Starting phenix.real_space_refine on Wed Jul 30 19:49:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bze_7314/07_2025/6bze_7314.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bze_7314/07_2025/6bze_7314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6bze_7314/07_2025/6bze_7314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bze_7314/07_2025/6bze_7314.map" model { file = "/net/cci-nas-00/data/ceres_data/6bze_7314/07_2025/6bze_7314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bze_7314/07_2025/6bze_7314.cif" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.006 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7072 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 4408 2.51 5 N 1296 2.21 5 O 1352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7072 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "B" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "C" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "D" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "E" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "F" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "G" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "H" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Time building chain proxies: 6.02, per 1000 atoms: 0.85 Number of scatterers: 7072 At special positions: 0 Unit cell: (105.7, 105.7, 87.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 1352 8.00 N 1296 7.00 C 4408 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=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 880.5 milliseconds 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 74.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.778A pdb=" N VAL A 16 " --> pdb=" O ASP A 12 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS A 18 " --> pdb=" O THR A 14 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 38 through 44 removed outlier: 4.213A pdb=" N ARG A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 58 removed outlier: 3.834A pdb=" N GLU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 73 removed outlier: 3.709A pdb=" N LEU A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.521A pdb=" N VAL A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 115 removed outlier: 3.568A pdb=" N LEU A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 25 removed outlier: 3.691A pdb=" N VAL B 16 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 18 " --> pdb=" O THR B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 38 through 44 removed outlier: 4.184A pdb=" N ARG B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 44 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 58 removed outlier: 3.922A pdb=" N GLU B 53 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 73 removed outlier: 3.927A pdb=" N LEU B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 Processing helix chain 'B' and resid 95 through 115 removed outlier: 3.808A pdb=" N LEU B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 25 removed outlier: 3.634A pdb=" N VAL C 16 " --> pdb=" O ASP C 12 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS C 18 " --> pdb=" O THR C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'C' and resid 38 through 44 removed outlier: 4.216A pdb=" N ARG C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 44 " --> pdb=" O HIS C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 58 removed outlier: 3.844A pdb=" N GLU C 53 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 73 removed outlier: 3.891A pdb=" N LEU C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 removed outlier: 3.502A pdb=" N VAL C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 115 removed outlier: 3.649A pdb=" N LEU C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 25 removed outlier: 3.810A pdb=" N VAL D 16 " --> pdb=" O ASP D 12 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS D 18 " --> pdb=" O THR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 38 Processing helix chain 'D' and resid 38 through 44 removed outlier: 4.478A pdb=" N ARG D 42 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS D 44 " --> pdb=" O HIS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 58 removed outlier: 3.530A pdb=" N GLU D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 75 removed outlier: 4.003A pdb=" N LEU D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU D 74 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN D 75 " --> pdb=" O TYR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 Processing helix chain 'D' and resid 95 through 115 removed outlier: 3.684A pdb=" N LEU D 114 " --> pdb=" O LYS D 110 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 25 removed outlier: 3.736A pdb=" N VAL E 16 " --> pdb=" O ASP E 12 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS E 18 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP E 19 " --> pdb=" O GLU E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 38 Processing helix chain 'E' and resid 38 through 44 removed outlier: 4.343A pdb=" N ARG E 42 " --> pdb=" O PHE E 38 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS E 44 " --> pdb=" O HIS E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 58 removed outlier: 3.862A pdb=" N GLU E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG E 58 " --> pdb=" O GLU E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 72 removed outlier: 4.102A pdb=" N LEU E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 87 Processing helix chain 'E' and resid 95 through 115 removed outlier: 3.658A pdb=" N LEU E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 25 removed outlier: 3.650A pdb=" N VAL F 16 " --> pdb=" O ASP F 12 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS F 18 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP F 19 " --> pdb=" O GLU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 38 Processing helix chain 'F' and resid 38 through 44 removed outlier: 4.390A pdb=" N ARG F 42 " --> pdb=" O PHE F 38 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS F 44 " --> pdb=" O HIS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 58 removed outlier: 3.881A pdb=" N GLU F 53 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG F 58 " --> pdb=" O GLU F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 72 removed outlier: 4.089A pdb=" N LEU F 72 " --> pdb=" O LEU F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 87 Processing helix chain 'F' and resid 95 through 115 removed outlier: 3.702A pdb=" N LEU F 114 " --> pdb=" O LYS F 110 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 25 removed outlier: 3.914A pdb=" N VAL G 16 " --> pdb=" O ASP G 12 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP G 19 " --> pdb=" O