc_final: 0.8065 (t70) REVERT: C 112 LYS cc_start: 0.7923 (mmtm) cc_final: 0.7405 (mtmt) REVERT: C 113 ASP cc_start: 0.8654 (t70) cc_final: 0.8452 (t70) REVERT: D 1 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7200 (ptt) REVERT: D 5 LYS cc_start: 0.7241 (mppt) cc_final: 0.6866 (mptp) REVERT: D 24 GLN cc_start: 0.8581 (tt0) cc_final: 0.8203 (tt0) REVERT: D 42 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7159 (mt-10) REVERT: D 52 LYS cc_start: 0.7480 (tptp) cc_final: 0.6017 (mtmm) REVERT: D 66 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: D 88 ARG cc_start: 0.7940 (mtm110) cc_final: 0.7337 (mmt-90) REVERT: D 117 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7885 (ttt90) REVERT: D 118 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6430 (mt-10) REVERT: D 125 ASP cc_start: 0.8113 (t70) cc_final: 0.7849 (t0) REVERT: E 122 VAL cc_start: 0.8275 (OUTLIER) cc_final: 0.7994 (m) REVERT: E 136 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7938 (mp0) REVERT: F 22 MET cc_start: 0.7762 (ttp) cc_final: 0.7322 (ttm) REVERT: F 52 LYS cc_start: 0.7051 (tptt) cc_final: 0.6762 (tptt) REVERT: F 103 LYS cc_start: 0.7844 (mtmt) cc_final: 0.7383 (ttpt) REVERT: F 115 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7809 (tm130) REVERT: F 118 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.5947 (mp0) REVERT: G 13 ARG cc_start: 0.7594 (mtm110) cc_final: 0.7319 (mtm-85) REVERT: G 50 ASP cc_start: 0.6919 (m-30) cc_final: 0.5943 (t0) REVERT: G 66 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7868 (mp0) REVERT: G 96 LYS cc_start: 0.7942 (ttpp) cc_final: 0.7235 (tmtm) REVERT: G 100 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7410 (m-30) REVERT: G 112 LYS cc_start: 0.8155 (mmtm) cc_final: 0.7789 (mmmt) REVERT: G 115 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7733 (tm-30) REVERT: H 66 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7957 (mt-10) REVERT: H 96 LYS cc_start: 0.8166 (tttm) cc_final: 0.7772 (ttpt) REVERT: H 125 ASP cc_start: 0.8128 (t0) cc_final: 0.7832 (t70) REVERT: I 1 MET cc_start: 0.6831 (ptm) cc_final: 0.6448 (ptm) REVERT: I 9 ASP cc_start: 0.7964 (m-30) cc_final: 0.7679 (m-30) REVERT: I 50 ASP cc_start: 0.6372 (m-30) cc_final: 0.5678 (t70) REVERT: I 75 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7364 (mm-30) REVERT: I 112 LYS cc_start: 0.8248 (mmtm) cc_final: 0.7522 (mtpm) REVERT: I 113 ASP cc_start: 0.8498 (t0) cc_final: 0.8298 (t0) REVERT: J 1 MET cc_start: 0.6954 (ptm) cc_final: 0.6715 (ptt) REVERT: J 50 ASP cc_start: 0.7170 (m-30) cc_final: 0.6907 (m-30) REVERT: J 57 LYS cc_start: 0.7690 (mtmt) cc_final: 0.7413 (mttm) REVERT: J 103 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7353 (mmtt) REVERT: J 110 GLN cc_start: 0.7522 (mt0) cc_final: 0.7239 (mt0) REVERT: K 1 MET cc_start: 0.6938 (ptm) cc_final: 0.6692 (ptm) REVERT: K 52 LYS cc_start: 0.6641 (tptt) cc_final: 0.5581 (mtmm) REVERT: K 66 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7939 (mp0) REVERT: K 88 ARG cc_start: 0.7283 (mtm110) cc_final: 0.6899 (mmt180) REVERT: K 96 LYS cc_start: 0.8063 (mtpp) cc_final: 0.7455 (mtmm) REVERT: K 103 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7262 (mmtt) REVERT: K 110 GLN cc_start: 0.7668 (tt0) cc_final: 0.7451 (tt0) REVERT: L 1 MET cc_start: 0.6836 (ptm) cc_final: 0.6363 (ptt) REVERT: L 42 GLU cc_start: 0.7643 (mt-10) cc_final: 0.6813 (pp20) REVERT: L 52 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.5972 (mtmm) REVERT: L 66 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7515 (mp0) REVERT: L 112 LYS cc_start: 0.8552 (mppt) cc_final: 0.7723 (mtmt) REVERT: N 1 MET cc_start: 0.5978 (ptt) cc_final: 0.5763 (ptt) REVERT: N 76 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8119 (tptp) REVERT: O 1 MET cc_start: 0.6867 (ttp) cc_final: 0.6000 (ptp) REVERT: O 68 LEU cc_start: 0.8415 (mt) cc_final: 0.8125 (mm) REVERT: O 96 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7025 (tm-30) REVERT: O 138 ARG cc_start: 0.7543 (ttm-80) cc_final: 0.6729 (ttm-80) REVERT: P 57 LYS cc_start: 0.7619 (mtmt) cc_final: 0.7337 (mttm) REVERT: Q 39 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8194 (mtpt) REVERT: Q 52 MET cc_start: 0.7962 (mtt) cc_final: 0.7704 (ttm) REVERT: Q 57 LYS cc_start: 0.7841 (mtmt) cc_final: 0.7559 (mttt) REVERT: Q 81 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: Q 98 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7525 (mp) REVERT: Q 125 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6919 (mt-10) REVERT: Q 139 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.6976 (tm-30) REVERT: R 6 LYS cc_start: 0.8033 (mmtp) cc_final: 0.7722 (mttp) REVERT: R 97 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7122 (tm-30) REVERT: R 129 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: S 1 MET cc_start: 0.6573 (ptm) cc_final: 0.6273 (ptt) REVERT: S 45 TYR cc_start: 0.7934 (t80) cc_final: 0.7696 (t80) REVERT: S 96 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7019 (tm-30) REVERT: T 6 LYS cc_start: 0.7884 (mmtp) cc_final: 0.7367 (mtmm) REVERT: T 13 ARG cc_start: 0.7458 (ttm-80) cc_final: 0.6878 (mtm-85) REVERT: T 53 LYS cc_start: 0.8028 (mttp) cc_final: 0.7677 (mtmt) REVERT: T 73 GLN cc_start: 0.7455 (mm-40) cc_final: 0.6880 (tp-100) REVERT: T 96 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7216 (mt-10) REVERT: T 103 ASP cc_start: 0.8162 (m-30) cc_final: 0.7804 (m-30) REVERT: U 6 LYS cc_start: 0.8052 (mptm) cc_final: 0.7647 (mtmm) REVERT: U 10 GLN cc_start: 0.8004 (mm110) cc_final: 0.7740 (mm110) REVERT: U 33 LYS cc_start: 0.8246 (ttpp) cc_final: 0.7539 (ttpp) REVERT: U 68 LEU cc_start: 0.8744 (mt) cc_final: 0.8505 (mm) REVERT: U 91 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7595 (tp) REVERT: U 113 ASP cc_start: 0.8356 (t70) cc_final: 0.7971 (t0) REVERT: V 33 LYS cc_start: 0.8389 (tttt) cc_final: 0.7729 (ttpp) REVERT: V 81 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7504 (mt-10) REVERT: V 96 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7144 (pt0) REVERT: V 129 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6423 (tm-30) REVERT: W 6 LYS cc_start: 0.7764 (mmtp) cc_final: 0.7353 (mtmm) REVERT: W 46 LYS cc_start: 0.7466 (pttt) cc_final: 0.7188 (mmmt) REVERT: W 52 MET cc_start: 0.7376 (ttm) cc_final: 0.6990 (ttt) REVERT: W 66 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7600 (mm-30) REVERT: W 75 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7336 (mt-10) REVERT: W 88 ASP cc_start: 0.8178 (m-30) cc_final: 0.7842 (m-30) REVERT: W 135 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7910 (mt-10) REVERT: W 148 ASN cc_start: 0.8213 (m-40) cc_final: 0.7871 (m-40) REVERT: W 151 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: X 1 MET cc_start: 0.6357 (ttp) cc_final: 0.6101 (ptt) REVERT: X 66 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8066 (mt-10) outliers start: 77 outliers final: 20 residues processed: 906 average time/residue: 1.5630 time to fit residues: 1646.1118 Evaluate side-chains 856 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 815 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain E residue 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 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 N residue 76 LYS Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 139 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain R residue 97 GLN Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain S residue 73 GLN 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 151 GLN Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain X residue 94 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 73 optimal weight: 6.9990 chunk 320 optimal weight: 5.9990 chunk 308 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 223 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 258 optimal weight: 6.9990 chunk 329 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 F 131 HIS G 60 GLN I 60 GLN J 149 ASN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 GLN K 115 GLN L 60 GLN ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 ASN N 70 ASN O 148 ASN P 97 GLN P 148 ASN R 148 ASN S 148 ASN T 42 HIS V 4 HIS V 10 GLN ** W 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 130 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.139391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.127464 restraints weight = 29480.975| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.21 r_work: 0.3328 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.696 31374 Z= 0.211 Angle : 0.593 18.757 42360 Z= 0.277 Chirality : 0.037 0.193 4656 Planarity : 0.004 0.050 5484 Dihedral : 5.629 82.222 4116 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 2.53 % Allowed : 15.22 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.05 (0.13), residues: 3696 helix: 3.19 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.70 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP S 35 HIS 0.009 0.001 HIS T 42 PHE 0.034 0.002 PHE U 26 TYR 0.024 0.002 TYR F 93 ARG 0.006 0.001 ARG X 30 Details of bonding type rmsd hydrogen bonds : bond 0.04758 ( 2652) hydrogen bonds : angle 3.70908 ( 7956) covalent geometry : bond 0.00489 (31368) covalent geometry : angle 0.59312 (42360) Misc. bond : bond 0.52542 ( 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: 84 poor density : 833 time to evaluate : 3.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7184 (tm-30) REVERT: B 112 LYS cc_start: 0.8294 (mptt) cc_final: 0.7595 (mtmt) REVERT: C 50 ASP cc_start: 0.7376 (m-30) cc_final: 0.6687 (t0) REVERT: C 52 LYS cc_start: 0.6874 (tptt) cc_final: 0.5990 (mtmm) REVERT: C 66 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7546 (mp0) REVERT: C 75 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7804 (mt-10) REVERT: C 112 LYS cc_start: 0.8004 (mmtm) cc_final: 0.7485 (mtmt) REVERT: D 1 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7537 (ptt) REVERT: D 5 LYS cc_start: 0.7328 (mppt) cc_final: 0.6970 (mptp) REVERT: D 42 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7192 (mt-10) REVERT: D 52 LYS cc_start: 0.7413 (tptp) cc_final: 0.6074 (mtmm) REVERT: D 88 ARG cc_start: 0.7949 (mtm110) cc_final: 0.7396 (mmt-90) REVERT: D 117 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7799 (ttt90) REVERT: D 118 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6486 (mt-10) REVERT: D 125 ASP cc_start: 0.8166 (t70) cc_final: 0.7946 (t70) REVERT: E 113 ASP cc_start: 0.8789 (t0) cc_final: 0.8440 (t70) REVERT: E 136 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7945 (mp0) REVERT: E 152 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: F 22 MET cc_start: 0.7894 (ttp) cc_final: 0.7427 (ttp) REVERT: F 52 LYS cc_start: 0.7061 (tptt) cc_final: 0.6707 (tptt) REVERT: F 96 LYS cc_start: 0.7995 (ttpp) cc_final: 0.7710 (tttm) REVERT: F 100 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7328 (t0) REVERT: F 103 LYS cc_start: 0.7936 (mtmt) cc_final: 0.7441 (ttmt) REVERT: F 115 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7785 (tm130) REVERT: F 118 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.6008 (mp0) REVERT: G 13 ARG cc_start: 0.7674 (mtm110) cc_final: 0.7396 (mtm-85) REVERT: G 66 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7900 (mp0) REVERT: G 96 LYS cc_start: 0.7976 (ttpp) cc_final: 0.7394 (tmtm) REVERT: G 100 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7429 (m-30) REVERT: G 112 LYS cc_start: 0.8290 (mmtm) cc_final: 0.7858 (mmmt) REVERT: G 115 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: H 57 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7801 (mtpt) REVERT: H 96 LYS cc_start: 0.8201 (tttm) cc_final: 0.7779 (ttpt) REVERT: H 103 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7807 (tttm) REVERT: I 1 MET cc_start: 0.6842 (ptm) cc_final: 0.6449 (ptm) REVERT: I 9 ASP cc_start: 0.8059 (m-30) cc_final: 0.7840 (m-30) REVERT: I 42 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7080 (mt-10) REVERT: I 50 ASP cc_start: 0.6483 (m-30) cc_final: 0.5871 (t70) REVERT: I 75 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7520 (mm-30) REVERT: I 112 LYS cc_start: 0.8315 (mmtm) cc_final: 0.7549 (mtpm) REVERT: I 118 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7123 (pt0) REVERT: J 1 MET cc_start: 0.7055 (ptm) cc_final: 0.6795 (ptt) REVERT: J 50 ASP cc_start: 0.7204 (m-30) cc_final: 0.6922 (m-30) REVERT: J 57 LYS cc_start: 0.7761 (mtmt) cc_final: 0.7467 (mttm) REVERT: J 96 LYS cc_start: 0.7967 (ttpp) cc_final: 