Starting phenix.real_space_refine on Tue Mar 3 13:06:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q66_13853/03_2026/7q66_13853.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q66_13853/03_2026/7q66_13853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q66_13853/03_2026/7q66_13853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q66_13853/03_2026/7q66_13853.map" model { file = "/net/cci-nas-00/data/ceres_data/7q66_13853/03_2026/7q66_13853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q66_13853/03_2026/7q66_13853.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 2959 2.51 5 N 814 2.21 5 O 1034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4807 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 262 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "B" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 175 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, U, D, F, H, J, L, N, P, R, T, V Time building chain proxies: 0.53, per 1000 atoms: 0.11 Number of scatterers: 4807 At special positions: 0 Unit cell: (66.15, 61.95, 72.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1034 8.00 N 814 7.00 C 2959 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: 0.42 Conformation dependent library (CDL) restraints added in 221.5 milliseconds 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 53.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 92 removed outlier: 6.095A pdb=" N ALA A 88 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU C 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR A 90 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA C 88 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU E 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR C 90 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA E 88 " --> pdb=" O ASN G 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU G 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR E 90 " --> pdb=" O LEU G 91 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA G 88 " --> pdb=" O ASN I 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU I 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR G 90 " --> pdb=" O LEU I 91 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA I 88 " --> pdb=" O ASN K 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU K 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N THR I 90 " --> pdb=" O LEU K 91 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA K 88 " --> pdb=" O ASN M 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU M 91 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N THR K 90 " --> pdb=" O LEU M 91 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA M 88 " --> pdb=" O ASN O 89 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU O 91 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR M 90 " --> pdb=" O LEU O 91 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA O 88 " --> pdb=" O ASN Q 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU Q 91 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR O 90 " --> pdb=" O LEU Q 91 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA Q 88 " --> pdb=" O ASN S 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU S 91 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR Q 90 " --> pdb=" O LEU S 91 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA S 88 " --> pdb=" O ASN U 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU U 91 " --> pdb=" O ALA S 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR S 90 " --> pdb=" O LEU U 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 removed outlier: 6.382A pdb=" N ALA A 95 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA C 95 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA E 95 " --> pdb=" O SER G 96 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA G 95 " --> pdb=" O SER I 96 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA I 95 " --> pdb=" O SER K 96 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA K 95 " --> pdb=" O SER M 96 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA M 95 " --> pdb=" O SER O 96 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA O 95 " --> pdb=" O SER Q 96 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA Q 95 " --> pdb=" O SER S 96 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA S 95 " --> pdb=" O SER U 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 112 removed outlier: 6.882A pdb=" N ASN A 106 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE C 109 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA A 108 " --> pdb=" O PHE C 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN C 111 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA A 110 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN C 106 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N PHE E 109 " --> pdb=" O ASN C 106 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA C 108 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN E 111 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA C 110 " --> pdb=" O GLN E 111 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN E 106 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE G 109 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA E 108 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN G 111 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA E 110 