Starting phenix.real_space_refine on Thu Sep 26 09:08:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/09_2024/6bze_7314.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/09_2024/6bze_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/09_2024/6bze_7314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/09_2024/6bze_7314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/09_2024/6bze_7314.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/09_2024/6bze_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 4.65, per 1000 atoms: 0.66 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: 1.96 Conformation dependent library (CDL) restraints added in 925.4 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: 0.87 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: 1.73 Time building geometry restraints manager: 2.24 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: 0.00 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: 0.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.020 Find NCS groups from input model: 0.250 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.580 ------------------------------------------------------------------------------- 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= 0.563 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 *********************** 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 fitting. rotamer outliers: 72 poor density : 426 time to evaluate : 0.955 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: 0.2803 time to fit residues: 158.8722 Evaluate side-chains 317 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 294 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4971 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= 0.343 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 *********************** 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 fitting. rotamer outliers: 70 poor density : 389 time to evaluate : 0.923 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 12 ASP cc_start: 0.7888 (m-30) cc_final: 0.7595 (p0) REVERT: A 30 GLU cc_start: 0.5496 (mm-30) cc_final: 0.5172 (mt-10) REVERT: A 63 LYS cc_start: 0.8336 (mmtt) cc_final: 0.7822 (mtmt) REVERT: A 70 ASP cc_start: 0.7008 (t70) cc_final: 0.6759 (t0) REVERT: A 84 GLU cc_start: 0.6654 (tp30) cc_final: 0.6173 (mm-30) REVERT: A 104 LEU cc_start: 0.8282 (mt) cc_final: 0.8058 (mt) REVERT: B 11 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8888 (tm-30) REVERT: B 25 ARG cc_start: 0.2813 (OUTLIER) cc_final: 0.2191 (tpt-90) REVERT: B 28 LEU cc_start: 0.6351 (tt) cc_final: 0.5780 (tt) REVERT: B 42 ARG cc_start: 0.8030 (tpt-90) cc_final: 0.7565 (mmt180) REVERT: B 49 ARG cc_start: 0.6692 (tpt90) cc_final: 0.6208 (tmt-80) REVERT: B 70 ASP cc_start: 0.7118 (t70) cc_final: 0.6656 (t70) REVERT: B 75 ASN cc_start: 0.6218 (OUTLIER) cc_final: 0.5552 (m-40) REVERT: B 84 GLU cc_start: 0.7615 (tp30) cc_final: 0.7247 (mm-30) REVERT: B 101 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7703 (t0) REVERT: B 112 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8618 (tm-30) REVERT: B 113 HIS cc_start: 0.8310 (t-170) cc_final: 0.8102 (t-170) REVERT: C 11 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7773 (tm-30) REVERT: C 16 VAL cc_start: 0.7630 (OUTLIER) cc_final: 0.7239 (p) REVERT: C 23 ASN cc_start: 0.7721 (m-40) cc_final: 0.7366 (m-40) REVERT: C 24 LEU cc_start: 0.7269 (mm) cc_final: 0.6072 (mm) REVERT: C 105 LYS cc_start: 0.7701 (mmmt) cc_final: 0.7480 (mmmt) REVERT: C 109 ILE cc_start: 0.7293 (mp) cc_final: 0.6737 (mp) REVERT: C 112 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8701 (tm-30) REVERT: D 16 VAL cc_start: 0.7020 (OUTLIER) cc_final: 0.6650 (p) REVERT: D 28 LEU cc_start: 0.6219 (tp) cc_final: 0.5235 (tp) REVERT: D 35 GLU cc_start: 0.0612 (pt0) cc_final: -0.0230 (mt-10) REVERT: D 37 HIS cc_start: 0.1279 (OUTLIER) cc_final: 0.0895 (t-170) REVERT: D 56 SER cc_start: 0.8094 (t) cc_final: 0.7746 (p) REVERT: D 73 GLN cc_start: 0.7460 (mt0) cc_final: 0.6884 (mt0) REVERT: D 74 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8399 (mt-10) REVERT: E 11 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8145 (tm-30) REVERT: E 37 HIS cc_start: 0.3337 (OUTLIER) cc_final: 0.2877 (t70) REVERT: E 62 ARG cc_start: 0.8182 (mmt90) cc_final: 0.7810 (mmm-85) REVERT: E 84 GLU cc_start: 0.7895 (tp30) cc_final: 0.7546 (tm-30) REVERT: E 90 LYS cc_start: 0.3029 (mttt) cc_final: 0.1601 (mttp) REVERT: E 105 LYS cc_start: 0.6546 (mmmt) cc_final: 0.6330 (mmtt) REVERT: F 25 ARG cc_start: 0.5243 (OUTLIER) cc_final: 0.4390 (tmt170) REVERT: F 37 HIS cc_start: 0.4460 (t70) cc_final: 0.3705 (t70) REVERT: F 63 LYS cc_start: 0.7418 (mmtt) cc_final: 0.6599 (mtmt) REVERT: F 90 LYS cc_start: 0.1125 (ttmt) cc_final: 0.0641 (ttmt) REVERT: G 42 ARG cc_start: 0.7199 (ttt-90) cc_final: 0.6853 (ttt-90) REVERT: G 50 GLU cc_start: 0.5917 (pm20) cc_final: 0.5713 (pm20) REVERT: G 53 GLU cc_start: 0.6591 (mt-10) cc_final: 0.6205 (tm-30) REVERT: G 63 LYS cc_start: 0.6205 (mmtt) cc_final: 0.5658 (mtmt) REVERT: G 81 THR cc_start: 0.7587 (p) cc_final: 0.7316 (m) REVERT: G 105 LYS cc_start: 0.7170 (mmmt) cc_final: 0.6670 (tptt) REVERT: G 113 HIS cc_start: 0.8707 (t70) cc_final: 0.8463 (t-170) REVERT: H 105 LYS cc_start: 0.6971 (mmmt) cc_final: 0.6526 (mmmt) outliers start: 70 outliers final: 31 residues processed: 425 average time/residue: 0.2808 time to fit residues: 143.1002 Evaluate side-chains 316 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 277 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 40 HIS Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain B residue 25 ARG 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 16 VAL 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 16 VAL Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 40 HIS 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 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 40 optimal weight: 40.0000 chunk 22 optimal weight: 5.9990 chunk 60 optimal weight: 30.0000 chunk 49 optimal weight: 7.9990 chunk 20 optimal weight: 30.0000 chunk 72 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS C 108 ASN ** D 92 GLN ** 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** ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 GLN ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5057 moved from start: 0.8567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7128 Z= 0.283 Angle : 0.905 12.059 9520 Z= 0.475 Chirality : 0.052 0.297 1104 Planarity : 0.005 0.037 1216 Dihedral : 8.402 59.452 972 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 26.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 8.12 % Allowed : 28.12 % Favored : 63.75 % 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: -2.25 (0.28), residues: 832 helix: -0.86 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -2.78 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 37 PHE 0.018 0.004 PHE E 94 TYR 0.008 0.001 TYR B 27 ARG 0.012 0.001 ARG F 107 *********************** 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 409 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 344 time to evaluate : 0.867 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 28 LEU cc_start: 0.3088 (tp) cc_final: 0.2487 (tp) REVERT: A 30 GLU cc_start: 0.5239 (mm-30) cc_final: 0.4905 (mt-10) REVERT: A 32 ILE cc_start: 0.1947 (mm) cc_final: 0.1744 (mm) REVERT: A 42 ARG cc_start: 0.6922 (tmt170) cc_final: 0.6566 (mmt180) REVERT: A 70 ASP cc_start: 0.7143 (t70) cc_final: 0.6653 (t0) REVERT: B 11 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8904 (tm-30) REVERT: B 75 ASN cc_start: 0.6527 (OUTLIER) cc_final: 0.5631 (m-40) REVERT: C 16 VAL cc_start: 0.7829 (OUTLIER) cc_final: 0.7413 (p) REVERT: C 23 ASN cc_start: 0.7520 (m-40) cc_final: 0.7284 (m-40) REVERT: C 24 LEU cc_start: 0.7187 (mm) cc_final: 0.6132 (mm) REVERT: C 25 ARG cc_start: 0.6241 (OUTLIER) cc_final: 0.5919 (mmm-85) REVERT: C 40 HIS cc_start: 0.6233 (OUTLIER) cc_final: 0.6015 (m-70) REVERT: C 105 LYS cc_start: 0.7393 (mmmt) cc_final: 0.7176 (mmmt) REVERT: C 107 ARG cc_start: 0.8802 (tpp80) cc_final: 0.8448 (tpp-160) REVERT: C 109 ILE cc_start: 0.7562 (mp) cc_final: 0.7362 (mp) REVERT: D 16 VAL cc_start: 0.7149 (OUTLIER) cc_final: 0.6685 (p) REVERT: D 52 THR cc_start: 0.7168 (p) cc_final: 0.6956 (p) REVERT: D 112 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8087 (tm-30) REVERT: E 15 GLU cc_start: 0.8564 (mp0) cc_final: 0.8270 (pm20) REVERT: E 18 LYS cc_start: 0.7447 (mtpp) cc_final: 0.7241 (mtpp) REVERT: E 30 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6432 (mm-30) REVERT: E 58 ARG cc_start: 0.4679 (OUTLIER) cc_final: 0.4338 (ttt180) REVERT: E 84 GLU cc_start: 0.7999 (tp30) cc_final: 0.7163 (tp30) REVERT: E 90 LYS cc_start: 0.2606 (mttt) cc_final: 0.1539 (mttt) REVERT: F 25 ARG cc_start: 0.5216 (OUTLIER) cc_final: 0.4353 (ttt180) REVERT: F 95 LEU cc_start: 0.8608 (tp) cc_final: 0.8349 (tp) REVERT: G 15 GLU cc_start: 0.8241 (mp0) cc_final: 0.7728 (tm-30) REVERT: G 53 GLU cc_start: 0.6729 (mt-10) cc_final: 0.6235 (tm-30) REVERT: G 62 ARG cc_start: 0.8687 (mmm-85) cc_final: 0.8155 (mmm-85) REVERT: G 81 THR cc_start: 0.7614 (p) cc_final: 0.7346 (m) REVERT: G 99 ILE cc_start: 0.7558 (pt) cc_final: 0.7325 (pt) REVERT: G 105 LYS cc_start: 0.7770 (mmmt) cc_final: 0.7467 (tppt) REVERT: H 105 LYS cc_start: 0.7554 (mmmt) cc_final: 0.7301 (mmmt) REVERT: H 106 LEU cc_start: 0.6596 (tp) cc_final: 0.6120 (mt) REVERT: H 109 ILE cc_start: 0.7756 (mt) cc_final: 0.7480 (pt) outliers start: 65 outliers final: 30 residues processed: 376 average time/residue: 0.2802 time to fit residues: 126.6582 Evaluate side-chains 331 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 294 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 40 HIS Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ARG 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 D residue 16 VAL 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 D residue 80 ASP Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 16 VAL 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 G residue 26 VAL Chi-restraints excluded: chain G residue 29 CYS 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 54 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 0.0030 chunk 48 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 20 optimal weight: 30.0000 chunk 64 optimal weight: 30.0000 overall best weight: 3.