0.7753 (ttpp) REVERT: J 103 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7395 (mmtt) REVERT: J 110 GLN cc_start: 0.7520 (mt0) cc_final: 0.7201 (mt0) REVERT: K 42 GLU cc_start: 0.7605 (mt-10) cc_final: 0.6701 (tm-30) REVERT: K 66 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7964 (mp0) REVERT: K 88 ARG cc_start: 0.7374 (mtm110) cc_final: 0.6964 (mmt180) REVERT: K 103 LYS cc_start: 0.8269 (mtmt) cc_final: 0.7332 (mmtt) REVERT: K 110 GLN cc_start: 0.7680 (tt0) cc_final: 0.7479 (tt0) REVERT: L 1 MET cc_start: 0.6918 (ptm) cc_final: 0.6535 (ptt) REVERT: L 42 GLU cc_start: 0.7773 (mt-10) cc_final: 0.6941 (pp20) REVERT: L 52 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.5930 (mtmm) REVERT: L 57 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7779 (mppt) REVERT: L 112 LYS cc_start: 0.8578 (mppt) cc_final: 0.7741 (mmmt) REVERT: N 1 MET cc_start: 0.6125 (ptt) cc_final: 0.5857 (ptt) REVERT: N 76 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8141 (tptm) REVERT: O 68 LEU cc_start: 0.8461 (mt) cc_final: 0.8149 (mm) REVERT: O 96 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7011 (tm-30) REVERT: O 138 ARG cc_start: 0.7622 (ttm-80) cc_final: 0.6768 (ttm-80) REVERT: P 57 LYS cc_start: 0.7665 (mtmt) cc_final: 0.7389 (mttm) REVERT: P 97 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7221 (tp-100) REVERT: P 127 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7273 (mm-30) REVERT: Q 38 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7709 (mm-30) REVERT: Q 57 LYS cc_start: 0.7925 (mtmt) cc_final: 0.7591 (mttt) REVERT: Q 81 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: Q 98 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7566 (mp) REVERT: Q 125 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6938 (mt-10) REVERT: Q 139 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: R 6 LYS cc_start: 0.8020 (mmtp) cc_final: 0.7704 (mttp) REVERT: R 13 ARG cc_start: 0.7725 (ttm-80) cc_final: 0.7420 (mtp85) REVERT: R 81 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: R 97 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7175 (tm-30) REVERT: R 129 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6733 (tm-30) REVERT: S 1 MET cc_start: 0.6838 (ptm) cc_final: 0.6463 (ptt) REVERT: S 6 LYS cc_start: 0.8170 (mmtp) cc_final: 0.7727 (mmtm) REVERT: S 57 LYS cc_start: 0.8177 (mttm) cc_final: 0.7915 (mttp) REVERT: S 96 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7095 (tm-30) REVERT: T 6 LYS cc_start: 0.7931 (mmtp) cc_final: 0.7399 (mtmm) REVERT: T 53 LYS cc_start: 0.8109 (mttp) cc_final: 0.7814 (mttt) REVERT: T 73 GLN cc_start: 0.7558 (mm-40) cc_final: 0.6974 (tp40) REVERT: T 75 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: T 96 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7150 (tt0) REVERT: T 103 ASP cc_start: 0.8244 (m-30) cc_final: 0.7912 (m-30) REVERT: U 10 GLN cc_start: 0.8038 (mm110) cc_final: 0.7747 (mm110) REVERT: U 33 LYS cc_start: 0.8320 (ttpp) cc_final: 0.7763 (ttpp) REVERT: U 45 TYR cc_start: 0.8187 (t80) cc_final: 0.7358 (t80) REVERT: U 68 LEU cc_start: 0.8799 (mt) cc_final: 0.8532 (mm) REVERT: U 91 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7700 (tt) REVERT: V 33 LYS cc_start: 0.8457 (tttt) cc_final: 0.7807 (ttpp) REVERT: V 81 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7637 (mt-10) REVERT: V 129 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6389 (tm-30) REVERT: W 6 LYS cc_start: 0.7794 (mmtp) cc_final: 0.7418 (mtmm) REVERT: W 46 LYS cc_start: 0.7638 (pttt) cc_final: 0.7275 (mmmt) REVERT: W 88 ASP cc_start: 0.8171 (m-30) cc_final: 0.7927 (m-30) REVERT: W 135 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7975 (mt-10) REVERT: W 151 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: X 1 MET cc_start: 0.6620 (ttp) cc_final: 0.6338 (ptt) REVERT: X 6 LYS cc_start: 0.7837 (mmtp) cc_final: 0.7193 (mmpt) REVERT: X 51 ASP cc_start: 0.7628 (m-30) cc_final: 0.7392 (m-30) outliers start: 84 outliers final: 25 residues processed: 871 average time/residue: 1.5738 time to fit residues: 1584.8090 Evaluate side-chains 855 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 802 time to evaluate : 3.532 ------------------------------------------------------------------------------- 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 117 ARG Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 57 LYS Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 17 CYS Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 97 GLN Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 139 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain R residue 97 GLN Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain S residue 73 GLN 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 151 GLN Chi-restraints excluded: chain X residue 94 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 271 optimal weight: 5.9990 chunk 213 optimal weight: 0.0970 chunk 305 optimal weight: 0.5980 chunk 192 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 281 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 322 optimal weight: 6.9990 chunk 309 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN E 70 ASN F 115 GLN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 ASN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 GLN K 89 ASN K 115 GLN L 60 GLN ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 ASN N 70 ASN O 10 GLN O 148 ASN P 73 GLN P 97 GLN Q 148 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 HIS V 10 GLN ** W 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 148 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.141629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.130165 restraints weight = 29357.182| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.13 r_work: 0.3357 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.669 31374 Z= 0.176 Angle : 0.563 19.708 42360 Z= 0.263 Chirality : 0.035 0.153 4656 Planarity : 0.003 0.046 5484 Dihedral : 5.546 80.916 4116 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.35 % Allowed : 16.03 % Favored : 81.62 % 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: 4.03 (0.13), residues: 3696 helix: 3.18 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.69 (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 0.030 0.002 PHE U 26 TYR 0.023 0.002 TYR K 133 ARG 0.011 0.001 ARG V 13 Details of bonding type rmsd hydrogen bonds : bond 0.04506 ( 2652) hydrogen bonds : angle 3.66471 ( 7956) covalent geometry : bond 0.00403 (31368) covalent geometry : angle 0.56285 (42360) Misc. bond : bond 0.48333 ( 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 896 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 818 time to evaluate : 3.