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN G 106 " --> pdb=" O ASN I 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE I 109 " --> pdb=" O ASN G 106 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA G 108 " --> pdb=" O PHE I 109 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLN I 111 " --> pdb=" O ALA G 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA G 110 " --> pdb=" O GLN I 111 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN I 106 " --> pdb=" O ASN K 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE K 109 " --> pdb=" O ASN I 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA I 108 " --> pdb=" O PHE K 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN K 111 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA I 110 " --> pdb=" O GLN K 111 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN K 106 " --> pdb=" O ASN M 107 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N PHE M 109 " --> pdb=" O ASN K 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA K 108 " --> pdb=" O PHE M 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN M 111 " --> pdb=" O ALA K 108 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA K 110 " --> pdb=" O GLN M 111 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN M 106 " --> pdb=" O ASN O 107 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N PHE O 109 " --> pdb=" O ASN M 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA M 108 " --> pdb=" O PHE O 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN O 111 " --> pdb=" O ALA M 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA M 110 " --> pdb=" O GLN O 111 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN O 106 " --> pdb=" O ASN Q 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE Q 109 " --> pdb=" O ASN O 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA O 108 " --> pdb=" O PHE Q 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN Q 111 " --> pdb=" O ALA O 108 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA O 110 " --> pdb=" O GLN Q 111 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN Q 106 " --> pdb=" O ASN S 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE S 109 " --> pdb=" O ASN Q 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA Q 108 " --> pdb=" O PHE S 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN S 111 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA Q 110 " --> pdb=" O GLN S 111 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN S 106 " --> pdb=" O ASN U 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE U 109 " --> pdb=" O ASN S 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA S 108 " --> pdb=" O PHE U 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN U 111 " --> pdb=" O ALA S 108 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA S 110 " --> pdb=" O GLN U 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 115 through 120 removed outlier: 6.517A pdb=" N THR A 115 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY C 118 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A 117 " --> pdb=" O GLY C 118 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N PHE C 120 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN A 119 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR C 115 " --> pdb=" O GLY E 116 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLY E 118 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE C 117 " --> pdb=" O GLY E 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE E 120 " --> pdb=" O PHE C 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN C 119 " --> pdb=" O PHE E 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR E 115 " --> pdb=" O GLY G 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY G 118 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE E 117 " --> pdb=" O GLY G 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE G 120 " --> pdb=" O PHE E 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN E 119 " --> pdb=" O PHE G 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR G 115 " --> pdb=" O GLY I 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY I 118 " --> pdb=" O THR G 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE G 117 " --> pdb=" O GLY I 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE I 120 " --> pdb=" O PHE G 117 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASN G 119 " --> pdb=" O PHE I 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR I 115 " --> pdb=" O GLY K 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY K 118 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE I 117 " --> pdb=" O GLY K 118 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N PHE K 120 " --> pdb=" O PHE I 117 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASN I 119 " --> pdb=" O PHE K 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR K 115 " --> pdb=" O GLY M 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY M 118 " --> pdb=" O THR K 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE K 117 " --> pdb=" O GLY M 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE M 120 " --> pdb=" O PHE K 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN K 119 " --> pdb=" O PHE M 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR M 115 " --> pdb=" O GLY O 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY O 118 " --> pdb=" O THR M 115 