GLU G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 38 Processing helix chain 'G' and resid 38 through 44 removed outlier: 4.369A pdb=" N ARG G 42 " --> pdb=" O PHE G 38 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS G 44 " --> pdb=" O HIS G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 58 removed outlier: 3.820A pdb=" N GLU G 53 " --> pdb=" O ARG G 49 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG G 58 " --> pdb=" O GLU G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 72 removed outlier: 4.103A pdb=" N LEU G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 87 Processing helix chain 'G' and resid 95 through 115 removed outlier: 3.580A pdb=" N LEU G 114 " --> pdb=" O LYS G 110 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 25 removed outlier: 3.699A pdb=" N VAL H 16 " --> pdb=" O ASP H 12 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS H 18 " --> pdb=" O THR H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 36 Processing helix chain 'H' and resid 38 through 44 removed outlier: 4.412A pdb=" N ARG H 42 " --> pdb=" O PHE H 38 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS H 44 " --> pdb=" O HIS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 58 removed outlier: 3.790A pdb=" N GLU H 53 " --> pdb=" O ARG H 49 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG H 58 " --> pdb=" O GLU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 72 removed outlier: 3.856A pdb=" N LEU H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 87 Processing helix chain 'H' and resid 95 through 115 removed outlier: 3.778A pdb=" N LEU H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 963 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: 1.85 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1247 1.28 - 1.41: 1457 1.41 - 1.54: 4361 1.54 - 1.68: 47 1.68 - 1.81: 16 Bond restraints: 7128 Sorted by residual: bond pdb=" C GLU B 74 " pdb=" O GLU B 74 " ideal model delta sigma weight residual 1.235 1.145 0.091 1.26e-02 6.30e+03 5.18e+01 bond pdb=" C GLU D 74 " pdb=" O GLU D 74 " ideal model delta sigma weight residual 1.235 1.151 0.084 1.26e-02 6.30e+03 4.49e+01 bond pdb=" C GLU A 74 " pdb=" O GLU A 74 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.26e-02 6.30e+03 3.46e+01 bond pdb=" C GLU C 74 " pdb=" O GLU C 74 " ideal model delta sigma weight residual 1.235 1.164 0.071 1.26e-02 6.30e+03 3.19e+01 bond pdb=" ND1 HIS G 40 " pdb=" CE1 HIS G 40 " ideal model delta sigma weight residual 1.321 1.359 -0.038 1.00e-02 1.00e+04 1.46e+01 ... (remaining 7123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 8406 2.07 - 4.15: 966 4.15 - 6.22: 110 6.22 - 8.30: 24 8.30 - 10.37: 14 Bond angle restraints: 9520 Sorted by residual: angle pdb=" N THR F 100 " pdb=" CA THR F 100 " pdb=" C THR F 100 " ideal model delta sigma weight residual 111.36 101.89 9.47 1.09e+00 8.42e-01 7.55e+01 angle pdb=" N THR H 100 " pdb=" CA THR H 100 " pdb=" C THR H 100 " ideal model delta sigma weight residual 111.82 101.98 9.84 1.16e+00 7.43e-01 7.20e+01 angle pdb=" N THR G 100 " pdb=" CA THR G 100 " pdb=" C THR G 100 " ideal model delta sigma weight residual 111.36 102.22 9.14 1.09e+00 8.42e-01 7.03e+01 angle pdb=" N THR A 100 " pdb=" CA THR A 100 " pdb=" C THR A 100 " ideal model delta sigma weight residual 111.36 102.30 9.06 1.09e+00 8.42e-01 6.91e+01 angle pdb=" N THR C 100 " pdb=" CA THR C 100 " pdb=" C THR C 100 " ideal model delta sigma weight residual 111.36 102.68 8.68 1.09e+00 8.42e-01 6.35e+01 ... (remaining 9515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 3971 17.56 - 35.13: 430 35.13 - 52.69: 124 52.69 - 70.25: 42 70.25 - 87.81: 17 Dihedral angle restraints: 4584 sinusoidal: 2064 harmonic: 2520 Sorted by residual: dihedral pdb=" CA SER A 56 " pdb=" C SER A 56 " pdb=" N CYS A 57 " pdb=" CA CYS A 57 " ideal model delta harmonic sigma weight residual -180.00 -162.05 -17.95 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" C PHE B 38 " pdb=" N PHE B 38 " pdb=" CA PHE B 38 " pdb=" CB PHE B 38 " ideal model delta harmonic sigma weight residual -122.60 -131.30 8.70 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" CG ARG D 49 " pdb=" CD ARG D 49 " pdb=" NE ARG D 49 " pdb=" CZ ARG D 49 " ideal model delta sinusoidal sigma weight residual 90.00 41.95 48.05 2 1.50e+01 4.44e-03 1.18e+01 ... (remaining 4581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 756 0.079 - 0.157: 286 0.157 - 0.236: 54 0.236 - 0.315: 5 0.315 - 0.394: 3 Chirality restraints: 1104 Sorted by residual: chirality pdb=" CA PHE B 38 " pdb=" N PHE B 38 " pdb=" C PHE B 38 " pdb=" CB PHE B 38 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CA PHE D 38 " pdb=" N PHE D 38 " pdb=" C PHE D 38 " pdb=" CB PHE D 38 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA PHE A 38 " pdb=" N PHE A 38 " pdb=" C PHE A 38 " pdb=" CB PHE A 38 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 1101 not shown) Planarity restraints: 1216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 94 " 0.036 2.00e-02 2.50e+03 2.58e-02 1.17e+01 pdb=" CG PHE F 94 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE F 94 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE F 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE F 94 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE F 94 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 94 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 92 " 0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C GLN B 92 " -0.058 2.00e-02 2.50e+03 pdb=" O GLN B 92 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN B 93 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS F 37 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.49e+00 pdb=" C HIS F 37 " -0.053 2.00e-02 2.50e+03 pdb=" O HIS F 37 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE F 38 " 0.018 2.00e-02 2.50e+03 ... (remaining 1213 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 87 2.30 - 2.95: 4208 2.95 - 3.60: 11653 3.60 - 4.25: 17484 4.25 - 4.90: 26284 Nonbonded interactions: 59716 Sorted by model distance: nonbonded pdb=" OG SER D 48 " pdb=" NE2 HIS H 37 " model vdw 1.648 3.120 nonbonded pdb=" OD2 ASP A 70 " pdb=" NH2 ARG D 49 " model vdw 1.789 3.120 nonbonded pdb=" OG SER A 48 " pdb=" NE2 HIS E 37 " model vdw 1.793 3.120 nonbonded pdb=" O ARG F 49 " pdb=" NH1 ARG F 49 " model vdw 1.879 3.120 nonbonded pdb=" O ARG C 49 " pdb=" NH1 ARG C 49 " model vdw 1.883 3.120 ... (remaining 59711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 group one per residue 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: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.340 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4815 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 : 0.009 0.091 