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: A 126 ASP cc_start: 0.7884 (m-30) cc_final: 0.7594 (t0) REVERT: B 43 ARG cc_start: 0.7561 (tpt170) cc_final: 0.7261 (tpt170) REVERT: B 112 LYS cc_start: 0.8180 (mptt) cc_final: 0.7441 (mtmt) REVERT: C 50 ASP cc_start: 0.7249 (m-30) cc_final: 0.6531 (t0) REVERT: C 52 LYS cc_start: 0.6745 (tptt) cc_final: 0.5815 (mtmm) REVERT: C 66 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7443 (mp0) REVERT: C 75 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7731 (mt-10) REVERT: C 112 LYS cc_start: 0.7858 (mmtm) cc_final: 0.7258 (mtpt) REVERT: D 1 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7457 (ptt) REVERT: D 5 LYS cc_start: 0.7251 (mppt) cc_final: 0.6898 (mptp) REVERT: D 42 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7055 (mt-10) REVERT: D 52 LYS cc_start: 0.7299 (tptp) cc_final: 0.5881 (mtmm) REVERT: D 88 ARG cc_start: 0.7849 (mtm110) cc_final: 0.7247 (mmt-90) REVERT: D 117 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7730 (ttt90) REVERT: D 118 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6292 (mt-10) REVERT: E 122 VAL cc_start: 0.8178 (p) cc_final: 0.7912 (m) REVERT: E 136 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7833 (mp0) REVERT: F 22 MET cc_start: 0.7778 (ttp) cc_final: 0.7280 (ttp) REVERT: F 52 LYS cc_start: 0.6951 (tptt) cc_final: 0.6569 (tptt) REVERT: F 96 LYS cc_start: 0.7832 (ttpp) cc_final: 0.7541 (tttm) REVERT: F 103 LYS cc_start: 0.7795 (mtmt) cc_final: 0.7289 (ttmt) REVERT: F 115 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7789 (tm130) REVERT: F 118 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.6101 (mt-10) REVERT: G 13 ARG cc_start: 0.7544 (mtm110) cc_final: 0.7261 (mtm-85) REVERT: G 66 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7781 (mp0) REVERT: G 96 LYS cc_start: 0.7848 (ttpp) cc_final: 0.7230 (tmtm) REVERT: G 100 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7314 (m-30) REVERT: G 112 LYS cc_start: 0.8220 (mmtm) cc_final: 0.7752 (mmmt) REVERT: G 115 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7686 (tm-30) REVERT: H 57 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7641 (mtpt) REVERT: H 96 LYS cc_start: 0.8088 (tttm) cc_final: 0.7660 (ttpt) REVERT: H 103 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7681 (tttm) REVERT: I 1 MET cc_start: 0.6779 (ptm) cc_final: 0.6329 (ptt) REVERT: I 9 ASP cc_start: 0.7956 (m-30) cc_final: 0.7729 (m-30) REVERT: I 42 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7006 (mt-10) REVERT: I 50 ASP cc_start: 0.6371 (m-30) cc_final: 0.5694 (t0) REVERT: I 75 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7450 (mm-30) REVERT: I 112 LYS cc_start: 0.8226 (mmtm) cc_final: 0.7426 (mtpm) REVERT: J 1 MET cc_start: 0.6957 (ptm) cc_final: 0.6706 (ptt) REVERT: J 50 ASP cc_start: 0.7103 (m-30) cc_final: 0.6778 (m-30) REVERT: J 57 LYS cc_start: 0.7602 (mtmt) cc_final: 0.7276 (mttm) REVERT: J 103 LYS cc_start: 0.7912 (mtmt) cc_final: 0.7213 (mmtt) REVERT: J 110 GLN cc_start: 0.7397 (mt0) cc_final: 0.7055 (mt0) REVERT: K 1 MET cc_start: 0.7202 (ptm) cc_final: 0.6746 (ptt) REVERT: K 42 GLU cc_start: 0.7532 (mt-10) cc_final: 0.6567 (tm-30) REVERT: K 66 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7914 (mp0) REVERT: K 88 ARG cc_start: 0.7219 (mtm110) cc_final: 0.6798 (mmt180) REVERT: K 103 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7143 (mmtt) REVERT: K 110 GLN cc_start: 0.7585 (tt0) cc_final: 0.7366 (tt0) REVERT: L 1 MET cc_start: 0.6806 (ptm) cc_final: 0.6405 (ptm) REVERT: L 42 GLU cc_start: 0.7657 (mt-10) cc_final: 0.6788 (pp20) REVERT: L 52 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.5794 (mtmm) REVERT: L 57 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7617 (mppt) REVERT: L 112 LYS cc_start: 0.8497 (mppt) cc_final: 0.7563 (mtmt) REVERT: N 1 MET cc_start: 0.5953 (ptt) cc_final: 0.5652 (ptt) REVERT: N 76 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8204 (tmtt) REVERT: O 1 MET cc_start: 0.6920 (ttp) cc_final: 0.5879 (ptp) REVERT: O 13 ARG cc_start: 0.7342 (mtm-85) cc_final: 0.6963 (mtm-85) REVERT: O 68 LEU cc_start: 0.8390 (mt) cc_final: 0.8074 (mm) REVERT: O 96 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6857 (tm-30) REVERT: O 138 ARG cc_start: 0.7524 (ttm-80) cc_final: 0.6621 (ttm-80) REVERT: P 57 LYS cc_start: 0.7514 (mtmt) cc_final: 0.7216 (mttm) REVERT: P 97 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7000 (tp-100) REVERT: P 127 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7124 (mm-30) REVERT: Q 38 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7582 (mm-30) REVERT: Q 39 LYS cc_start: 0.8676 (ttmm) cc_final: 0.8177 (mtpt) REVERT: Q 57 LYS cc_start: 0.7799 (mtmt) cc_final: 0.7463 (mttt) REVERT: Q 81 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: Q 98 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7463 (mp) REVERT: Q 125 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6797 (mt-10) REVERT: Q 139 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.6884 (tm-30) REVERT: R 6 LYS cc_start: 0.7917 (mmtp) cc_final: 0.7580 (mttp) REVERT: R 13 ARG cc_start: 0.7494 (ttm-80) cc_final: 0.7210 (mtp85) REVERT: R 75 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7967 (mt-10) REVERT: R 129 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6584 (tm-30) REVERT: S 1 MET cc_start: 0.6723 (ptm) cc_final: 0.6368 (ptt) REVERT: S 6 LYS cc_start: 0.8054 (mmtp) cc_final: 0.7588 (mmtm) REVERT: S 57 LYS cc_start: 0.8025 (mttm) cc_final: 0.7744 (mttp) REVERT: S 96 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6950 (tm-30) REVERT: T 6 LYS cc_start: 0.7830 (mmtp) cc_final: 0.7338 (mttp) REVERT: T 53 LYS cc_start: 0.7929 (mttp) cc_final: 0.7627 (mttt) REVERT: T 73 GLN cc_start: 0.7490 (mm-40) cc_final: 