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE M 117 " --> pdb=" O GLY O 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE O 120 " --> pdb=" O PHE M 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN M 119 " --> pdb=" O PHE O 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR O 115 " --> pdb=" O GLY Q 116 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N GLY Q 118 " --> pdb=" O THR O 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE O 117 " --> pdb=" O GLY Q 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE Q 120 " --> pdb=" O PHE O 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN O 119 " --> pdb=" O PHE Q 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR Q 115 " --> pdb=" O GLY S 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY S 118 " --> pdb=" O THR Q 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE Q 117 " --> pdb=" O GLY S 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE S 120 " --> pdb=" O PHE Q 117 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASN Q 119 " --> pdb=" O PHE S 120 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR S 115 " --> pdb=" O GLY U 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY U 118 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE S 117 " --> pdb=" O GLY U 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE U 120 " --> pdb=" O PHE S 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN S 119 " --> pdb=" O PHE U 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 87 through 92 Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 108 160 hydrogen bonds defined for protein. 480 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: 0.88 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.27: 803 1.27 - 1.34: 803 1.34 - 1.41: 594 1.41 - 1.47: 979 1.47 - 1.54: 1705 Bond restraints: 4884 Sorted by residual: bond pdb=" CB THR A 90 " pdb=" CG2 THR A 90 " ideal model delta sigma weight residual 1.521 1.354 0.167 3.30e-02 9.18e+02 2.57e+01 bond pdb=" CB THR C 90 " pdb=" CG2 THR C 90 " ideal model delta sigma weight residual 1.521 1.354 0.167 3.30e-02 9.18e+02 2.56e+01 bond pdb=" CB THR K 90 " pdb=" CG2 THR K 90 " ideal model delta sigma weight residual 1.521 1.354 0.167 3.30e-02 9.18e+02 2.56e+01 bond pdb=" CB THR O 90 " pdb=" CG2 THR O 90 " ideal model delta sigma weight residual 1.521 1.354 0.167 3.30e-02 9.18e+02 2.56e+01 bond pdb=" CB THR M 90 " pdb=" CG2 THR M 90 " ideal model delta sigma weight residual 1.521 1.354 0.167 3.30e-02 9.18e+02 2.56e+01 ... (remaining 4879 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 5817 1.89 - 3.78: 563 3.78 - 5.67: 176 5.67 - 7.56: 33 7.56 - 9.45: 22 Bond angle restraints: 6611 Sorted by residual: angle pdb=" N LYS A 113 " pdb=" CA LYS A 113 " pdb=" C LYS A 113 " ideal model delta sigma weight residual 111.53 119.09 -7.56 2.18e+00 2.10e-01 1.20e+01 angle pdb=" N LYS G 113 " pdb=" CA LYS G 113 " pdb=" C LYS G 113 " ideal model delta sigma weight residual 111.53 119.08 -7.55 2.18e+00 2.10e-01 1.20e+01 angle pdb=" N LYS U 113 " pdb=" CA LYS U 113 " pdb=" C LYS U 113 " ideal model delta sigma weight residual 111.53 119.08 -7.55 2.18e+00 2.10e-01 1.20e+01 angle pdb=" N LYS K 113 " pdb=" CA LYS K 113 " pdb=" C LYS K 113 " ideal model delta sigma weight residual 111.53 119.08 -7.55 2.18e+00 2.10e-01 1.20e+01 angle pdb=" N LYS O 113 " pdb=" CA LYS O 113 " pdb=" C LYS O 113 " ideal model delta sigma weight residual 111.53 119.07 -7.54 2.18e+00 2.10e-01 1.20e+01 ... (remaining 6606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.71: 2376 12.71 - 25.42: 209 25.42 - 38.13: 66 38.13 - 50.84: 11 50.84 - 63.55: 11 Dihedral angle restraints: 2673 sinusoidal: 847 harmonic: 1826 Sorted by residual: dihedral pdb=" C LYS K 113 " pdb=" N LYS K 113 " pdb=" CA LYS K 113 " pdb=" CB LYS K 113 " ideal model delta harmonic sigma weight residual -122.60 -131.58 8.98 0 2.50e+00 1.60e-01 1.29e+01 dihedral pdb=" C LYS M 113 " pdb=" N LYS M 113 " pdb=" CA LYS M 113 " pdb=" CB LYS M 113 " ideal model delta harmonic sigma weight residual -122.60 -131.54 8.94 0 2.50e+00 1.60e-01 1.28e+01 dihedral pdb=" C LYS I 113 " pdb=" N LYS I 113 " pdb=" CA LYS I 113 " pdb=" CB LYS I 113 " ideal model delta harmonic sigma weight residual -122.60 -131.54 8.94 0 2.50e+00 1.60e-01 1.28e+01 ... (remaining 2670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 638 0.096 - 0.191: 66 0.191 - 0.287: 33 0.287 - 0.383: 11 0.383 - 0.478: 22 Chirality restraints: 770 Sorted by residual: chirality pdb=" CG LEU B 101 " pdb=" CB LEU B 101 " pdb=" CD1 LEU B 101 " pdb=" CD2 LEU B 101 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CG LEU T 101 " pdb=" CB LEU T 101 " pdb=" CD1 LEU T 101 " pdb=" CD2 LEU T 101 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CG LEU F 101 " pdb=" CB LEU F 101 " pdb=" CD1 LEU F 101 " pdb=" CD2 LEU F 101 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.71e+00 ... (remaining 767 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 110 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C ALA Q 110 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA Q 110 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN Q 111 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA U 110 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C ALA U 110 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA U 110 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN U 111 