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS B 113 HIS D 73 GLN E 37 HIS ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5048 moved from start: 0.9431 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= 0.219 Angle : 0.835 10.548 9520 Z= 0.437 Chirality : 0.048 0.276 1104 Planarity : 0.005 0.046 1216 Dihedral : 7.922 59.364 964 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 24.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 8.00 % Allowed : 29.88 % Favored : 62.12 % 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: -2.10 (0.28), residues: 832 helix: -0.58 (0.22), residues: 584 sheet: None (None), residues: 0 loop : -3.24 (0.33), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS G 113 PHE 0.015 0.002 PHE H 94 TYR 0.008 0.001 TYR B 27 ARG 0.007 0.001 ARG E 64 *********************** 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 407 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 343 time to evaluate : 0.807 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: A 30 GLU cc_start: 0.5430 (mm-30) cc_final: 0.5093 (mt-10) REVERT: A 42 ARG cc_start: 0.7241 (tmt170) cc_final: 0.6964 (mmt180) REVERT: A 63 LYS cc_start: 0.8297 (mmtt) cc_final: 0.7799 (mtmt) REVERT: B 17 LYS cc_start: 0.8389 (mmmm) cc_final: 0.7748 (tmtt) REVERT: B 75 ASN cc_start: 0.6700 (t0) cc_final: 0.5663 (m-40) REVERT: C 23 ASN cc_start: 0.7619 (m-40) cc_final: 0.7361 (m-40) REVERT: C 24 LEU cc_start: 0.7436 (mm) cc_final: 0.6542 (mm) REVERT: C 25 ARG cc_start: 0.6243 (tpt90) cc_final: 0.5644 (mmm-85) REVERT: C 49 ARG cc_start: 0.7363 (tpt90) cc_final: 0.7128 (tpt90) REVERT: C 107 ARG cc_start: 0.8773 (tpp80) cc_final: 0.8445 (mmm-85) REVERT: D 16 VAL cc_start: 0.7151 (OUTLIER) cc_final: 0.6768 (p) REVERT: D 35 GLU cc_start: 0.0873 (pt0) cc_final: 0.0612 (pt0) REVERT: D 52 THR cc_start: 0.7019 (p) cc_final: 0.6661 (p) REVERT: D 58 ARG cc_start: 0.3627 (mmt180) cc_final: 0.3235 (tpp-160) REVERT: D 73 GLN cc_start: 0.6890 (mt0) cc_final: 0.6067 (mt0) REVERT: D 74 GLU cc_start: 0.8257 (mp0) cc_final: 0.7955 (mt-10) REVERT: D 112 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8159 (tm-30) REVERT: D 113 HIS cc_start: 0.8976 (t-90) cc_final: 0.8651 (t-170) REVERT: E 30 GLU cc_start: 0.6649 (mm-30) cc_final: 0.6265 (tp30) REVERT: E 58 ARG cc_start: 0.4398 (OUTLIER) cc_final: 0.3953 (ttt180) REVERT: E 90 LYS cc_start: 0.2351 (mttt) cc_final: 0.2030 (mttt) REVERT: E 105 LYS cc_start: 0.6982 (mmtt) cc_final: 0.6690 (tppt) REVERT: G 42 ARG cc_start: 0.7136 (ttt-90) cc_final: 0.6811 (ttt-90) REVERT: G 53 GLU cc_start: 0.6620 (mt-10) cc_final: 0.6026 (tm-30) REVERT: G 62 ARG cc_start: 0.8615 (mmm-85) cc_final: 0.8302 (mmm-85) REVERT: G 81 THR cc_start: 0.7657 (p) cc_final: 0.7262 (m) REVERT: G 105 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7650 (tppt) REVERT: G 107 ARG cc_start: 0.8225 (tmm-80) cc_final: 0.7961 (tmm-80) REVERT: H 24 LEU cc_start: 0.7286 (mm) cc_final: 0.6834 (mm) REVERT: H 82 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8099 (mm) REVERT: H 105 LYS cc_start: 0.7692 (mmmt) cc_final: 0.7380 (mtpp) REVERT: H 106 LEU cc_start: 0.6752 (tp) cc_final: 0.6051 (mt) REVERT: H 107 ARG cc_start: 0.7833 (ttp80) cc_final: 0.7483 (ttp80) outliers start: 64 outliers final: 35 residues processed: 373 average time/residue: 0.2835 time to fit residues: 126.6196 Evaluate side-chains 324 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 286 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 40 HIS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 27 TYR Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 16 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 80 ASP 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 58 ARG 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 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 75 ASN Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 82 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS B 40 HIS E 37 HIS ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5059 moved from start: 1.0038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7128 Z= 0.226 Angle : 0.830 7.959 9520 Z= 0.437 Chirality : 0.048 0.297 1104 Planarity : 0.005 0.062 1216 Dihedral : 7.459 59.993 958 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 23.