0.6888 (tp40) REVERT: T 75 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7381 (mm-30) REVERT: T 96 GLU cc_start: 0.7330 (tm-30) cc_final: 0.7016 (tt0) REVERT: T 97 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: T 103 ASP cc_start: 0.8102 (m-30) cc_final: 0.7734 (m-30) REVERT: U 10 GLN cc_start: 0.7921 (mm110) cc_final: 0.7633 (mm110) REVERT: U 33 LYS cc_start: 0.8226 (ttpp) cc_final: 0.7663 (ttpp) REVERT: U 45 TYR cc_start: 0.8084 (t80) cc_final: 0.7330 (t80) REVERT: U 68 LEU cc_start: 0.8744 (mt) cc_final: 0.8472 (mm) REVERT: U 91 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7545 (tt) REVERT: V 33 LYS cc_start: 0.8357 (tttt) cc_final: 0.7667 (ttpp) REVERT: V 76 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7564 (tmmt) REVERT: V 81 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7543 (mt-10) REVERT: V 129 GLU cc_start: 0.6656 (mt-10) cc_final: 0.6233 (tm-30) REVERT: W 6 LYS cc_start: 0.7693 (mmtp) cc_final: 0.7297 (mtmm) REVERT: W 46 LYS cc_start: 0.7509 (pttt) cc_final: 0.7141 (mmmt) REVERT: W 52 MET cc_start: 0.7460 (ttm) cc_final: 0.6976 (ttt) REVERT: W 88 ASP cc_start: 0.8071 (m-30) cc_final: 0.7803 (m-30) REVERT: W 135 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7895 (mt-10) REVERT: W 151 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: X 1 MET cc_start: 0.6510 (ttp) cc_final: 0.6225 (ptt) REVERT: X 6 LYS cc_start: 0.7753 (mmtp) cc_final: 0.7078 (mmpt) REVERT: X 51 ASP cc_start: 0.7547 (m-30) cc_final: 0.7313 (m-30) outliers start: 78 outliers final: 26 residues processed: 854 average time/residue: 1.5923 time to fit residues: 1568.8212 Evaluate side-chains 847 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 796 time to evaluate : 3.290 ------------------------------------------------------------------------------- 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 117 ARG Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 39 GLU 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 68 VAL Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 57 LYS Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 17 CYS Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 97 GLN Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 139 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain T residue 97 GLN Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 155 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 76 LYS Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 119 LEU Chi-restraints excluded: chain W residue 151 GLN Chi-restraints excluded: chain X residue 94 VAL Chi-restraints excluded: chain X residue 106 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 179 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 299 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN E 70 ASN E 115 GLN F 115 GLN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 ASN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN L 60 GLN ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 ASN N 70 ASN N 151 GLN O 10 GLN O 148 ASN P 97 GLN Q 148 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 148 ASN T 42 HIS V 10 GLN ** W 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 148 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.142243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.130649 restraints weight = 29152.255| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.15 r_work: 0.3359 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.669 31374 Z= 0.164 Angle : 0.550 17.955 42360 Z= 0.262 Chirality : 0.035 0.175 4656 Planarity : 0.003 0.044 5484 Dihedral : 5.471 78.922 4116 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 2.05 % Allowed : 16.70 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.04 (0.13), residues: 3696 helix: 3.18 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.67 (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 0.030 0.002 PHE U 26 TYR 0.024 0.002 TYR K 133 ARG 0.006 0.001 ARG C 74 Details of bonding type rmsd hydrogen bonds : bond 0.04423 ( 2652) hydrogen bonds : angle 3.63939 ( 7956) covalent geometry : bond 0.00371 (31368) covalent geometry : angle 0.55013 (42360) Misc. bond : bond 0.47761 ( 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 878 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 810 time to evaluate : 3.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6986 (mm-30) REVERT: A 115 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: A 126 ASP cc_start: 0.7877 (m-30) cc_final: 0.7602 (t0) REVERT: B 43 ARG cc_start: 0.7576 (tpt170) cc_final: 0.7255 (tpt170) REVERT: B 112 LYS cc_start: 0.8192 (mptt) cc_final: 0.7456 (mtmt) REVERT: C 50 ASP cc_start: 0.7259 (m-30) cc_final: 0.6546 (t0) REVERT: C 66 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7469 (mp0) REVERT: C 75 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7782 (mt-10) REVERT: C 112 LYS cc_start: 0.7828 (mmtm) cc_final: 0.7241 (mtpt) REVERT: D 1 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7452 (ptt) REVERT: D 5 LYS cc_start: 0.7246 (mppt) cc_final: 0.6907 (mptp) REVERT: D 42 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7062 (mt-10) REVERT: D 52 LYS cc_start: 0.7313 (tptp) cc_final: 0.5881 (mtmm) REVERT: D 88 ARG cc_start: 0.7865 (mtm110) cc_final: 0.7257 (mmt-90) REVERT: D 117 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7731 (ttt90) REVERT: D 118 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6337 (mt-10) REVERT: E 122 VAL cc_start: 0.8181 (p) cc_final: 0.7920 (m) REVERT: E 136 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7925 (mt-10) REVERT: F 22 MET cc_start: 0.7803 (ttp) cc_final: 0.7285 (ttp) REVERT: F 52 LYS cc_start: 0.6958 (tptt) cc_final: 0.6601 (tptt) REVERT: F 96 LYS cc_start: 0.7848 (ttpp) cc_final: 0.7557 (tttm) REVERT: F 103 LYS cc_start: 0.7804 (mtmt) cc_final: 0.7301 (ttmt) REVERT: F 115 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7728 (tm130) REVERT: F 118 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.6143 (mt-10) REVERT: G 13 ARG cc_start: 0.7563 (mtm110) cc_final: 0.7284 (mtm-85) REVERT: G 66 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7782 (mp0) REVERT: G 96 LYS cc_start: 0.7852 (ttpp) cc_final: 0.7227 (tmtm) REVERT: G 100 