7128 Z= 0.561 Angle : 1.421 10.371 9520 Z= 1.027 Chirality : 0.082 0.394 1104 Planarity : 0.005 0.033 1216 Dihedral : 17.335 87.814 2920 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 79.81 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.22 % Favored : 86.42 % Rotamer: Outliers : 9.00 % Allowed : 19.62 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.34 (0.22), residues: 832 helix: -4.12 (0.14), residues: 528 sheet: None (None), residues: 0 loop : -1.99 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS H 37 PHE 0.055 0.006 PHE F 94 TYR 0.006 0.001 TYR H 71 ARG 0.005 0.001 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.42477 ( 323) hydrogen bonds : angle 9.43892 ( 963) covalent geometry : bond 0.00859 ( 7128) covalent geometry : angle 1.42118 ( 9520) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 426 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7730 (tm-30) REVERT: A 24 LEU cc_start: 0.7077 (tp) cc_final: 0.6803 (tt) REVERT: A 28 LEU cc_start: 0.4443 (tp) cc_final: 0.3725 (tp) REVERT: A 70 ASP cc_start: 0.7043 (t70) cc_final: 0.6809 (t70) REVERT: A 84 GLU cc_start: 0.7343 (tp30) cc_final: 0.7140 (pp20) REVERT: B 11 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8899 (tm-30) REVERT: B 12 ASP cc_start: 0.8451 (m-30) cc_final: 0.7930 (p0) REVERT: B 23 ASN cc_start: 0.6061 (m110) cc_final: 0.5856 (m-40) REVERT: B 37 HIS cc_start: 0.3331 (OUTLIER) cc_final: 0.2945 (m-70) REVERT: B 55 ILE cc_start: 0.7265 (mt) cc_final: 0.6801 (tt) REVERT: B 70 ASP cc_start: 0.7059 (t70) cc_final: 0.6615 (t0) REVERT: B 74 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7983 (mt-10) REVERT: B 84 GLU cc_start: 0.8286 (tp30) cc_final: 0.7993 (tp30) REVERT: B 107 ARG cc_start: 0.8124 (tpp-160) cc_final: 0.7894 (tpp80) REVERT: B 113 HIS cc_start: 0.8341 (t-170) cc_final: 0.8029 (t70) REVERT: C 11 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7568 (tm-30) REVERT: C 12 ASP cc_start: 0.8377 (m-30) cc_final: 0.7728 (p0) REVERT: C 16 VAL cc_start: 0.6605 (OUTLIER) cc_final: 0.6369 (p) REVERT: C 30 GLU cc_start: 0.4359 (mm-30) cc_final: 0.3486 (mt-10) REVERT: C 74 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7277 (tm-30) REVERT: D 30 GLU cc_start: 0.5060 (mm-30) cc_final: 0.4691 (mm-30) REVERT: D 35 GLU cc_start: 0.0530 (pt0) cc_final: 0.0044 (pt0) REVERT: D 70 ASP cc_start: 0.7040 (t70) cc_final: 0.6499 (t0) REVERT: D 73 GLN cc_start: 0.6688 (mt0) cc_final: 0.5842 (mt0) REVERT: D 74 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8160 (mt-10) REVERT: D 80 ASP cc_start: 0.7408 (m-30) cc_final: 0.7079 (m-30) REVERT: D 95 LEU cc_start: 0.8740 (tp) cc_final: 0.8530 (tp) REVERT: E 11 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8392 (tm-30) REVERT: E 16 VAL cc_start: 0.5912 (OUTLIER) cc_final: 0.5416 (p) REVERT: E 32 ILE cc_start: 0.4377 (mm) cc_final: 0.2905 (mm) REVERT: E 48 SER cc_start: 0.4230 (t) cc_final: 0.3264 (p) REVERT: E 49 ARG cc_start: 0.6146 (tpt90) cc_final: 0.5866 (tpt90) REVERT: E 80 ASP cc_start: 0.7311 (m-30) cc_final: 0.6582 (m-30) REVERT: E 84 GLU cc_start: 0.7833 (tp30) cc_final: 0.7390 (tm-30) REVERT: F 18 LYS cc_start: 0.7595 (mtmp) cc_final: 0.7208 (mtpp) REVERT: F 25 ARG cc_start: 0.5008 (OUTLIER) cc_final: 0.4575 (tmt170) REVERT: F 62 ARG cc_start: 0.7242 (mmt90) cc_final: 0.6865 (mmm-85) REVERT: F 69 LEU cc_start: 0.7620 (mp) cc_final: 0.7392 (mp) REVERT: F 104 LEU cc_start: 0.9153 (mt) cc_final: 0.8878 (mt) REVERT: G 16 VAL cc_start: 0.3522 (OUTLIER) cc_final: 0.3317 (p) REVERT: G 32 ILE cc_start: 0.2041 (mm) cc_final: 0.1805 (mm) REVERT: G 55 ILE cc_start: 0.6531 (mt) cc_final: 0.5707 (mt) REVERT: H 26 VAL cc_start: 0.8649 (t) cc_final: 0.8410 (p) REVERT: H 63 LYS cc_start: 0.6063 (mmtt) cc_final: 0.5595 (mtmm) REVERT: H 95 LEU cc_start: 0.8964 (tp) cc_final: 0.8630 (pt) REVERT: H 96 ILE cc_start: 0.6795 (mm) cc_final: 0.6407 (mm) outliers start: 72 outliers final: 18 residues processed: 470 average time/residue: 0.3443 time to fit residues: 195.3911 Evaluate side-chains 317 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 294 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 49 ARG Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 49 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 9.9990 chunk 60 optimal weight: 30.0000 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 40 optimal weight: 30.0000 chunk 32 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 97 GLN B 92 GLN B 97 GLN C 92 GLN C 97 GLN D 37 HIS ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN E 40 HIS ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN E 113 HIS F 23 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN F 113 HIS ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 113 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.133251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.119873 restraints weight = 21481.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.122435 restraints weight = 14551.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.124264 restraints weight = 10590.169| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.6922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7128 Z= 0.251 Angle : 0.990 9.302 9520 Z= 0.531 Chirality : 0.053 0.304 1104 Planarity : 0.006 0.062 1216 Dihedral : 9.442 84.249 999 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 27.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 8.75 % Allowed : 25.88 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.26), residues: 832 helix: -1.95 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -2.80 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS D 37 PHE 0.029 0.004 PHE H 94 TYR 0.015 0.002 TYR B 71 ARG 0.009 0.001 ARG G 87 Details of bonding type rmsd hydrogen bonds : bond 0.07992 ( 323) hydrogen bonds : angle 6.76187 ( 963) covalent geometry : bond 0.00521 ( 7128) covalent geometry : angle 0.99012 ( 9520) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 389 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9289 (mmmm) cc_final: 0.8933 (mmtp) REVERT: A 24 LEU cc_start: 0.8638 (tp) cc_final: 0.8263 (tt) REVERT: A 37 HIS cc_start: 0.6537 (OUTLIER) cc_final: 0.5865 (m90) REVERT: A 63 LYS cc_start: 0.8360 (mmtt) cc_final: 0.7918 (mtmt) REVERT: A 101 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7152 (t0) REVERT: B 49 ARG cc_start: 0.7817 (tpt90) cc_final: 0.7447 (tmt-80) REVERT: B 67 LYS cc_start: 0.9239 (mmmm) cc_final: 0.8995 (mtmt) REVERT: B 75 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7053 (m-40) REVERT: B 101 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7075 (t0) REVERT: C 39 ASP cc_start: 0.7963 (m-30) cc_final: 0.7650 (m-30) REVERT: C 51 ASP cc_start: 0.6962 (m-30) cc_final: 0.6199 (m-30) REVERT: D 28 LEU cc_start: 0.8621 (tp) cc_final: 0.8370 (tp) REVERT: D 37 HIS cc_start: 0.3140 (OUTLIER) cc_final: 0.2772 (t-170) REVERT: D 62 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6217 (mmt90) REVERT: D 80 ASP cc_start: 0.8845 (m-30) cc_final: 0.8544 (m-30) REVERT: D 90 LYS cc_start: 0.7244 (ttmt) cc_final: 0.6787 (ttmt) REVERT: E 23 ASN cc_start: 0.8966 (m-40) cc_final: 0.8740 (m-40) REVERT: E 37 HIS cc_start: 0.5718 (OUTLIER) cc_final: 0.5241 (t70) REVERT: E 62 ARG cc_start: 0.8346 (mmt90) cc_final: 0.7775 (mmm-85) REVERT: E 70 ASP cc_start: 0.7514 (t70) cc_final: 0.7262 (t70) REVERT: E 90 LYS cc_start: 0.7073 (mttt) cc_final: 0.6854 (mttp) REVERT: F 25 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.6127 (tmt170) REVERT: F 39 ASP cc_start: 0.7378 (m-30) cc_final: 0.7015 (m-30) REVERT: F 63 LYS cc_start: 0.8383 (mmtt) cc_final: 0.7800 (mtmt) REVERT: F 70 ASP cc_start: 0.7938 (t0) cc_final: 0.7677 (t0) REVERT: F 79 LEU cc_start: 0.8206 (mt) cc_final: 0.7982 (mm) REVERT: F 90 LYS cc_start: 0.7511 (ttmt) cc_final: 0.7069 (ttmt) REVERT: G 16 VAL cc_start: 0.7912 (OUTLIER) cc_final: 0.7656 (p) REVERT: G 17 LYS cc_start: 0.8420 (mttp) cc_final: 0.8036 (mttm) REVERT: G 42 ARG cc_start: 0.7989 (ttt-90) cc_final: 0.7689 (ttt-90) REVERT: G 53 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7406 (tm-30) REVERT: G 63 LYS cc_start: 0.8073 (mmtt) cc_final: 0.6852 (mtmt) REVERT: G 73 GLN cc_start: 0.8547 (mt0) cc_final: 0.8128 (mt0) REVERT: G 81 THR cc_start: 0.9190 (p) cc_final: 0.8868 (m) REVERT: G 105 LYS cc_start: 0.8465 (mmmt) cc_final: 0.7812 (tptt) REVERT: H 15 GLU cc_start: 0.8309 (mp0) cc_final: 0.8078 (mp0) outliers start: 70 outliers final: 31 residues processed: 425 average time/residue: 0.2833 time to fit residues: 144.6804 Evaluate side-chains 314 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 274 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 29 CYS Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 111 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.0670 chunk 11 optimal weight: 10.0000 chunk 20 optimal weight: 30.0000 chunk 43 optimal weight: 8.9990 chunk 33 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 40 optimal weight: 40.0000 chunk 10 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS D 37 HIS D 92 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 GLN G 113 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.132813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.118691 restraints weight = 21751.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.121344 restraints weight = 14366.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.123294 restraints weight = 10393.205| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.8665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7128 Z= 0.190 Angle : 0.908 11.980 9520 Z= 0.474 Chirality : 0.051 0.300 1104 Planarity : 0.005 0.038 1216 Dihedral : 8.395 59.898 973 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 25.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 7.38 % Allowed : 29.12 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.28), residues: 832 helix: -0.97 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -2.61 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS F 37 PHE 0.017 0.003 PHE E 94 TYR 0.009 0.001 TYR B 27 ARG 0.011 0.001 ARG F 107 Details of bonding type rmsd hydrogen bonds : bond 0.05537 ( 323) hydrogen bonds : angle 5.95500 ( 963) covalent geometry : bond 0.00404 ( 7128) covalent geometry : angle 0.90812 ( 9520) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 334 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8980 (mmmm) cc_final: 0.8742 (mmtp) REVERT: A 73 GLN cc_start: 0.8070 (mt0) cc_final: 0.7580 (mt0) REVERT: A 101 ASP cc_start: 0.7239 (OUTLIER) cc_final: 0.6894 (t0) REVERT: A 105 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8473 (mmmt) REVERT: B 17 LYS cc_start: 0.9210 (mmmm) cc_final: 0.8641 (mmtp) REVERT: B 28 LEU cc_start: 0.8631 (tt) cc_final: 0.8383 (tp) REVERT: B 51 ASP cc_start: 0.5448 (m-30) cc_final: 0.4599 (m-30) REVERT: B 54 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8679 (tm-30) REVERT: B 70 ASP cc_start: 0.8017 (t70) cc_final: 0.6513 (t0) REVERT: B 73 GLN cc_start: 0.8044 (mt0) cc_final: 0.7738 (mt0) REVERT: B 75 ASN cc_start: 0.7654 (t0) cc_final: 0.7086 (m-40) REVERT: B 101 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.6955 (t0) REVERT: C 35 GLU cc_start: 0.7030 (pt0) cc_final: 0.6624 (pt0) REVERT: C 40 HIS cc_start: 0.8811 (OUTLIER) cc_final: 0.7538 (m-70) REVERT: C 42 ARG cc_start: 0.6403 (tpp-160) cc_final: 0.6172 (tpp-160) REVERT: D 18 LYS cc_start: 0.8513 (mtpp) cc_final: 0.8271 (mtpp) REVERT: D 62 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.6031 (mmt90) REVERT: D 90 LYS cc_start: 0.7377 (ttmt) cc_final: 0.7021 (ttmt) REVERT: E 58 ARG cc_start: 0.6316 (OUTLIER) cc_final: 0.4936 (ttt180) REVERT: E 64 ARG cc_start: 0.8086 (ptp90) cc_final: 0.7316 (ptt-90) REVERT: F 25 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.5916 (tmt170) REVERT: F 37 HIS cc_start: 0.6227 (t70) cc_final: 0.5459 (t-170) REVERT: F 39 ASP cc_start: 0.7610 (m-30) cc_final: 0.7331 (m-30) REVERT: F 53 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7892 (mt-10) REVERT: F 87 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6641 (mpt180) REVERT: G 40 HIS cc_start: 0.8828 (m170) cc_final: 0.8617 (m170) REVERT: G 53 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7518 (tm-30) REVERT: G 73 GLN cc_start: 0.8146 (mt0) cc_final: 0.7909 (mt0) REVERT: G 81 THR cc_start: 0.9120 (p) cc_final: 0.8755 (m) REVERT: G 84 GLU cc_start: 0.6794 (tp30) cc_final: 0.6088 (tp30) REVERT: G 99 ILE cc_start: 0.8309 (pt) cc_final: 0.8006 (pt) REVERT: G 105 LYS cc_start: 0.8547 (mmmt) cc_final: 0.8023 (tppt) REVERT: H 18 LYS cc_start: 0.8724 (mtmm) cc_final: 0.8334 (mmtt) REVERT: H 94 PHE cc_start: 0.6442 (t80) cc_final: 0.6168 (t80) outliers start: 59 outliers final: 30 residues processed: 368 average time/residue: 0.3047 time to fit residues: 134.7667 Evaluate side-chains 315 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 278 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 87 ARG Chi-restraints excluded: chain G residue 29 CYS Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 29 CYS Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 80 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 0.0060 chunk 3 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 40 optimal weight: 40.0000 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS D 37 HIS ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 ASN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS G 37 HIS G 113 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.137486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.123089 restraints weight = 21867.