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA S 110 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C ALA S 110 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA S 110 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN S 111 " 0.014 2.00e-02 2.50e+03 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1632 2.80 - 3.33: 4132 3.33 - 3.85: 9177 3.85 - 4.38: 11100 4.38 - 4.90: 21252 Nonbonded interactions: 47293 Sorted by model distance: nonbonded pdb=" ND2 ASN A 106 " pdb=" OG SER B 103 " model vdw 2.277 3.120 nonbonded pdb=" ND2 ASN G 106 " pdb=" OG SER H 103 " model vdw 2.277 3.120 nonbonded pdb=" ND2 ASN S 106 " pdb=" OG SER T 103 " model vdw 2.278 3.120 nonbonded pdb=" ND2 ASN O 106 " pdb=" OG SER P 103 " model vdw 2.278 3.120 nonbonded pdb=" ND2 ASN U 106 " pdb=" OG SER V 103 " model vdw 2.278 3.120 ... (remaining 47288 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.020 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:8.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 : 0.021 0.167 4884 Z= 0.896 Angle : 1.424 9.452 6611 Z= 0.782 Chirality : 0.115 0.478 770 Planarity : 0.007 0.024 880 Dihedral : 12.578 63.547 1507 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.52 % Allowed : 4.35 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.18 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.034 0.006 PHE S 109 Details of bonding type rmsd covalent geometry : bond 0.02061 ( 4884) covalent geometry : angle 1.42395 ( 6611) hydrogen bonds : bond 0.13764 ( 160) hydrogen bonds : angle 8.38790 ( 480) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 258 time to evaluate : 0.222 Fit side-chains REVERT: H 105 GLN cc_start: 0.8627 (tt0) cc_final: 0.8409 (tt0) REVERT: K 107 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8226 (p0) REVERT: M 105 GLN cc_start: 0.8601 (tm130) cc_final: 0.8332 (tm-30) REVERT: O 107 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8262 (p0) REVERT: P 105 GLN cc_start: 0.8903 (tt0) cc_final: 0.8616 (tt0) REVERT: R 87 THR cc_start: 0.8477 (p) cc_final: 0.8115 (t) REVERT: S 105 GLN cc_start: 0.8773 (tm130) cc_final: 0.8526 (tm130) outliers start: 33 outliers final: 6 residues processed: 269 average time/residue: 0.2179 time to fit residues: 63.5521 Evaluate side-chains 184 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 101 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain R residue 101 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN B 105 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN E 112 ASN F 105 GLN G 112 ASN H 105 GLN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 ASN K 112 ASN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 105 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN T 105 GLN U 106 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.072265 restraints weight = 7742.892| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.69 r_work: 0.3038 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4884 Z= 0.189 Angle : 0.706 9.581 6611 Z= 0.338 Chirality : 0.045 0.211 770 Planarity : 0.003 0.019 880 Dihedral : 6.352 47.856 676 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 17.39 % Allowed : 15.81 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.25 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.12), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE G 109 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 4884) covalent geometry : angle 0.70610 ( 6611) hydrogen bonds : bond 0.04269 ( 160) hydrogen bonds : angle 5.58332 ( 480) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 208 time to evaluate : 0.123 Fit side-chains REVERT: B 91 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8349 (tt) REVERT: D 91 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8183 (tt) REVERT: H 105 GLN cc_start: 0.8911 (tt0) cc_final: 0.8710 (tt0) REVERT: I 107 ASN cc_start: 0.8706 (p0) cc_final: 0.8186 (p0) REVERT: J 91 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8311 (tt) REVERT: K 107 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8297 (p0) REVERT: M 106 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8110 (p0) REVERT: M 107 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8600 (p0) REVERT: M 119 ASN cc_start: 0.8697 (m110) cc_final: 0.8419 (m-40) REVERT: R 91 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8065 (tt) REVERT: T 91 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8394 (mm) outliers start: 88 outliers final: 50 residues processed: 249 average time/residue: 0.1536 time to fit residues: 43.0680 Evaluate side-chains 230 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 172 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 106 ASN Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 100 SER Chi-restraints excluded: chain V residue 101 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 12 optimal weight: 0.0370 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN B 89 ASN B 105 GLN B 107 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN D 89 ASN F 89 ASN F 105 GLN H 89 ASN H 105 GLN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN L 89 ASN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 ASN N 89 ASN N 105 GLN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 119 ASN P 89 ASN R 89 ASN R 105 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.079444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.071295 