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7294 (m-30) REVERT: G 112 LYS cc_start: 0.8224 (mmtm) cc_final: 0.7767 (mmmt) REVERT: G 115 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: H 57 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7673 (mtpt) REVERT: H 96 LYS cc_start: 0.8102 (tttm) cc_final: 0.7687 (ttpt) REVERT: H 103 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7689 (tttm) REVERT: I 1 MET cc_start: 0.6773 (ptm) cc_final: 0.6420 (ptm) REVERT: I 9 ASP cc_start: 0.7962 (m-30) cc_final: 0.7751 (m-30) REVERT: I 42 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7025 (mt-10) REVERT: I 50 ASP cc_start: 0.6352 (m-30) cc_final: 0.5706 (t70) REVERT: I 75 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7467 (mm-30) REVERT: I 112 LYS cc_start: 0.8235 (mmtm) cc_final: 0.7451 (mtpm) REVERT: I 113 ASP cc_start: 0.8455 (t0) cc_final: 0.8247 (t0) REVERT: J 1 MET cc_start: 0.6927 (ptm) cc_final: 0.6680 (ptt) REVERT: J 50 ASP cc_start: 0.7132 (m-30) cc_final: 0.6812 (m-30) REVERT: J 57 LYS cc_start: 0.7614 (mtmt) cc_final: 0.7287 (mttm) REVERT: J 103 LYS cc_start: 0.7941 (mtmt) cc_final: 0.7247 (mmtt) REVERT: J 110 GLN cc_start: 0.7428 (mt0) cc_final: 0.7137 (mt0) REVERT: K 1 MET cc_start: 0.7206 (ptm) cc_final: 0.6768 (ptt) REVERT: K 42 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6578 (tm-30) REVERT: K 66 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7926 (mp0) REVERT: K 88 ARG cc_start: 0.7223 (mtm110) cc_final: 0.6802 (mmt180) REVERT: K 103 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7149 (mmtt) REVERT: K 110 GLN cc_start: 0.7572 (tt0) cc_final: 0.7344 (tt0) REVERT: L 1 MET cc_start: 0.6798 (ptm) cc_final: 0.6399 (ptm) REVERT: L 42 GLU cc_start: 0.7656 (mt-10) cc_final: 0.6783 (pp20) REVERT: L 52 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.5806 (mtmm) REVERT: L 57 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7620 (mppt) REVERT: L 112 LYS cc_start: 0.8506 (mppt) cc_final: 0.7573 (mtmt) REVERT: N 1 MET cc_start: 0.5945 (ptt) cc_final: 0.5652 (ptt) REVERT: N 76 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8207 (tmtt) REVERT: N 81 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: O 1 MET cc_start: 0.6903 (ttp) cc_final: 0.5874 (ptp) REVERT: O 68 LEU cc_start: 0.8385 (mt) cc_final: 0.8070 (mm) REVERT: O 96 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6891 (tm-30) REVERT: O 138 ARG cc_start: 0.7540 (ttm-80) cc_final: 0.6644 (ttm-80) REVERT: P 57 LYS cc_start: 0.7527 (mtmt) cc_final: 0.7227 (mttm) REVERT: Q 38 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7594 (mm-30) REVERT: Q 39 LYS cc_start: 0.8678 (ttmm) cc_final: 0.8168 (mtpt) REVERT: Q 53 LYS cc_start: 0.8051 (mttp) cc_final: 0.7646 (mttt) REVERT: Q 57 LYS cc_start: 0.7799 (mtmt) cc_final: 0.7466 (mttt) REVERT: Q 81 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: Q 98 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7487 (mp) REVERT: Q 125 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6814 (mt-10) REVERT: Q 139 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.6886 (tm-30) REVERT: R 6 LYS cc_start: 0.7919 (mmtp) cc_final: 0.7587 (mttp) REVERT: R 13 ARG cc_start: 0.7464 (ttm-80) cc_final: 0.7214 (mtp85) REVERT: R 75 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7941 (mt-10) REVERT: R 129 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6604 (tm-30) REVERT: S 1 MET cc_start: 0.6729 (ptm) cc_final: 0.6414 (ptt) REVERT: S 96 GLU cc_start: 0.7384 (tm-30) cc_final: 0.7033 (tm-30) REVERT: T 6 LYS cc_start: 0.7831 (mmtp) cc_final: 0.7317 (mttp) REVERT: T 53 LYS cc_start: 0.7921 (mttp) cc_final: 0.7599 (mttt) REVERT: T 57 LYS cc_start: 0.8107 (mtmt) cc_final: 0.7538 (mmtt) REVERT: T 73 GLN cc_start: 0.7494 (mm-40) cc_final: 0.6896 (tp40) REVERT: T 74 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7043 (mp) REVERT: T 75 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7350 (mm-30) REVERT: T 96 GLU cc_start: 0.7342 (tm-30) cc_final: 0.7025 (tt0) REVERT: T 97 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7908 (tt0) REVERT: T 103 ASP cc_start: 0.8120 (m-30) cc_final: 0.7744 (m-30) REVERT: U 10 GLN cc_start: 0.7921 (mm110) cc_final: 0.7649 (mm110) REVERT: U 33 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7675 (ttpp) REVERT: U 45 TYR cc_start: 0.8081 (t80) cc_final: 0.7283 (t80) REVERT: U 68 LEU cc_start: 0.8739 (mt) cc_final: 0.8470 (mm) REVERT: U 91 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7548 (tt) REVERT: U 113 ASP cc_start: 0.8397 (t70) cc_final: 0.7972 (t70) REVERT: V 13 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.7281 (ttm110) REVERT: V 33 LYS cc_start: 0.8366 (tttt) cc_final: 0.7680 (ttpp) REVERT: V 76 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7583 (tmmt) REVERT: V 81 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7566 (mt-10) REVERT: V 129 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6246 (tm-30) REVERT: W 6 LYS cc_start: 0.7707 (mmtp) cc_final: 0.7318 (mtmm) REVERT: W 46 LYS cc_start: 0.7520 (pttt) cc_final: 0.7160 (mmmt) REVERT: W 52 MET cc_start: 0.7486 (ttm) cc_final: 0.6994 (ttt) REVERT: W 88 ASP cc_start: 0.8086 (m-30) cc_final: 0.7815 (m-30) REVERT: W 100 LEU cc_start: 0.8301 (tt) cc_final: 0.8099 (tp) REVERT: W 135 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7889 (mt-10) REVERT: W 151 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: X 1 MET cc_start: 0.6492 (ttp) cc_final: 0.6226 (ptt) REVERT: X 2 LYS cc_start: 0.8234 (tptt) cc_final: 0.7420 (tmtt) REVERT: X 6 LYS cc_start: 0.7752 (mmtp) cc_final: 0.7076 (mmpt) REVERT: X 51 ASP cc_start: 0.7507 (m-30) cc_final: 0.7283 (m-30) REVERT: X 66 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8122 (mt-10) outliers start: 68 outliers final: 27 residues processed: 844 average time/residue: 1.6045 time to fit residues: 1566.7553 Evaluate side-chains 847 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 793 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 39 GLU 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 68 VAL Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 57 LYS Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 17 CYS Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 139 