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.125834 restraints weight = 14558.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.127746 restraints weight = 10534.006| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.9588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7128 Z= 0.156 Angle : 0.864 12.098 9520 Z= 0.442 Chirality : 0.049 0.263 1104 Planarity : 0.005 0.044 1216 Dihedral : 7.983 60.293 966 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 8.62 % Allowed : 29.62 % Favored : 61.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.41 (0.28), residues: 832 helix: -0.83 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -3.38 (0.32), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS G 113 PHE 0.016 0.002 PHE E 38 TYR 0.008 0.001 TYR H 27 ARG 0.008 0.001 ARG C 107 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 323) hydrogen bonds : angle 5.40005 ( 963) covalent geometry : bond 0.00332 ( 7128) covalent geometry : angle 0.86402 ( 9520) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 344 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9126 (mmmm) cc_final: 0.8891 (mmtp) REVERT: A 105 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8426 (mmmt) REVERT: B 51 ASP cc_start: 0.5517 (m-30) cc_final: 0.4956 (m-30) REVERT: B 70 ASP cc_start: 0.7872 (t70) cc_final: 0.6677 (t0) REVERT: B 73 GLN cc_start: 0.8003 (mt0) cc_final: 0.7752 (mt0) REVERT: B 75 ASN cc_start: 0.7370 (t0) cc_final: 0.6745 (m-40) REVERT: B 101 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.6839 (t0) REVERT: C 18 LYS cc_start: 0.8471 (mtmm) cc_final: 0.8136 (mtmm) REVERT: C 35 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6933 (pt0) REVERT: C 40 HIS cc_start: 0.8814 (OUTLIER) cc_final: 0.7435 (m-70) REVERT: C 49 ARG cc_start: 0.8005 (tpt90) cc_final: 0.7668 (tpt90) REVERT: C 74 GLU cc_start: 0.7945 (mp0) cc_final: 0.7078 (mt-10) REVERT: C 105 LYS cc_start: 0.8513 (mmmt) cc_final: 0.7849 (mttt) REVERT: D 53 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7082 (tt0) REVERT: D 62 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6607 (mmt90) REVERT: D 105 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8341 (mmmt) REVERT: E 53 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8069 (mt-10) REVERT: E 58 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.4937 (ttt180) REVERT: E 64 ARG cc_start: 0.7881 (ptp90) cc_final: 0.7289 (ptp90) REVERT: E 105 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8507 (mmtt) REVERT: F 37 HIS cc_start: 0.6048 (t70) cc_final: 0.5522 (t-170) REVERT: F 39 ASP cc_start: 0.7725 (m-30) cc_final: 0.7198 (m-30) REVERT: F 49 ARG cc_start: 0.6208 (tpt90) cc_final: 0.5818 (tpt-90) REVERT: F 53 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7984 (mt-10) REVERT: F 87 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6905 (mpt180) REVERT: F 99 ILE cc_start: 0.8519 (pt) cc_final: 0.8256 (pt) REVERT: G 25 ARG cc_start: 0.1306 (tmt170) cc_final: 0.0817 (tmt170) REVERT: G 53 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7624 (tm-30) REVERT: G 73 GLN cc_start: 0.8398 (mt0) cc_final: 0.7992 (mt0) REVERT: G 81 THR cc_start: 0.9101 (p) cc_final: 0.8876 (m) REVERT: G 104 LEU cc_start: 0.8254 (mt) cc_final: 0.7384 (mt) REVERT: G 107 ARG cc_start: 0.7803 (tmm-80) cc_final: 0.7029 (tmm-80) REVERT: H 82 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8137 (mm) REVERT: H 111 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7799 (mt) outliers start: 69 outliers final: 34 residues processed: 374 average time/residue: 0.2917 time to fit residues: 131.4221 Evaluate side-chains 326 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 284 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 64 ARG Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 87 ARG Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 51 optimal weight: 0.3980 chunk 27 optimal weight: 8.9990 chunk 40 optimal weight: 40.0000 chunk 5 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS D 73 GLN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.138468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.124407 restraints weight = 21411.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.127146 restraints weight = 14205.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.129096 restraints weight = 10239.298| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 1.0189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7128 Z= 0.144 Angle : 0.823 12.352 9520 Z= 0.422 Chirality : 0.047 0.294 1104 Planarity : 0.004 0.034 1216 Dihedral : 7.573 59.515 960 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 22.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 7.25 % Allowed : 32.38 % Favored : 60.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.29), residues: 832 helix: -0.74 (0.22), residues: 576 sheet: None (None), residues: 0 loop : -2.81 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS G 113 PHE 0.011 0.002 PHE F 38 TYR 0.006 0.001 TYR B 27 ARG 0.008 0.001 ARG D 88 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 323) hydrogen bonds : angle 5.09148 ( 963) covalent geometry : bond 0.00305 ( 7128) covalent geometry : angle 0.82349 ( 9520) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 317 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8831 (mmmm) cc_final: 0.8626 (mmtp) REVERT: A 30 GLU cc_start: 0.6117 (mt-10) cc_final: 0.5451 (mm-30) REVERT: B 18 LYS cc_start: 0.9041 (mtmm) cc_final: 0.8745 (mtmm) REVERT: B 51 ASP cc_start: 0.5359 (m-30) cc_final: 0.4602 (m-30) REVERT: B 75 ASN cc_start: 0.7214 (t0) cc_final: 0.6689 (m-40) REVERT: C 18 LYS cc_start: 0.8487 (mtmm) cc_final: 0.8094 (mtmm) REVERT: C 49 ARG cc_start: 0.8056 (tpt90) cc_final: 0.7711 (tpt90) REVERT: C 105 LYS cc_start: 0.8508 (mmmt) cc_final: 0.8001 (mttt) REVERT: D 27 TYR cc_start: 0.6407 (m-80) cc_final: 0.6063 (m-80) REVERT: D 53 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6759 (tt0) REVERT: D 62 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6306 (mmt90) REVERT: E 18 LYS cc_start: 0.9083 (tttm) cc_final: 0.8826 (mmmt) REVERT: E 53 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7935 (mt-10) REVERT: E 70 ASP cc_start: 0.7295 (t70) cc_final: 0.6292 (t70) REVERT: F 22 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7071 (mm-30) REVERT: F 37 HIS cc_start: 0.6292 (t70) cc_final: 0.5733 (t-170) REVERT: F 39 ASP cc_start: 0.7701 (m-30) cc_final: 0.7474 (m-30) REVERT: F 49 ARG cc_start: 0.6064 (tpt90) cc_final: 0.5645 (tpt-90) REVERT: F 53 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8011 (mt-10) REVERT: G 17 LYS cc_start: 0.8511 (mmtp) cc_final: 0.8244 (mmtp) REVERT: G 53 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7686 (tm-30) REVERT: G 64 ARG cc_start: 0.6186 (ptp90) cc_final: 0.5910 (ptp90) REVERT: G 102 GLU cc_start: 0.8140 (pp20) cc_final: 0.7784 (pp20) REVERT: G 104 LEU cc_start: 0.8169 (mt) cc_final: 0.7832 (mt) REVERT: G 107 ARG cc_start: 0.7506 (tmm-80) cc_final: 0.7296 (ttp80) REVERT: H 104 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8551 (tt) outliers start: 58 outliers final: 35 residues processed: 340 average time/residue: 0.2793 time to fit residues: 114.9315 Evaluate side-chains 317 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 280 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain B residue 27 TYR Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 64 ARG Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 98 LYS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 33 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 chunk 15 optimal weight: 0.0770 chunk 26 optimal weight: 0.0980 chunk 40 optimal weight: 50.0000 chunk 77 optimal weight: 0.0980 chunk 53 optimal weight: 10.0000 chunk 44 optimal weight: 0.0050 chunk 35 optimal weight: 20.0000 overall best weight: 2.0554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS D 23 ASN F 113 HIS H 37 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.138232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.124122 restraints weight = 21271.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.126959 restraints weight = 13758.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.128963 restraints weight = 9761.918| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 1.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7128 Z= 0.151 Angle : 0.834 11.626 9520 Z= 0.429 Chirality : 0.047 0.289 1104 Planarity : 0.004 0.044 1216 Dihedral : 7.432 58.280 960 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 22.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 7.00 % Allowed : 33.88 % Favored : 59.12 % 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: -2.01 (0.29), residues: 832 helix: -0.60 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -2.83 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.001 HIS B 40 PHE 0.008 0.002 PHE E 38 TYR 0.008 0.001 TYR B 27 ARG 0.015 0.001 ARG H 107 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 323) hydrogen bonds : angle 4.87320 ( 963) covalent geometry : bond 0.00318 ( 7128) covalent geometry : angle 0.83445 ( 9520) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 300 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.5961 (mt-10) cc_final: 0.4933 (tp30) REVERT: A 79 LEU cc_start: 0.8738 (mp) cc_final: 0.8370 (mm) REVERT: A 99 ILE cc_start: 0.6716 (OUTLIER) cc_final: 0.6351 (pt) REVERT: B 17 LYS cc_start: 0.8799 (mmmm) cc_final: 0.8018 (tptt) REVERT: B 18 LYS cc_start: 0.9122 (mtmm) cc_final: 0.8691 (mtmm) REVERT: B 51 ASP cc_start: 0.5633 (m-30) cc_final: 0.5103 (m-30) REVERT: B 53 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7755 (pt0) REVERT: B 104 LEU cc_start: 0.8800 (mt) cc_final: 0.8594 (mm) REVERT: C 18 LYS cc_start: 0.8627 (mtmm) cc_final: 0.7925 (mtmm) REVERT: C 49 ARG cc_start: 0.8095 (tpt90) cc_final: 0.6799 (tpt90) REVERT: C 53 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7467 (mt-10) REVERT: C 74 GLU cc_start: 0.8199 (mp0) cc_final: 0.7472 (mp0) REVERT: C 105 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8191 (mttt) REVERT: C 107 ARG cc_start: 0.8444 (mmm160) cc_final: 0.8135 (mmm160) REVERT: D 27 TYR cc_start: 0.6389 (m-80) cc_final: 0.6069 (m-80) REVERT: D 50 GLU cc_start: 0.7861 (mp0) cc_final: 0.7419 (mp0) REVERT: D 53 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6466 (pt0) REVERT: D 62 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6422 (mmt90) REVERT: F 37 HIS cc_start: 0.6455 (t70) cc_final: 0.6021 (t-170) REVERT: F 39 ASP cc_start: 0.8228 (m-30) cc_final: 0.7791 (m-30) REVERT: F 53 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7988 (mt-10) REVERT: G 17 LYS cc_start: 0.8615 (mmtp) cc_final: 0.8256 (mmtp) REVERT: G 18 LYS cc_start: 0.9100 (mtpp) cc_final: 0.8875 (mmmt) REVERT: G 64 ARG cc_start: 0.6331 (ptp90) cc_final: 0.5891 (ptp90) REVERT: G 73 GLN cc_start: 0.8680 (mt0) cc_final: 0.8281 (mt0) REVERT: G 102 GLU cc_start: 0.8118 (pp20) cc_final: 0.7888 (pp20) REVERT: G 104 LEU cc_start: 0.7984 (mt) cc_final: 0.7496 (mp) REVERT: G 107 ARG cc_start: 0.7769 (tmm-80) cc_final: 0.7539 (ttp80) REVERT: H 30 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7360 (mp0) REVERT: H 82 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8304 (mm) REVERT: H 104 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8599 (tp) outliers start: 56 outliers final: 33 residues processed: 328 average time/residue: 0.2732 time to fit residues: 109.8400 Evaluate side-chains 296 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 259 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 37 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 chunk 48 optimal weight: 0.0070 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN D 40 HIS E 92 GLN F 92 GLN F 113 HIS ** H 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.137877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.123885 restraints weight = 21377.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.126497 restraints weight = 14486.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.128413 restraints weight = 10659.600| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 1.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7128 Z= 0.153 Angle : 0.869 11.120 9520 Z= 0.448 Chirality : 0.049 0.270 1104 Planarity : 0.004 0.041 1216 Dihedral : 7.389 59.793 958 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 5.88 % Allowed : 35.38 % Favored : 58.