restraints weight = 7623.630| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.66 r_work: 0.3033 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4884 Z= 0.182 Angle : 0.689 9.249 6611 Z= 0.317 Chirality : 0.045 0.209 770 Planarity : 0.003 0.014 880 Dihedral : 5.883 58.818 672 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 13.83 % Allowed : 23.12 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.14), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE U 109 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 4884) covalent geometry : angle 0.68891 ( 6611) hydrogen bonds : bond 0.02981 ( 160) hydrogen bonds : angle 4.93593 ( 480) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 188 time to evaluate : 0.125 Fit side-chains REVERT: B 91 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8425 (tt) REVERT: C 106 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8724 (p0) REVERT: D 91 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8281 (tt) REVERT: E 101 LEU cc_start: 0.9367 (tt) cc_final: 0.9122 (tm) REVERT: F 91 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8323 (tt) REVERT: I 96 SER cc_start: 0.9122 (t) cc_final: 0.8837 (p) REVERT: J 91 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8359 (tt) REVERT: M 106 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8311 (p0) REVERT: N 91 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8288 (tt) REVERT: O 107 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8586 (p0) REVERT: R 91 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8152 (tt) REVERT: S 107 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8276 (p0) REVERT: T 91 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8399 (mm) outliers start: 70 outliers final: 46 residues processed: 219 average time/residue: 0.1639 time to fit residues: 40.0518 Evaluate side-chains 225 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 168 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 100 SER Chi-restraints excluded: chain V residue 101 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 13 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN B 89 ASN D 89 ASN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN I 112 ASN J 89 ASN J 105 GLN J 107 ASN K 112 ASN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 ASN O 119 ASN P 89 ASN R 89 ASN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 105 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.075740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.067466 restraints weight = 7719.020| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.64 r_work: 0.2951 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4884 Z= 0.241 Angle : 0.689 8.993 6611 Z= 0.315 Chirality : 0.045 0.240 770 Planarity : 0.002 0.015 880 Dihedral : 5.369 26.031 670 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 15.02 % Allowed : 22.33 % Favored : 62.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.23 (0.14), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.001 PHE U 109 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 4884) covalent geometry : angle 0.68922 ( 6611) hydrogen bonds : bond 0.02786 ( 160) hydrogen bonds : angle 4.79445 ( 480) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 179 time to evaluate : 0.142 Fit side-chains REVERT: B 91 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8402 (tt) REVERT: C 106 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8599 (p0) REVERT: D 91 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8253 (tt) REVERT: D 106 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8404 (m110) REVERT: E 101 LEU cc_start: 0.9391 (tt) cc_final: 0.9123 (tm) REVERT: E 106 ASN cc_start: 0.9005 (OUTLIER) cc_final: 0.8648 (p0) REVERT: F 91 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8313 (tt) REVERT: G 94 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8909 (m) REVERT: I 96 SER cc_start: 0.9137 (OUTLIER) cc_final: 0.8896 (p) REVERT: I 99 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.8957 (p) REVERT: J 91 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8327 (tt) REVERT: M 106 ASN cc_start: 0.9099 (OUTLIER) cc_final: 0.8391 (p0) REVERT: N 91 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8291 (tt) REVERT: N 106 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8259 (m110) REVERT: O 107 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8497 (p0) REVERT: R 91 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8179 (tt) REVERT: R 106 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8412 (m110) REVERT: S 107 ASN cc_start: 0.8886 (OUTLIER) cc_final: 0.8367 (p0) REVERT: T 91 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8426 (mm) outliers start: 76 outliers final: 47 residues processed: 214 average time/residue: 0.1361 time to fit residues: 33.0072 Evaluate side-chains 224 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 159 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 100 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 32 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN J 105 GLN ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 ASN N 105 GLN N 107 ASN P 89 ASN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.076817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.068625 restraints weight = 7731.564| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.66 r_work: 0.2976 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4884 Z= 0.176 Angle : 0.654 8.655 6611 Z= 0.296 Chirality : 0.043 0.218 770 Planarity : 0.002 0.016 880 Dihedral : 5.234 27.231 670 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 14.23 % Allowed : 24.11 % Favored : 61.