Starting phenix.real_space_refine on Tue Mar 3 12:23:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yat_33719/03_2026/7yat_33719.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yat_33719/03_2026/7yat_33719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yat_33719/03_2026/7yat_33719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yat_33719/03_2026/7yat_33719.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yat_33719/03_2026/7yat_33719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yat_33719/03_2026/7yat_33719.map" } resolution = 2.2 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= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 2568 2.51 5 N 744 2.21 5 O 721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s 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: 4129 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, X, Y Time building chain proxies: 0.46, per 1000 atoms: 0.11 Number of scatterers: 4129 At special positions: 0 Unit cell: (77.19, 77.19, 47.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 721 8.00 N 744 7.00 C 2568 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: 0.31 Conformation dependent library (CDL) restraints added in 166.2 milliseconds 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 864 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 43.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 121 through 122 removed outlier: 6.521A pdb=" N VAL B 121 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 121 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 125 through 130 removed outlier: 6.629A pdb=" N GLY B 126 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N MET E 129 " --> pdb=" O GLY B 126 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR B 128 " --> pdb=" O MET E 129 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU B 125 " --> pdb=" O GLY C 126 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N TYR C 128 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY B 127 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU C 130 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N MET B 129 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU C 125 " --> pdb=" O GLY D 126 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR D 128 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY C 127 " --> pdb=" O TYR D 128 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU D 130 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N MET C 129 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU A 125 " --> pdb=" O GLY F 126 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N TYR F 128 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY A 127 " --> pdb=" O TYR F 128 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU F 130 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N MET A 129 " --> pdb=" O LEU F 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 133 through 135 removed outlier: 6.347A pdb=" N ALA B 133 " --> pdb=" O MET E 134 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA A 133 " --> pdb=" O MET D 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 138 through 141 removed outlier: 6.366A pdb=" N MET B 138 " --> pdb=" O MET E 139 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N PHE E 141 " --> pdb=" O MET B 138 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N HIS B 140 " --> pdb=" O PHE E 141 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N MET A 138 " --> pdb=" O MET D 139 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N PHE D 141 " --> pdb=" O MET A 138 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS A 140 " --> pdb=" O PHE D 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 121 through 122 removed outlier: 6.690A pdb=" N VAL G 121 " --> pdb=" O VAL H 122 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL H 121 " --> pdb=" O VAL I 122 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL I 121 " --> pdb=" O VAL J 122 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL J 121 " --> pdb=" O VAL K 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'K' and resid 125 through 130 removed outlier: 6.612A pdb=" N GLY I 126 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N MET J 129 " --> pdb=" O GLY I 126 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR I 128 " --> pdb=" O MET J 129 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 133 through 135 removed outlier: 6.402A pdb=" N ALA J 133 " --> pdb=" O MET K 134 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA I 133 " --> pdb=" O MET J 134 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA H 133 " --> pdb=" O MET I 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 138 through 141 removed outlier: 6.275A pdb=" N MET J 138 " --> pdb=" O MET K 139 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N PHE K 141 " --> pdb=" O MET J 138 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N HIS J 140 " --> pdb=" O PHE K 141 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N MET I 138 " --> pdb=" O MET J 139 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE J 141 " --> pdb=" O MET I 138 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS I 140 " --> pdb=" O PHE J 141 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N MET H 138 " --> pdb=" O MET I 139 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N PHE I 141 " --> pdb=" O MET H 138 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS H 140 " --> pdb=" O PHE I 141 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N MET G 138 " --> pdb=" O MET H 139 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N PHE H 141 " --> pdb=" O MET G 138 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N HIS G 140 " --> pdb=" O PHE H 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Q' and resid 121 through 122 removed outlier: 6.698A pdb=" N VAL P 121 " --> pdb=" O VAL Q 122 