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.81 (0.29), residues: 832 helix: -0.47 (0.22), residues: 568 sheet: None (None), residues: 0 loop : -2.71 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS F 113 PHE 0.012 0.002 PHE H 94 TYR 0.008 0.001 TYR B 27 ARG 0.010 0.001 ARG D 88 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 323) hydrogen bonds : angle 4.85394 ( 963) covalent geometry : bond 0.00339 ( 7128) covalent geometry : angle 0.86946 ( 9520) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 286 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.5693 (mt-10) cc_final: 0.4846 (tp30) REVERT: B 17 LYS cc_start: 0.8813 (mmmm) cc_final: 0.8011 (tptp) REVERT: B 18 LYS cc_start: 0.9097 (mtmm) cc_final: 0.8687 (mtmm) REVERT: B 53 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7674 (pt0) REVERT: B 70 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.6621 (t70) REVERT: B 71 TYR cc_start: 0.7875 (m-80) cc_final: 0.7648 (m-80) REVERT: B 73 GLN cc_start: 0.7447 (mt0) cc_final: 0.7012 (mp10) REVERT: C 18 LYS cc_start: 0.8487 (mtmm) cc_final: 0.7909 (mtmm) REVERT: C 49 ARG cc_start: 0.7763 (tpt90) cc_final: 0.6296 (tpt90) REVERT: C 53 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7279 (mt-10) REVERT: C 74 GLU cc_start: 0.8067 (mp0) cc_final: 0.7778 (mp0) REVERT: C 105 LYS cc_start: 0.8673 (mmmt) cc_final: 0.8039 (mttt) REVERT: D 27 TYR cc_start: 0.6328 (m-80) cc_final: 0.6050 (m-80) REVERT: D 53 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6967 (tt0) REVERT: E 71 TYR cc_start: 0.8046 (m-80) cc_final: 0.7837 (m-80) REVERT: F 39 ASP cc_start: 0.8379 (m-30) cc_final: 0.8020 (m-30) REVERT: F 53 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8008 (mt-10) REVERT: F 73 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8045 (mm110) REVERT: G 73 GLN cc_start: 0.8633 (mt0) cc_final: 0.8310 (mt0) REVERT: G 104 LEU cc_start: 0.8061 (mt) cc_final: 0.7514 (mp) REVERT: H 82 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8233 (mm) REVERT: H 104 LEU cc_start: 0.8765 (mm) cc_final: 0.8226 (tp) REVERT: H 108 ASN cc_start: 0.9005 (m-40) cc_final: 0.8596 (m-40) outliers start: 47 outliers final: 34 residues processed: 308 average time/residue: 0.2584 time to fit residues: 96.8739 Evaluate side-chains 299 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 263 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain B residue 27 TYR Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 82 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 30 optimal weight: 50.0000 chunk 21 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 28 optimal weight: 0.3980 chunk 0 optimal weight: 30.0000 chunk 22 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 40 HIS D 40 HIS ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN F 113 HIS ** H 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.134884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.121211 restraints weight = 21500.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.123887 restraints weight = 14206.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.125824 restraints weight = 10261.885| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 1.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7128 Z= 0.174 Angle : 0.909 13.358 9520 Z= 0.472 Chirality : 0.049 0.199 1104 Planarity : 0.005 0.048 1216 Dihedral : 7.494 59.212 958 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 24.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 6.12 % Allowed : 36.62 % Favored : 57.25 % 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: -1.32 (0.30), residues: 832 helix: -0.02 (0.24), residues: 528 sheet: None (None), residues: 0 loop : -2.40 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.020 0.002 HIS F 113 PHE 0.013 0.002 PHE A 38 TYR 0.014 0.001 TYR B 27 ARG 0.017 0.001 ARG G 107 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 323) hydrogen bonds : angle 4.94951 ( 963) covalent geometry : bond 0.00387 ( 7128) covalent geometry : angle 0.90933 ( 9520) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 274 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6236 (mt-10) cc_final: 0.5579 (tp30) REVERT: A 64 ARG cc_start: 0.8592 (ptp-170) cc_final: 0.7294 (ptp-170) REVERT: B 17 LYS cc_start: 0.8818 (mmmm) cc_final: 0.7942 (tptp) REVERT: B 18 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8752 (mtmm) REVERT: B 24 LEU cc_start: 0.9100 (mm) cc_final: 0.8807 (mm) REVERT: B 50 GLU cc_start: 0.7761 (mp0) cc_final: 0.7339 (mp0) REVERT: B 53 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7638 (pt0) REVERT: B 70 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.7571 (t70) REVERT: B 73 GLN cc_start: 0.7740 (mt0) cc_final: 0.7159 (mt0) REVERT: C 18 LYS cc_start: 0.8658 (mtmm) cc_final: 0.8313 (mtmm) REVERT: C 37 HIS cc_start: 0.6224 (OUTLIER) cc_final: 0.5941 (m-70) REVERT: C 49 ARG cc_start: 0.7845 (tpt90) cc_final: 0.7226 (tpt90) REVERT: C 53 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8004 (mt-10) REVERT: C 105 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8016 (mttt) REVERT: D 27 TYR cc_start: 0.6563 (m-80) cc_final: 0.6319 (m-80) REVERT: D 53 GLU cc_start: 0.7679 (mt-10) cc_final: 0.6520 (pt0) REVERT: E 49 ARG cc_start: 0.7141 (tpt90) cc_final: 0.6709 (tpt90) REVERT: F 39 ASP cc_start: 0.8733 (m-30) cc_final: 0.8312 (m-30) REVERT: F 53 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7996 (mt-10) REVERT: F 73 GLN cc_start: 0.8514 (mm110) cc_final: 0.8132 (mm110) REVERT: G 70 ASP cc_start: 0.8080 (t70) cc_final: 0.7864 (t0) REVERT: H 49 ARG cc_start: 0.8045 (mmm160) cc_final: 0.7797 (tpp80) REVERT: H 82 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8381 (mm) REVERT: H 104 LEU cc_start: 0.8830 (mm) cc_final: 0.8087 (tp) outliers start: 49 outliers final: 37 residues processed: 297 average time/residue: 0.2659 time to fit residues: 96.8118 Evaluate side-chains 295 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 82 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 70 optimal weight: 30.0000 chunk 12 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 chunk 60 optimal weight: 40.0000 chunk 22 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.136484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.122589 restraints weight = 21172.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.125313 restraints weight = 14162.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.127285 restraints weight = 10293.183| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 1.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7128 Z= 0.172 Angle : 0.968 14.229 9520 Z= 0.493 Chirality : 0.050 0.227 1104 Planarity : 0.005 0.062 1216 Dihedral : 7.559 59.755 958 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 25.