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.23 (0.14), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE Q 109 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 4884) covalent geometry : angle 0.65418 ( 6611) hydrogen bonds : bond 0.02482 ( 160) hydrogen bonds : angle 4.72809 ( 480) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 174 time to evaluate : 0.169 Fit side-chains REVERT: C 106 ASN cc_start: 0.9137 (OUTLIER) cc_final: 0.8645 (p0) REVERT: D 87 THR cc_start: 0.9336 (t) cc_final: 0.9117 (t) REVERT: D 91 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8260 (tt) REVERT: E 101 LEU cc_start: 0.9365 (tt) cc_final: 0.9090 (tm) REVERT: F 91 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8305 (tt) REVERT: I 96 SER cc_start: 0.9086 (OUTLIER) cc_final: 0.8836 (p) REVERT: I 99 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.8983 (p) REVERT: J 91 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8326 (tt) REVERT: M 106 ASN cc_start: 0.9113 (OUTLIER) cc_final: 0.8593 (p0) REVERT: N 91 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8292 (tt) REVERT: N 106 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8191 (m110) REVERT: O 107 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8359 (p0) REVERT: P 91 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8266 (tt) REVERT: R 91 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8200 (tt) REVERT: R 106 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8370 (m110) REVERT: T 91 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8233 (tt) outliers start: 72 outliers final: 47 residues processed: 207 average time/residue: 0.1474 time to fit residues: 34.4166 Evaluate side-chains 227 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 166 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 100 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 41 optimal weight: 6.9990 chunk 10 optimal weight: 0.1980 chunk 50 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 12 optimal weight: 0.0170 chunk 2 optimal weight: 0.0170 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN G 112 ASN I 112 ASN J 105 GLN J 107 ASN ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN L 107 ASN M 112 ASN N 105 GLN P 89 ASN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.079520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.071525 restraints weight = 7866.782| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.74 r_work: 0.3044 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4884 Z= 0.124 Angle : 0.631 9.244 6611 Z= 0.281 Chirality : 0.041 0.196 770 Planarity : 0.002 0.013 880 Dihedral : 4.894 30.070 668 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 13.04 % Allowed : 24.70 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.24 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE Q 109 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4884) covalent geometry : angle 0.63059 ( 6611) hydrogen bonds : bond 0.02150 ( 160) hydrogen bonds : angle 4.62007 ( 480) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 168 time to evaluate : 0.197 Fit side-chains REVERT: C 106 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8690 (p0) REVERT: D 87 THR cc_start: 0.9343 (t) cc_final: 0.9070 (t) REVERT: F 91 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8328 (tt) REVERT: G 94 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8952 (m) REVERT: I 96 SER cc_start: 0.9069 (t) cc_final: 0.8818 (p) REVERT: I 99 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.9028 (p) REVERT: J 91 LEU cc_start: 0.8561 (mm) cc_final: 0.8345 (tt) REVERT: K 107 ASN cc_start: 0.8784 (m110) cc_final: 0.8544 (m110) REVERT: M 101 LEU cc_start: 0.9252 (tt) cc_final: 0.9003 (tm) REVERT: M 106 ASN cc_start: 0.9079 (OUTLIER) cc_final: 0.8631 (p0) REVERT: N 87 THR cc_start: 0.9139 (t) cc_final: 0.8938 (m) REVERT: N 106 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8194 (m110) REVERT: O 107 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8344 (p0) REVERT: R 91 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8197 (tt) REVERT: R 106 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8393 (m110) REVERT: T 91 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8118 (tt) outliers start: 66 outliers final: 41 residues processed: 202 average time/residue: 0.1471 time to fit residues: 33.7341 Evaluate side-chains 209 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 158 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 100 SER Chi-restraints excluded: chain V residue 101 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 9 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 17 optimal weight: 0.0670 chunk 20 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 overall best weight: 3.