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain T residue 97 GLN Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 155 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 76 LYS Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 119 LEU Chi-restraints excluded: chain W residue 151 GLN Chi-restraints excluded: chain X residue 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: 0.1980 chunk 153 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 296 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 351 optimal weight: 0.0170 chunk 228 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 263 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 110 GLN B 110 GLN B 115 GLN B 149 ASN C 60 GLN E 70 ASN E 115 GLN F 115 GLN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 ASN J 149 ASN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN L 60 GLN ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 ASN N 70 ASN N 151 GLN O 10 GLN O 148 ASN Q 148 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 HIS ** W 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 148 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.143905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.131714 restraints weight = 29368.751| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.22 r_work: 0.3370 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.638 31374 Z= 0.129 Angle : 0.524 20.645 42360 Z= 0.248 Chirality : 0.034 0.183 4656 Planarity : 0.003 0.034 5484 Dihedral : 5.305 76.285 4116 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.65 % Allowed : 17.33 % Favored : 81.02 % 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: 4.20 (0.13), residues: 3696 helix: 3.29 (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 0.006 0.001 TRP S 133 HIS 0.009 0.001 HIS T 42 PHE 0.028 0.002 PHE U 26 TYR 0.024 0.002 TYR K 133 ARG 0.007 0.000 ARG C 74 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 2652) hydrogen bonds : angle 3.53926 ( 7956) covalent geometry : bond 0.00280 (31368) covalent geometry : angle 0.52431 (42360) Misc. bond : bond 0.44244 ( 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 881 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 826 time to evaluate : 3.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7181 (mm-30) REVERT: A 115 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.7204 (tm-30) REVERT: A 126 ASP cc_start: 0.7887 (m-30) cc_final: 0.7657 (t0) REVERT: B 43 ARG cc_start: 0.7661 (tpt170) cc_final: 0.7342 (tpt170) REVERT: B 112 LYS cc_start: 0.8231 (mptt) cc_final: 0.7550 (mtmt) REVERT: C 22 MET cc_start: 0.7672 (ttp) cc_final: 0.7316 (ttm) REVERT: C 50 ASP cc_start: 0.7358 (m-30) cc_final: 0.6656 (t0) REVERT: C 52 LYS cc_start: 0.6834 (tptt) cc_final: 0.5921 (mtpt) REVERT: C 66 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7571 (mp0) REVERT: C 75 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7808 (mt-10) REVERT: D 1 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7126 (ptt) REVERT: D 5 LYS cc_start: 0.7296 (mppt) cc_final: 0.6990 (mptp) REVERT: D 42 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7143 (mt-10) REVERT: D 52 LYS cc_start: 0.7424 (tptp) cc_final: 0.6046 (mtmm) REVERT: D 66 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8151 (mp0) REVERT: D 88 ARG cc_start: 0.7981 (mtm110) cc_final: 0.7395 (mmt-90) REVERT: D 117 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7715 (ttt90) REVERT: D 118 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6430 (mt-10) REVERT: D 125 ASP cc_start: 0.8090 (t70) cc_final: 0.7873 (t0) REVERT: E 122 VAL cc_start: 0.8304 (p) cc_final: 0.8036 (m) REVERT: E 136 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7867 (mp0) REVERT: F 22 MET cc_start: 0.7875 (ttp) cc_final: 0.7375 (ttp) REVERT: F 52 LYS cc_start: 0.7049 (tptt) cc_final: 0.6717 (tptt) REVERT: F 96 LYS cc_start: 0.7962 (ttpp) cc_final: 0.7676 (tttm) REVERT: F 103 LYS cc_start: 0.7886 (mtmt) cc_final: 0.7429 (ttmt) REVERT: F 115 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7945 (tm130) REVERT: F 118 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6269 (mt-10) REVERT: G 13 ARG cc_start: 0.7629 (mtm110) cc_final: 0.7373 (mtm-85) REVERT: G 50 ASP cc_start: 0.6949 (m-30) cc_final: 0.5976 (t0) REVERT: G 66 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7857 (mp0) REVERT: G 96 LYS cc_start: 0.7918 (ttpp) cc_final: 0.7238 (tmtm) REVERT: G 100 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7418 (m-30) REVERT: G 112 LYS cc_start: 0.8248 (mmtm) cc_final: 0.7852 (mmmt) REVERT: G 115 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: H 57 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7807 (mtpt) REVERT: H 96 LYS cc_start: 0.8185 (tttm) cc_final: 0.7804 (ttpt) REVERT: H 103 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7789 (tttm) REVERT: H 125 ASP cc_start: 0.8154 (t0) cc_final: 0.7838 (t70) REVERT: I 1 MET cc_start: 0.6835 (ptm) cc_final: 0.6494 (ptm) REVERT: I 9 ASP cc_start: 0.8053 (m-30) cc_final: 0.7715 (m-30) REVERT: I 42 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7022 (mt-10) REVERT: I 50 ASP cc_start: 0.6412 (m-30) cc_final: 0.5693 (t70) REVERT: I 75 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7482 (mm-30) REVERT: I 112 LYS cc_start: 0.8279 (mmtm) cc_final: 0.7604 (mtpm) REVERT: J 50 ASP cc_start: 0.7200 (m-30) cc_final: 0.6893 (m-30) REVERT: J 57 LYS cc_start: 0.7730 (mtmt) cc_final: 0.7445 (mttm) REVERT: J 103 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7395 (mmtt) REVERT: J 110 GLN cc_start: 0.7560 (mt0) cc_final: 0.7297 (mt0) REVERT: K 1 MET cc_start: 0.7256 (ptm) cc_final: 0.6783 (ptt) REVERT: K 42 GLU cc_start: 0.7588 (mt-10) cc_final: 0.6666 (tm-30) REVERT: K 66 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8032 (mp0) REVERT: K 88 ARG cc_start: 0.7322 (mtm110) cc_final: 0.6934 (mmt180) REVERT: K 103 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7294 (mmtt) REVERT: K 110 GLN cc_start: 0.7651 (tt0) cc_final: 0.7430 (tt0) REVERT: L 1 MET cc_start: 0.6858 (ptm) cc_final: 0.6340 (ptt) REVERT: L 42 GLU cc_start: 0.7685 (mt-10) cc_final: 0.6870 (pp20) REVERT: L 52 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.5901 (mtmm) REVERT: L 57 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7904 (mppt) REVERT: L 66 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7567 (mp0) REVERT: L 112 LYS cc_start: 0.8584 (mppt) cc_final: 0.7713 (mtmt) REVERT: N 1 MET cc_start: 0.5992 (ptt) cc_final: 0.5747 (ptt) REVERT: N 76 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8251 (tmtt) REVERT: O 1 MET cc_start: 0.6913 (ttp) cc_final: 0.5917 (ptp) REVERT: O 13 ARG cc_start: 0.7166 (mtm-85) cc_final: 0.6845 (mtm-85) REVERT: O 50 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6885 (pp20) REVERT: O 68 LEU cc_start: 0.8425 (mt) cc_final: 0.8130 (mm) REVERT: O 96 GLU cc_start: 0.7456 (tm-30) cc_final: 0.7015 (tm-30) REVERT: O 138 ARG cc_start: 0.7590 (ttm-80) cc_final: 0.6754 (ttm-80) REVERT: P 57 LYS cc_start: 0.7649 (mtmt) cc_final: 0.7365 (mttm) REVERT: Q 38 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7668 (mm-30) REVERT: Q 39 LYS cc_start: 0.8712 (ttmm) cc_final: 0.8225 (mtpt) REVERT: Q 53 LYS cc_start: 0.8071 (mttp) cc_final: 0.7691 (mttp) REVERT: Q 57 LYS cc_start: 0.7856 (mtmt) cc_final: 0.7570 (mttt) REVERT: Q 81 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: Q 125 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6950 (mt-10) REVERT: Q 139 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.6927 (tm-30) REVERT: R 6 LYS cc_start: 0.8030 (mmtp) cc_final: 0.7726 (mttp) REVERT: R 13 ARG cc_start: 0.7569 (ttm-80) cc_final: 0.7354 (mtp85) REVERT: R 75 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7984 (mt-10) REVERT: R 129 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: S 1 MET cc_start: 0.6677 (ptm) cc_final: 0.6430 (ptt) REVERT: S 57 LYS cc_start: 0.8123 (mttm) cc_final: 0.7868 (mttp) REVERT: S 96 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7090 (tm-30) REVERT: T 6 LYS cc_start: 0.7960 (mmtp) cc_final: 0.7433 (mttp) REVERT: T 53 LYS cc_start: 0.8004 (mttp) cc_final: 0.7678 (mtmt) REVERT: T 57 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7674 (mmtt) REVERT: T 73 GLN cc_start: 0.7525 (mm-40) cc_final: 0.6948 (tp40) REVERT: T 74 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7072 (mp) REVERT: T 75 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7351 (mm-30) REVERT: T 96 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7218 (mt-10) REVERT: T 97 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: T 103 ASP cc_start: 0.8179 (m-30) cc_final: 0.7846 (m-30) REVERT: U 10 GLN cc_start: 0.8017 (mm110) cc_final: 0.7776 (mm110) REVERT: U 33 LYS cc_start: 0.8285 (ttpp) cc_final: 0.7639 (ttpp) REVERT: U 45 TYR cc_start: 0.8105 (t80) cc_final: 0.7339 (t80) REVERT: U 68 LEU cc_start: 0.8770 (mt) cc_final: 0.8523 (mm) REVERT: U 91 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7596 (tt) REVERT: U 113 ASP cc_start: 0.8388 (t70) cc_final: 0.8022 (t70) REVERT: V 33 LYS cc_start: 0.8426 (tttt) cc_final: 0.7780 (ttpp) REVERT: V 81 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7590 (mt-10) REVERT: V 129 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6423 (tm-30) REVERT: W 6 LYS cc_start: 0.7770 (mmtp) cc_final: 0.7371 (mtmm) REVERT: W 46 LYS cc_start: 0.7545 (pttt) cc_final: 0.7255 (mmmt) REVERT: W 88 ASP cc_start: 0.8201 (m-30) cc_final: 0.7921 (m-30) REVERT: W 100 LEU cc_start: 0.8355 (tt) cc_final: 0.8128 (tp) REVERT: W 135 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7969 (mt-10) REVERT: X 1 MET cc_start: 0.6505 (ttp) cc_final: 0.6225 (ptt) REVERT: X 66 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8159 (mt-10) outliers start: 55 outliers final: 20 residues processed: 851 average time/residue: 1.5582 time to fit residues: 1538.5897 Evaluate side-chains 839 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 795 time to evaluate : 3.489 ------------------------------------------------------------------------------- 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 117 ARG 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 57 LYS Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 17 CYS Chi-restraints excluded: chain N residue 76 LYS 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 76 LYS Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 139 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 96 GLU Chi-restraints excluded: chain R residue 129 GLU Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 75 GLU Chi-restraints excluded: chain T residue 97 GLN 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 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: 7.9990 chunk 204 optimal weight: 4.9990 chunk 305 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 200 optimal weight: 0.0870 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 296 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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 70 ASN E 115 GLN F 115 GLN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 GLN I 131 HIS J 89 ASN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN L 60 GLN L 115 GLN M 148 ASN N 70 ASN N 151 GLN O 10 GLN O 148 ASN P 73 GLN P 97 GLN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 148 ASN T 42 HIS ** W 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.146129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.134021 restraints weight = 29221.007| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.18 r_work: 0.3399 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.609 31374 Z= 0.123 Angle : 0.512 17.641 42360 Z= 0.248 Chirality : 0.034 0.197 4656 Planarity : 0.003 0.032 5484 Dihedral : 5.199 73.540 4116 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.74 % Allowed : 17.69 % Favored : 80.57 % 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: 4.27 (0.13), residues: 3696 helix: 3.33 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.58 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP S 133 HIS 0.009 0.001 HIS T 42 PHE 0.027 0.002 PHE U 26 TYR 0.024 0.001 TYR K 133 ARG 0.010 0.000 ARG V 13 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 2652) hydrogen bonds : angle 3.50970 ( 7956) covalent geometry : bond 0.00263 (31368) covalent geometry : angle 0.51233 (42360) Misc. bond : bond 0.40099 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31423.70 seconds wall clock time: 539 minutes 4.49 seconds (32344.49 seconds total)