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.62 % Favored : 90.26 % Rotamer: Outliers : 6.12 % Allowed : 37.62 % Favored : 56.25 % 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: -1.50 (0.29), residues: 832 helix: -0.03 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -2.74 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.002 HIS F 113 PHE 0.022 0.003 PHE E 94 TYR 0.012 0.001 TYR B 27 ARG 0.009 0.001 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 323) hydrogen bonds : angle 4.96623 ( 963) covalent geometry : bond 0.00382 ( 7128) covalent geometry : angle 0.96836 ( 9520) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 276 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6083 (mt-10) cc_final: 0.5842 (tp30) REVERT: A 64 ARG cc_start: 0.8670 (ptp-170) cc_final: 0.7556 (ptp-170) REVERT: B 17 LYS cc_start: 0.8832 (mmmm) cc_final: 0.7937 (tptp) REVERT: B 18 LYS cc_start: 0.9198 (mtmm) cc_final: 0.8808 (mtmm) REVERT: B 53 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7704 (pt0) REVERT: B 70 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.7999 (t0) REVERT: B 73 GLN cc_start: 0.7764 (mt0) cc_final: 0.7505 (mt0) REVERT: B 105 LYS cc_start: 0.8458 (mmmm) cc_final: 0.7776 (mmmt) REVERT: C 18 LYS cc_start: 0.8773 (mtmm) cc_final: 0.8470 (mtmm) REVERT: C 49 ARG cc_start: 0.7774 (tpt90) cc_final: 0.7527 (tpt90) REVERT: C 63 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8339 (mtmt) REVERT: C 105 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8019 (mttt) REVERT: D 27 TYR cc_start: 0.6727 (m-80) cc_final: 0.6480 (m-80) REVERT: D 50 GLU cc_start: 0.8048 (mp0) cc_final: 0.7826 (mp0) REVERT: D 53 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7042 (tt0) REVERT: E 41 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8791 (tp) REVERT: F 39 ASP cc_start: 0.8575 (m-30) cc_final: 0.8202 (m-30) REVERT: F 53 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7998 (mt-10) REVERT: F 63 LYS cc_start: 0.8339 (mtmt) cc_final: 0.8048 (mtmm) REVERT: G 70 ASP cc_start: 0.8193 (t70) cc_final: 0.7958 (t0) REVERT: H 70 ASP cc_start: 0.7966 (t70) cc_final: 0.7700 (t0) REVERT: H 82 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8337 (mm) REVERT: H 89 GLU cc_start: 0.7525 (tp30) cc_final: 0.7264 (tp30) REVERT: H 104 LEU cc_start: 0.8768 (mm) cc_final: 0.8292 (tp) outliers start: 49 outliers final: 36 residues processed: 303 average time/residue: 0.2542 time to fit residues: 94.7971 Evaluate side-chains 296 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 257 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 82 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 72 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN D 40 HIS ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 113 HIS ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.137943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.123465 restraints weight = 21577.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.126295 restraints weight = 14339.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.128370 restraints weight = 10392.969| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 1.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7128 Z= 0.171 Angle : 1.024 16.198 9520 Z= 0.512 Chirality : 0.053 0.326 1104 Planarity : 0.005 0.050 1216 Dihedral : 7.477 58.755 956 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 25.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.89 % Favored : 90.99 % Rotamer: Outliers : 5.25 % Allowed : 38.12 % Favored : 56.62 % 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: -1.53 (0.29), residues: 832 helix: -0.07 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -2.65 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.001 HIS F 113 PHE 0.030 0.002 PHE E 94 TYR 0.010 0.001 TYR B 27 ARG 0.013 0.001 ARG C 88 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 323) hydrogen bonds : angle 4.94081 ( 963) covalent geometry : bond 0.00371 ( 7128) covalent geometry : angle 1.02434 ( 9520) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 281 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.5916 (mt-10) cc_final: 0.5555 (tp30) REVERT: A 70 ASP cc_start: 0.8413 (t70) cc_final: 0.8009 (t70) REVERT: B 17 LYS cc_start: 0.8892 (mmmm) cc_final: 0.8070 (tptt) REVERT: B 18 LYS cc_start: 0.9205 (mtmm) cc_final: 0.8779 (mtmm) REVERT: B 53 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7704 (pt0) REVERT: B 70 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8071 (t0) REVERT: B 73 GLN cc_start: 0.7844 (mt0) cc_final: 0.7582 (mt0) REVERT: B 105 LYS cc_start: 0.8397 (mmmm) cc_final: 0.7836 (mmmt) REVERT: C 18 LYS cc_start: 0.8817 (mtmm) cc_final: 0.8417 (mtmm) REVERT: C 23 ASN cc_start: 0.8594 (m-40) cc_final: 0.8355 (m110) REVERT: E 41 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8654 (tp) REVERT: F 39 ASP cc_start: 0.8282 (m-30) cc_final: 0.7919 (m-30) REVERT: F 49 ARG cc_start: 0.6400 (tpt-90) cc_final: 0.5949 (tpt-90) REVERT: F 53 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8008 (mt-10) REVERT: F 63 LYS cc_start: 0.8113 (mtmt) cc_final: 0.7871 (mtmm) REVERT: G 15 GLU cc_start: 0.7851 (pm20) cc_final: 0.7214 (pm20) REVERT: G 19 ASP cc_start: 0.8362 (m-30) cc_final: 0.8063 (p0) REVERT: G 67 LYS cc_start: 0.9035 (mptt) cc_final: 0.8832 (mttt) REVERT: H 70 ASP cc_start: 0.8063 (t70) cc_final: 0.7806 (t0) REVERT: H 82 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8295 (mm) REVERT: H 89 GLU cc_start: 0.7816 (tp30) cc_final: 0.7612 (tp30) REVERT: H 104 LEU cc_start: 0.8726 (mm) cc_final: 0.8367 (tp) outliers start: 42 outliers final: 34 residues processed: 299 average time/residue: 0.2578 time to fit residues: 94.8849 Evaluate side-chains 303 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 266 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 82 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 72 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.0570 chunk 71 optimal weight: 10.0000 chunk 20 optimal weight: 40.0000 chunk 76 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 58 optimal weight: 30.0000 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 92 GLN F 113 HIS ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.138386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.124009 restraints weight = 21085.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.126852 restraints weight = 14042.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.128902 restraints weight = 10149.310| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 1.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7128 Z= 0.176 Angle : 1.035 15.705 9520 Z= 0.520 Chirality : 0.052 0.271 1104 Planarity : 0.005 0.054 1216 Dihedral : 7.512 58.476 956 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 24.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.25 % Favored : 90.62 % Rotamer: Outliers : 4.88 % Allowed : 38.88 % Favored : 56.25 % 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: -1.65 (0.29), residues: 832 helix: -0.16 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -2.72 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.021 0.002 HIS F 113 PHE 0.013 0.002 PHE E 94 TYR 0.011 0.001 TYR D 27 ARG 0.013 0.001 ARG C 88 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 323) hydrogen bonds : angle 4.98335 ( 963) covalent geometry : bond 0.00392 ( 7128) covalent geometry : angle 1.03521 ( 9520) =============================================================================== Job complete usr+sys time: 3023.40 seconds wall clock time: 54 minutes 13.01 seconds (3253.01 seconds total)