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 8.12 % Allowed : 31.62 % Favored : 60.25 % 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: -2.26 (0.29), residues: 832 helix: -0.60 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -3.69 (0.32), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS G 113 PHE 0.014 0.002 PHE E 38 TYR 0.008 0.001 TYR B 27 ARG 0.011 0.001 ARG A 87 *********************** 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 fitting. rotamer outliers: 65 poor density : 310 time to evaluate : 0.956 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: A 30 GLU cc_start: 0.4831 (mm-30) cc_final: 0.4491 (mt-10) REVERT: A 46 ILE cc_start: 0.4408 (mp) cc_final: 0.4092 (mp) REVERT: A 63 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7825 (mtmt) REVERT: A 74 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8161 (tm-30) REVERT: A 84 GLU cc_start: 0.6052 (OUTLIER) cc_final: 0.5552 (mm-30) REVERT: B 17 LYS cc_start: 0.7731 (mmmm) cc_final: 0.6976 (tptp) REVERT: B 50 GLU cc_start: 0.6997 (mp0) cc_final: 0.6587 (mp0) REVERT: B 53 GLU cc_start: 0.6716 (mt-10) cc_final: 0.6426 (pt0) REVERT: B 75 ASN cc_start: 0.6931 (t0) cc_final: 0.5865 (m-40) REVERT: C 16 VAL cc_start: 0.8047 (OUTLIER) cc_final: 0.7650 (p) REVERT: C 24 LEU cc_start: 0.7443 (mm) cc_final: 0.6231 (mm) REVERT: C 25 ARG cc_start: 0.6616 (OUTLIER) cc_final: 0.6245 (mmm-85) REVERT: C 49 ARG cc_start: 0.7305 (tpt90) cc_final: 0.7023 (tpt90) REVERT: C 105 LYS cc_start: 0.7482 (mmmt) cc_final: 0.7193 (mttt) REVERT: C 107 ARG cc_start: 0.8828 (tpp80) cc_final: 0.8562 (mmm160) REVERT: D 16 VAL cc_start: 0.7134 (OUTLIER) cc_final: 0.6651 (p) REVERT: D 52 THR cc_start: 0.7022 (p) cc_final: 0.6775 (p) REVERT: D 63 LYS cc_start: 0.7666 (mmtt) cc_final: 0.7360 (mtmt) REVERT: D 74 GLU cc_start: 0.8288 (mp0) cc_final: 0.8042 (mt-10) REVERT: D 112 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7950 (tm-30) REVERT: E 30 GLU cc_start: 0.6661 (mm-30) cc_final: 0.6436 (mm-30) REVERT: E 31 LYS cc_start: 0.5808 (mmtt) cc_final: 0.5531 (mtpt) REVERT: E 37 HIS cc_start: 0.4473 (OUTLIER) cc_final: 0.3991 (t-170) REVERT: E 105 LYS cc_start: 0.7410 (mmtt) cc_final: 0.7154 (tppt) REVERT: G 42 ARG cc_start: 0.7485 (ttt-90) cc_final: 0.7178 (ttt-90) REVERT: G 53 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6595 (tm-30) REVERT: G 81 THR cc_start: 0.7572 (p) cc_final: 0.7118 (m) REVERT: G 102 GLU cc_start: 0.8592 (pp20) cc_final: 0.8324 (pp20) REVERT: G 105 LYS cc_start: 0.8434 (mmmt) cc_final: 0.8076 (ttmm) REVERT: H 19 ASP cc_start: 0.8575 (m-30) cc_final: 0.8247 (p0) REVERT: H 105 LYS cc_start: 0.8055 (mmmt) cc_final: 0.7707 (tttp) REVERT: H 106 LEU cc_start: 0.7555 (tp) cc_final: 0.7206 (mt) REVERT: H 109 ILE cc_start: 0.8006 (pt) cc_final: 0.7346 (pt) outliers start: 65 outliers final: 38 residues processed: 346 average time/residue: 0.2813 time to fit residues: 117.9138 Evaluate side-chains 324 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 280 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 40 HIS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 16 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 90 LYS Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 37 HIS Chi-restraints excluded: chain E residue 46 ILE 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 14 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 40 optimal weight: 40.0000 chunk 74 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 73 GLN A 108 ASN B 73 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5037 moved from start: 1.0592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7128 Z= 0.286 Angle : 0.863 10.135 9520 Z= 0.454 Chirality : 0.049 0.237 1104 Planarity : 0.006 0.091 1216 Dihedral : 7.505 59.597 958 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 26.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 9.62 % Allowed : 32.12 % Favored : 58.25 % 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: -2.25 (0.28), residues: 832 helix: -0.68 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -2.91 (0.31), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.002 HIS E 37 PHE 0.019 0.002 PHE E 38 TYR 0.008 0.001 TYR A 27 ARG 0.011 0.001 ARG D 87 *********************** 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 378 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 301 time to evaluate : 0.872 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: 0.5457 (mm-30) cc_final: 0.5154 (mt-10) REVERT: A 50 GLU cc_start: 0.7732 (mp0) cc_final: 0.7210 (mt-10) REVERT: A 63 LYS cc_start: 0.8372 (mmtt) cc_final: 0.7956 (mtmt) REVERT: B 17 LYS cc_start: 0.7706 (mmmm) cc_final: 0.7096 (tptp) REVERT: B 35 GLU cc_start: 0.1210 (pt0) cc_final: 0.0902 (pt0) REVERT: B 50 GLU cc_start: 0.7019 (mp0) cc_final: 0.6622 (mp0) REVERT: B 53 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6442 (pt0) REVERT: B 74 GLU cc_start: 0.8370 (mp0) cc_final: 0.7921 (pm20) REVERT: B 75 ASN cc_start: 0.7397 (OUTLIER) cc_final: 0.6507 (m-40) REVERT: C 16 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7651 (p) REVERT: C 24 LEU cc_start: 0.7542 (mm) cc_final: 0.6382 (mm) REVERT: C 25 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.6071 (tpt-90) REVERT: C 49 ARG cc_start: 0.6999 (tpt90) cc_final: 0.6772 (tpt90) REVERT: C 105 LYS