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN F 105 GLN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 GLN ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 ASN P 89 ASN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN T 105 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.072599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.064674 restraints weight = 7874.245| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.64 r_work: 0.2896 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 4884 Z= 0.345 Angle : 0.749 10.817 6611 Z= 0.344 Chirality : 0.049 0.301 770 Planarity : 0.003 0.018 880 Dihedral : 5.080 27.566 666 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 14.03 % Allowed : 25.89 % Favored : 60.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.09 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.002 PHE Q 109 Details of bonding type rmsd covalent geometry : bond 0.00771 ( 4884) covalent geometry : angle 0.74950 ( 6611) hydrogen bonds : bond 0.02790 ( 160) hydrogen bonds : angle 4.60672 ( 480) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 165 time to evaluate : 0.179 Fit side-chains REVERT: C 106 ASN cc_start: 0.9129 (OUTLIER) cc_final: 0.8668 (p0) REVERT: D 87 THR cc_start: 0.9308 (t) cc_final: 0.9013 (t) REVERT: D 106 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8389 (m110) REVERT: E 101 LEU cc_start: 0.9394 (tt) cc_final: 0.9145 (tm) REVERT: G 94 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8971 (m) REVERT: I 96 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8864 (p) REVERT: I 99 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.9066 (p) REVERT: K 107 ASN cc_start: 0.8931 (m110) cc_final: 0.8716 (m110) REVERT: M 106 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8630 (p0) REVERT: N 106 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8171 (m110) REVERT: O 107 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8341 (p0) REVERT: R 91 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8191 (tt) REVERT: R 106 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8369 (m110) REVERT: T 91 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8533 (mm) outliers start: 71 outliers final: 48 residues processed: 198 average time/residue: 0.1659 time to fit residues: 36.8369 Evaluate side-chains 217 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 158 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 100 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN F 105 GLN G 112 ASN I 112 ASN J 105 GLN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN M 112 ASN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 ASN R 105 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN T 105 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.076594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.068643 restraints weight = 7990.212| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.73 r_work: 0.2985 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4884 Z= 0.167 Angle : 0.674 9.701 6611 Z= 0.302 Chirality : 0.044 0.246 770 Planarity : 0.002 0.016 880 Dihedral : 4.950 31.746 666 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 12.45 % Allowed : 26.88 % Favored : 60.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.16 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE Q 109 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 4884) covalent geometry : angle 0.67432 ( 6611) hydrogen bonds : bond 0.02334 ( 160) hydrogen bonds : angle 4.58221 ( 480) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 167 time to evaluate : 0.162 Fit side-chains REVERT: C 106 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.8650 (p0) REVERT: D 87 THR cc_start: 0.9309 (t) cc_final: 0.9061 (t) REVERT: E 101 LEU cc_start: 0.9373 (tt) cc_final: 0.9145 (tm) REVERT: K 99 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.9067 (p) REVERT: K 112 ASN cc_start: 0.9041 (t0) cc_final: 0.8830 (t0) REVERT: M 101 LEU cc_start: 0.9255 (tt) cc_final: 0.9017 (tm) REVERT: N 87 THR cc_start: 0.9196 (t) cc_final: 0.8951 (m) REVERT: N 101 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9175 (tt) REVERT: N 106 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8135 (m110) REVERT: O 107 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8348 (p0) REVERT: R 91 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8253 (tt) REVERT: R 106 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8375 (m110) REVERT: S 107 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8649 (p0) REVERT: T 91 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8135 (tt) outliers start: 63 outliers final: 40 residues processed: 199 average time/residue: 0.1471 time to fit residues: 33.0396 Evaluate side-chains 206 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 157 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 29 optimal weight: 8.9990 chunk 21 optimal weight: 0.0170 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.0030 chunk 40 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.8032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 107 ASN A 112 ASN B 107 ASN E 105 GLN E 112 ASN F 105 GLN G 119 ASN I 105 GLN J 105 GLN J 107 ASN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 ASN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.078568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.070585 restraints weight = 7843.331| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.71 r_work: 0.3040 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4884 Z= 0.141 Angle : 0.657 9.278 6611 Z= 0.293 Chirality : 0.042 0.209 770 Planarity : 0.002 0.016 880 Dihedral : 4.841 34.958 666 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 11.07 % Allowed : 28.66 % Favored : 60.