cc_start: 0.7483 (mmmt) cc_final: 0.7066 (mttt) REVERT: C 107 ARG cc_start: 0.8814 (tpp80) cc_final: 0.8585 (tpp80) REVERT: D 16 VAL cc_start: 0.7054 (OUTLIER) cc_final: 0.6634 (p) REVERT: D 28 LEU cc_start: 0.6217 (OUTLIER) cc_final: 0.5353 (tp) REVERT: D 35 GLU cc_start: 0.6964 (pp20) cc_final: 0.6324 (pm20) REVERT: D 62 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7496 (mmm-85) REVERT: D 112 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7951 (tm-30) REVERT: F 98 LYS cc_start: 0.8911 (pttp) cc_final: 0.8647 (ptpp) REVERT: G 27 TYR cc_start: 0.7362 (m-10) cc_final: 0.7138 (m-10) REVERT: G 42 ARG cc_start: 0.7355 (ttt-90) cc_final: 0.7031 (ttt-90) REVERT: G 53 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6526 (tm-30) REVERT: G 105 LYS cc_start: 0.8448 (mmmt) cc_final: 0.8157 (tppt) REVERT: H 104 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8751 (tt) REVERT: H 105 LYS cc_start: 0.8282 (mmmt) cc_final: 0.7941 (tptp) outliers start: 77 outliers final: 49 residues processed: 335 average time/residue: 0.2627 time to fit residues: 107.0821 Evaluate side-chains 335 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 279 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 40 HIS Chi-restraints excluded: chain A residue 48 SER 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 106 LEU Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 80 ASP 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 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 110 LYS Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 24 LEU 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 67 LYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 98 LYS 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 8 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 30 optimal weight: 40.0000 chunk 46 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS B 73 GLN D 23 ASN D 40 HIS ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5041 moved from start: 1.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7128 Z= 0.243 Angle : 0.846 9.461 9520 Z= 0.443 Chirality : 0.048 0.205 1104 Planarity : 0.005 0.045 1216 Dihedral : 7.336 58.342 958 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 23.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 8.50 % Allowed : 34.00 % Favored : 57.50 % 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: -2.16 (0.29), residues: 832 helix: -0.61 (0.22), residues: 584 sheet: None (None), residues: 0 loop : -3.32 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.001 HIS F 113 PHE 0.018 0.002 PHE E 94 TYR 0.009 0.001 TYR B 27 ARG 0.016 0.001 ARG G 107 *********************** 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 368 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 300 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.5258 (mm-30) cc_final: 0.4944 (mt-10) REVERT: A 50 GLU cc_start: 0.7468 (mp0) cc_final: 0.7031 (mt-10) REVERT: A 63 LYS cc_start: 0.8310 (mmtt) cc_final: 0.7855 (mtmt) REVERT: B 17 LYS cc_start: 0.7555 (mmmm) cc_final: 0.7085 (tptp) REVERT: B 22 GLU cc_start: 0.5662 (tp30) cc_final: 0.5461 (tp30) REVERT: B 35 GLU cc_start: 0.1305 (pt0) cc_final: 0.0972 (pt0) REVERT: B 50 GLU cc_start: 0.7122 (mp0) cc_final: 0.6561 (mp0) REVERT: B 53 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6431 (pt0) REVERT: B 74 GLU cc_start: 0.8387 (mp0) cc_final: 0.7754 (pm20) REVERT: B 75 ASN cc_start: 0.7248 (OUTLIER) cc_final: 0.6344 (t0) REVERT: C 24 LEU cc_start: 0.7630 (mm) cc_final: 0.6333 (mm) REVERT: C 25 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6736 (mmm-85) REVERT: C 49 ARG cc_start: 0.7177 (tpt90) cc_final: 0.6950 (tpt90) REVERT: C 53 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6629 (mt-10) REVERT: C 62 ARG cc_start: 0.7827 (mmm-85) cc_final: 0.7454 (mmm-85) REVERT: C 63 LYS cc_start: 0.7714 (mmtt) cc_final: 0.7300 (mtmt) REVERT: C 105 LYS cc_start: 0.7504 (mmmt) cc_final: 0.7049 (mttt) REVERT: C 107 ARG cc_start: 0.8868 (tpp80) cc_final: 0.8643 (tpp80) REVERT: D 16 VAL cc_start: 0.7014 (OUTLIER) cc_final: 0.6608 (p) REVERT: D 19 ASP cc_start: 0.8302 (m-30) cc_final: 0.8090 (m-30) REVERT: D 35 GLU cc_start: 0.7367 (pp20) cc_final: 0.4616 (pt0) REVERT: D 37 HIS cc_start: 0.3898 (OUTLIER) cc_final: 0.3495 (t70) REVERT: D 62 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7673 (mmm-85) REVERT: D 71 TYR cc_start: 0.6811 (m-80) cc_final: 0.6534 (m-10) REVERT: D 72 LEU cc_start: 0.8224 (mt) cc_final: 0.7945 (mt) REVERT: D 74 GLU cc_start: 0.8280 (mp0) cc_final: 0.8020 (mt-10) REVERT: D 112 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7971 (tm-30) REVERT: F 98 LYS cc_start: 0.8904 (pttp) cc_final: 0.8637 (ptpp) REVERT: F 104 LEU cc_start: 0.8830 (mt) cc_final: 0.8608 (pp) REVERT: G 42 ARG cc_start: 0.7367 (ttt-90) cc_final: 0.7005 (ttt-90) REVERT: G 53 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6647 (tm-30) REVERT: G 105 LYS cc_start: 0.8413 (mmmt) cc_final: 0.8101 (tttp) REVERT: H 94 PHE cc_start: 0.7069 (t80) cc_final: 0.6851 (t80) REVERT: H 104 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8739 (tt) REVERT: H 105 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8216 (tptp) outliers start: 68 outliers final: 41 residues processed: 325 average time/residue: 0.2587 time to fit residues: 102.5159 Evaluate side-chains 325 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 278 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 40 HIS Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 37 HIS 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 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 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 59 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain G residue 14 THR 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 67 LYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.0170 chunk 15 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 38 optimal weight: 0.0980 chunk 7 optimal weight: 10.0000 chunk 60 optimal weight: 30.0000 chunk 70 optimal weight: 40.0000 chunk 73 optimal weight: 50.0000 chunk 67 optimal weight: 8.9990 overall best weight: 5.2224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5051 moved from start: 1.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7128 Z= 0.252 Angle : 0.863 10.052 9520 Z= 0.450 Chirality : 0.049 0.242 1104 Planarity : 0.005 0.060 1216 Dihedral : 7.215 59.121 955 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 24.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 7.25 % Allowed : 34.88 % Favored : 57.88 % 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: -2.14 (0.28), residues: 832 helix: -0.67 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -2.66 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.001 HIS F 113 PHE 0.013 0.002 PHE E 38 TYR 0.012 0.001 TYR D 27 ARG 0.015 0.001 ARG G 107 *********************** 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 355 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 297 time to evaluate : 0.951 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: 0.5270 (mm-30) cc_final: 0.4920 (mt-10) REVERT: A 50 GLU cc_start: 0.7347 (mp0) cc_final: 0.6901 (mt-10) REVERT: A 63 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7851 (mtmt) REVERT: B 17 LYS cc_start: 0.7571 (mmmm) cc_final: 0.7043 (tptp) REVERT: B 50 GLU cc_start: 0.7123 (mp0) cc_final: 0.6707 (mp0) REVERT: B 53 GLU cc_start: 0.6752 (mt-10) cc_final: 0.6467 (pt0) REVERT: B 62 ARG cc_start: 0.8429 (mmm-85) cc_final: 0.7410 (ttt180) REVERT: B 73 GLN cc_start: 0.7407 (mt0) cc_final: 0.7186 (mp10) REVERT: B 74 GLU cc_start: 0.8446 (mp0) cc_final: 0.7828 (pm20) REVERT: B 75 ASN cc_start: 0.7125 (OUTLIER) cc_final: 0.6129 (t0) REVERT: C 24 LEU cc_start: 0.7640 (mm) cc_final: 0.6461 (mm) REVERT: C 25 ARG cc_start: 0.6633 (OUTLIER) cc_final: 0.6182 (tpt-90) REVERT: C 105 LYS cc_start: 0.7626 (mmmt) cc_final: 0.7168 (mttt) REVERT: C 107 ARG cc_start: 0.8876 (tpp80) cc_final: 0.8627 (tpp80) REVERT: D 16 VAL cc_start: 0.6999 (OUTLIER) cc_final: 0.6595 (p) REVERT: D 19 ASP cc_start: 0.8310 (m-30) cc_final: 0.8100 (m-30) REVERT: D 28 LEU cc_start: 0.5997 (OUTLIER) cc_final: 0.4874 (tp) REVERT: D 35 GLU cc_start: 0.7292 (pp20) cc_final: 0.4668 (pt0) REVERT: D 37 HIS cc_start: 0.3895 (OUTLIER) cc_final: 0.3520 (t70) REVERT: D 62 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7758 (mmm-85) REVERT: D 71 TYR cc_start: 0.6816 (m-80) cc_final: 0.6574 (m-10) REVERT: D 74 GLU cc_start: 0.8296 (mp0) cc_final: 0.8086 (mt-10) REVERT: D 112 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7974 (tm-30) REVERT: E 88 ARG cc_start: 0.7370 (mtp85) cc_final: 0.7148 (mtt-85) REVERT: E 105 LYS cc_start: 0.7469 (mmtt) cc_final: 0.7240 (tppt) REVERT: F 12 ASP cc_start: 0.7948 (m-30) cc_final: 0.7553 (p0) REVERT: F 73 GLN cc_start: 0.7630 (mt0) cc_final: 0.7378 (mt0) REVERT: F 98 LYS cc_start: 0.8950 (pttp) cc_final: 0.8703 (ptpp) REVERT: G 42 ARG cc_start: 0.7357 (ttt-90) cc_final: 0.6987 (ttt-90) REVERT: G 53 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6668 (tm-30) REVERT: G 70 ASP cc_start: 0.7770 (t0) cc_final: 0.7513 (t0) REVERT: G 105 LYS cc_start: 0.8462 (mmmt) cc_final: 0.8135 (tptp) REVERT: H 94 PHE cc_start: 0.6895 (t80) cc_final: 0.6520 (t80) REVERT: H 102 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: H 105 LYS cc_start: 0.8426 (mmmt) cc_final: 0.8082 (tttm) outliers start: 58 outliers final: 40 residues processed: 318 average time/residue: 0.2823 time to fit residues: 108.6414 Evaluate side-chains 322 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 275 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 29 CYS Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 48 SER 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 106 LEU Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 79 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 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 24 LEU 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 67 LYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 93 ASN Chi-restraints excluded: chain H residue 102 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 20.0000 chunk 73 optimal weight: 0.0670 chunk 43 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 113 HIS ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5036 moved from start: 1.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7128 Z= 0.212 Angle : 0.894 14.552 9520 Z= 0.457 Chirality : 0.049 0.255 1104 Planarity : 0.005 0.057 1216 Dihedral : 7.183 57.361 955 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.89 % Favored : 90.99 % Rotamer: Outliers : 6.12 % Allowed : 37.25 % 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: -1.83 (0.28), residues: 832 helix: -0.20 (0.24), residues: 480 sheet: None (None), residues: 0 loop : -2.71 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.001 HIS F 113 PHE 0.011 0.002 PHE E 38 TYR 0.008 0.001 TYR B 27 ARG 0.015 0.001 ARG G 107 *********************** 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 351 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 302 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7462 (mp0) cc_final: 0.6976 (mt-10) REVERT: A 63 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7829 (mtmt) REVERT: B 17 LYS cc_start: 0.7325 (mmmm) cc_final: 0.6740 (tptp) REVERT: B 46 ILE cc_start: 0.5756 (mm) cc_final: 0.5472 (mp) REVERT: B 50 GLU cc_start: 0.7093 (mp0) cc_final: 0.6349 (pp20) REVERT: B 53 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6744 (pt0) REVERT: B 73 GLN cc_start: 0.7436 (mt0) cc_final: 0.7141 (mp10) REVERT: B 74 GLU cc_start: 0.8357 (mp0) cc_final: 0.7776 (pm20) REVERT: B 75 ASN cc_start: 0.7094 (t0) cc_final: 0.6424 (t0) REVERT: C 24 LEU cc_start: 0.7623 (mm) cc_final: 0.6389 (mm) REVERT: C 25 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.6302 (mmm-85) REVERT: C 53 GLU cc_start: 0.6689 (mt-10) cc_final: 0.6435 (pt0) REVERT: C 62 ARG cc_start: 0.7812 (mmm-85) cc_final: 0.7411 (ttt180) REVERT: C 63 LYS cc_start: 0.7547 (mmtt) cc_final: 0.7067 (mtmt) REVERT: C 102 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6911 (tm-30) REVERT: C 105 LYS cc_start: 0.7783 (mmmt) cc_final: 0.7450 (mttt) REVERT: D 16 VAL cc_start: 0.6970 (OUTLIER) cc_final: 0.6575 (p) REVERT: D 19 ASP cc_start: 0.8276 (m-30) cc_final: 0.8074 (m-30) REVERT: D 28 LEU cc_start: 0.5467 (OUTLIER) cc_final: 0.4758 (tp) REVERT: D 32 ILE cc_start: 0.4246 (mm) cc_final: 0.2903 (mp) REVERT: D 35 GLU cc_start: 0.7369 (pp20) cc_final: 0.4844 (pt0) REVERT: D 37 HIS cc_start: 0.3851 (OUTLIER) cc_final: 0.3457 (t70) REVERT: D 49 ARG cc_start: 0.6579 (tpt90) cc_final: 0.6214 (tpt90) REVERT: D 50 GLU cc_start: 0.7062 (mp0) cc_final: 0.5880 (mp0) REVERT: D 53 GLU cc_start: 0.7557 (tt0) cc_final: 0.6987 (pt0) REVERT: D 62 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7493 (mmm-85) REVERT: D 71 TYR cc_start: 0.6888 (m-80) cc_final: 0.6626 (m-10) REVERT: D 74 GLU cc_start: 0.8230 (mp0) cc_final: 0.7904 (mt-10) REVERT: D 112 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8152 (tm-30) REVERT: E 49 ARG cc_start: 0.7393 (mmm160) cc_final: 0.7188 (mmm160) REVERT: F 12 ASP cc_start: 0.7922 (m-30) cc_final: 0.7609 (p0) REVERT: F 37 HIS cc_start: 0.5568 (OUTLIER) cc_final: 0.5203 (m-70) REVERT: F 73 GLN cc_start: 0.7604 (mt0) cc_final: 0.7306 (mt0) REVERT: F 88 ARG cc_start: 0.7193 (mmm-85) cc_final: 0.6909 (mmm-85) REVERT: F 94 PHE cc_start: 0.7625 (t80) cc_final: 0.7240 (t80) REVERT: F 98 LYS cc_start: 0.8848 (pttp) cc_final: 0.8646 (ptpp) REVERT: G 42 ARG cc_start: 0.7387 (ttt-90) cc_final: 0.7132 (ttt-90) REVERT: G 70 ASP cc_start: 0.7805 (t0) cc_final: 0.7564 (t0) REVERT: G 94 PHE cc_start: 0.7085 (t80) cc_final: 0.6757 (t80) REVERT: G 105 LYS cc_start: 0.8454 (mmmt) cc_final: 0.8109 (tptp) REVERT: H 98 LYS cc_start: 0.8519 (ttpp) cc_final: 0.8145 (tptp) REVERT: H 105 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8348 (tttm) outliers start: 49 outliers final: 31 residues processed: 324 average time/residue: 0.2702 time to fit residues: 106.1740 Evaluate side-chains 313 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 275 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 90 LYS 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 27 TYR Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain G residue 24 LEU 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 18 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 80 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 79 optimal weight: 20.0000 chunk 73 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 50 optimal weight: 40.0000 chunk 67 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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** C 37 HIS ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 113 HIS ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5045 moved from start: 1.