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.22 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.12), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE Q 109 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4884) covalent geometry : angle 0.65653 ( 6611) hydrogen bonds : bond 0.02166 ( 160) hydrogen bonds : angle 4.44107 ( 480) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 156 time to evaluate : 0.191 Fit side-chains REVERT: C 106 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8676 (p0) REVERT: D 87 THR cc_start: 0.9309 (t) cc_final: 0.9069 (t) REVERT: D 106 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8318 (m110) REVERT: E 101 LEU cc_start: 0.9377 (tt) cc_final: 0.9148 (tm) REVERT: J 91 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8323 (tt) REVERT: J 97 THR cc_start: 0.9188 (m) cc_final: 0.8984 (t) REVERT: N 101 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9166 (tt) REVERT: N 106 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8135 (m110) REVERT: O 107 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8319 (p0) REVERT: R 106 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8349 (m110) REVERT: S 107 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8565 (p0) REVERT: T 91 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8188 (tt) REVERT: U 119 ASN cc_start: 0.8908 (m110) cc_final: 0.8657 (m-40) REVERT: V 106 ASN cc_start: 0.8548 (m110) cc_final: 0.8195 (t0) outliers start: 56 outliers final: 37 residues processed: 189 average time/residue: 0.1622 time to fit residues: 34.5329 Evaluate side-chains 200 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 43 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 2 optimal weight: 0.0370 chunk 20 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN E 112 ASN F 105 GLN G 112 ASN I 112 ASN J 105 GLN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN M 112 ASN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 105 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.080207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.072381 restraints weight = 7641.766| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.67 r_work: 0.3072 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4884 Z= 0.129 Angle : 0.657 9.399 6611 Z= 0.290 Chirality : 0.041 0.207 770 Planarity : 0.002 0.019 880 Dihedral : 4.805 42.853 666 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 11.07 % Allowed : 28.85 % Favored : 60.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.25 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE H 92 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4884) covalent geometry : angle 0.65689 ( 6611) hydrogen bonds : bond 0.02063 ( 160) hydrogen bonds : angle 4.36265 ( 480) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 163 time to evaluate : 0.197 Fit side-chains REVERT: B 97 THR cc_start: 0.9203 (m) cc_final: 0.8880 (t) REVERT: C 106 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8682 (p0) REVERT: D 87 THR cc_start: 0.9288 (t) cc_final: 0.9072 (t) REVERT: E 101 LEU cc_start: 0.9378 (tt) cc_final: 0.9141 (tm) REVERT: I 94 THR cc_start: 0.9265 (t) cc_final: 0.8857 (m) REVERT: I 96 SER cc_start: 0.9110 (t) cc_final: 0.8816 (p) REVERT: J 91 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8349 (tt) REVERT: K 99 THR cc_start: 0.9068 (p) cc_final: 0.8865 (m) REVERT: K 112 ASN cc_start: 0.9016 (t0) cc_final: 0.8794 (t0) REVERT: N 106 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.8103 (m110) REVERT: O 107 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8190 (p0) REVERT: R 106 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8356 (m110) REVERT: S 107 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8513 (p0) REVERT: T 91 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8202 (tt) REVERT: U 119 ASN cc_start: 0.8914 (m110) cc_final: 0.8660 (m-40) REVERT: V 106 ASN cc_start: 0.8530 (m110) cc_final: 0.8180 (t0) outliers start: 56 outliers final: 40 residues processed: 194 average time/residue: 0.1511 time to fit residues: 33.1030 Evaluate side-chains 207 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 100 SER Chi-restraints excluded: chain V residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN B 107 ASN E 107 ASN E 112 ASN F 105 GLN J 105 GLN J 107 ASN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 ASN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN T 105 GLN ** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.068694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.060652 restraints weight = 8083.652| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.65 r_work: 0.2817 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.097 4884 Z= 0.659 Angle : 0.927 11.635 6611 Z= 0.446 Chirality : 0.061 0.397 770 Planarity : 0.004 0.023 880 Dihedral : 5.416 22.136 664 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 11.07 % Allowed : 29.45 % Favored : 59.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.16 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.003 PHE K 109 Details of bonding type rmsd covalent geometry : bond 0.01475 ( 4884) covalent geometry : angle 0.92744 ( 6611) hydrogen bonds : bond 0.03349 ( 160) hydrogen bonds : angle 4.77410 ( 480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1553.08 seconds wall clock time: 27 minutes 36.97 seconds (1656.97 seconds total)