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7128 Z= 0.291 Angle : 0.963 15.629 9520 Z= 0.496 Chirality : 0.052 0.363 1104 Planarity : 0.006 0.064 1216 Dihedral : 7.418 60.677 955 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 27.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.02 % Favored : 87.86 % Rotamer: Outliers : 6.12 % Allowed : 38.00 % Favored : 55.88 % 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: -2.00 (0.28), residues: 832 helix: -0.42 (0.24), residues: 480 sheet: None (None), residues: 0 loop : -2.64 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.002 HIS F 113 PHE 0.013 0.003 PHE E 38 TYR 0.013 0.001 TYR B 27 ARG 0.015 0.001 ARG G 107 ********************** 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 332 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 283 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7352 (mp0) cc_final: 0.6885 (mt-10) REVERT: A 63 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7864 (mtmt) REVERT: B 17 LYS cc_start: 0.7656 (mmmm) cc_final: 0.7067 (tptp) REVERT: B 22 GLU cc_start: 0.4991 (tp30) cc_final: 0.4707 (tp30) REVERT: B 48 SER cc_start: 0.5749 (t) cc_final: 0.5536 (m) REVERT: B 50 GLU cc_start: 0.7208 (mp0) cc_final: 0.6105 (pp20) REVERT: B 53 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6891 (pt0) REVERT: B 71 TYR cc_start: 0.6812 (m-80) cc_final: 0.6522 (m-80) REVERT: B 74 GLU cc_start: 0.8306 (mp0) cc_final: 0.7585 (pm20) REVERT: B 75 ASN cc_start: 0.7206 (OUTLIER) cc_final: 0.6383 (t0) REVERT: C 24 LEU cc_start: 0.7695 (mm) cc_final: 0.6409 (mm) REVERT: C 25 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.6343 (mmm-85) REVERT: C 53 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6563 (pt0) REVERT: C 63 LYS cc_start: 0.7751 (mmtt) cc_final: 0.7176 (mtmt) REVERT: C 105 LYS cc_start: 0.7546 (mmmt) cc_final: 0.7034 (mttt) REVERT: C 107 ARG cc_start: 0.8846 (tpp80) cc_final: 0.8614 (tpp80) REVERT: D 12 ASP cc_start: 0.8731 (m-30) cc_final: 0.8524 (p0) REVERT: D 16 VAL cc_start: 0.6898 (OUTLIER) cc_final: 0.6536 (p) REVERT: D 19 ASP cc_start: 0.8326 (m-30) cc_final: 0.8111 (m-30) REVERT: D 28 LEU cc_start: 0.5521 (OUTLIER) cc_final: 0.4296 (tp) REVERT: D 35 GLU cc_start: 0.7324 (pp20) cc_final: 0.5092 (pt0) REVERT: D 37 HIS cc_start: 0.3900 (OUTLIER) cc_final: 0.3522 (t70) REVERT: D 62 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7696 (mmm-85) REVERT: D 71 TYR cc_start: 0.6850 (m-80) cc_final: 0.6591 (m-10) REVERT: D 74 GLU cc_start: 0.8187 (mp0) cc_final: 0.7842 (mt-10) REVERT: D 84 GLU cc_start: 0.7039 (pp20) cc_final: 0.6682 (pp20) REVERT: D 112 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7967 (tm-30) REVERT: F 12 ASP cc_start: 0.8201 (m-30) cc_final: 0.7693 (p0) REVERT: F 73 GLN cc_start: 0.7687 (mt0) cc_final: 0.7392 (mt0) REVERT: F 94 PHE cc_start: 0.7502 (t80) cc_final: 0.7106 (t80) REVERT: G 42 ARG cc_start: 0.7247 (ttt-90) cc_final: 0.6813 (ttt-90) REVERT: G 53 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6745 (tm-30) REVERT: G 70 ASP cc_start: 0.7762 (t0) cc_final: 0.7536 (t0) REVERT: G 94 PHE cc_start: 0.7792 (t80) cc_final: 0.7467 (t80) REVERT: G 105 LYS cc_start: 0.8449 (mmmt) cc_final: 0.8081 (tttp) outliers start: 49 outliers final: 36 residues processed: 303 average time/residue: 0.2581 time to fit residues: 95.4186 Evaluate side-chains 311 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 269 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 90 LYS 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 27 TYR Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain G residue 24 LEU 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 102 GLU Chi-restraints excluded: chain H residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 113 HIS ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 HIS ** 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 = 0.3970 r_free = 0.3970 target = 0.132778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.119289 restraints weight = 21355.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.122016 restraints weight = 13952.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.123961 restraints weight = 9970.500| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 1.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7128 Z= 0.247 Angle : 0.961 15.549 9520 Z= 0.490 Chirality : 0.050 0.221 1104 Planarity : 0.005 0.050 1216 Dihedral : 7.353 58.717 955 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 24.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.46 % Favored : 89.42 % Rotamer: Outliers : 5.38 % Allowed : 39.12 % Favored : 55.50 % 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: -1.91 (0.28), residues: 832 helix: -0.36 (0.24), residues: 472 sheet: None (None), residues: 0 loop : -2.54 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.022 0.002 HIS F 113 PHE 0.023 0.003 PHE E 94 TYR 0.010 0.001 TYR B 27 ARG 0.014 0.001 ARG G 107 =============================================================================== Job complete usr+sys time: 2227.65 seconds wall clock time: 40 minutes 18.50 seconds (2418.50 seconds total)