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL O 121 " --> pdb=" O VAL P 122 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL N 121 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL M 121 " --> pdb=" O VAL N 122 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 125 through 130 removed outlier: 6.608A pdb=" N GLY M 126 " --> pdb=" O GLY N 127 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N MET N 129 " --> pdb=" O GLY M 126 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR M 128 " --> pdb=" O MET N 129 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 133 through 135 removed outlier: 6.393A pdb=" N ALA P 133 " --> pdb=" O MET Q 134 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA O 133 " --> pdb=" O MET P 134 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA N 133 " --> pdb=" O MET O 134 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA M 133 " --> pdb=" O MET N 134 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 138 through 141 removed outlier: 6.237A pdb=" N MET P 138 " --> pdb=" O MET Q 139 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N PHE Q 141 " --> pdb=" O MET P 138 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N HIS P 140 " --> pdb=" O PHE Q 141 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET O 138 " --> pdb=" O MET P 139 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N PHE P 141 " --> pdb=" O MET O 138 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N HIS O 140 " --> pdb=" O PHE P 141 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N MET N 138 " --> pdb=" O MET O 139 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE O 141 " --> pdb=" O MET N 138 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N HIS N 140 " --> pdb=" O PHE O 141 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N MET M 138 " --> pdb=" O MET N 139 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE N 141 " --> pdb=" O MET M 138 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N HIS M 140 " --> pdb=" O PHE N 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'X' and resid 121 through 122 removed outlier: 6.713A pdb=" N VAL V 121 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL U 121 " --> pdb=" O VAL V 122 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL T 121 " --> pdb=" O VAL U 122 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL S 121 " --> pdb=" O VAL T 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'X' and resid 125 through 130 removed outlier: 6.550A pdb=" N GLY U 126 " --> pdb=" O GLY V 127 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N MET V 129 " --> pdb=" O GLY U 126 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR U 128 " --> pdb=" O MET V 129 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY S 126 " --> pdb=" O GLY T 127 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N MET T 129 " --> pdb=" O GLY S 126 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N TYR S 128 " --> pdb=" O MET T 129 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU S 125 " --> pdb=" O GLY Y 126 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N TYR Y 128 " --> pdb=" O LEU S 125 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY S 127 " --> pdb=" O TYR Y 128 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU Y 130 " --> pdb=" O GLY S 127 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N MET S 129 " --> pdb=" O LEU Y 130 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'X' and resid 133 through 135 removed outlier: 6.426A pdb=" N ALA V 133 " --> pdb=" O MET X 134 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA U 133 " --> pdb=" O MET V 134 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA T 133 " --> pdb=" O MET U 134 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA S 133 " --> pdb=" O MET T 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 138 through 141 removed outlier: 6.209A pdb=" N MET V 138 " --> pdb=" O MET X 139 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N PHE X 141 " --> pdb=" O MET V 138 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N HIS V 140 " --> pdb=" O PHE X 141 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N MET U 138 " --> pdb=" O MET V 139 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE V 141 " --> pdb=" O MET U 138 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N HIS U 140 " --> pdb=" O PHE V 141 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N MET T 138 " --> pdb=" O MET U 139 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE U 141 " --> pdb=" O MET T 138 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N HIS T 140 " --> pdb=" O PHE U 141 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N MET S 138 " --> pdb=" O MET T 139 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE T 141 " --> pdb=" O MET S 138 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N HIS S 140 " --> pdb=" O PHE T 141 " (cutoff:3.500A) 92 hydrogen bonds defined for protein. 276 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: 0.55 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1312 1.33 - 1.45: 663 1.45 - 1.57: 2009 1.57 - 1.69: 0 1.69 - 1.80: 192 Bond restraints: 4176 Sorted by residual: bond pdb=" CB MET Y 129 " pdb=" CG MET Y 129 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.04e+00 bond pdb=" CB MET M 129 " pdb=" CG MET M 129 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" CB MET K 129 " pdb=" CG MET K 129 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.02e+00 bond pdb=" CB MET H 129 " pdb=" CG MET H 129 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.02e+00 bond pdb=" CB MET D 129 " pdb=" CG MET D 129 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.02e+00 ... (remaining 4171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 4565 1.00 - 1.99: 625 1.99 - 2.99: 138 2.99 - 3.99: 72 3.99 - 4.99: 120 Bond angle restraints: 5520 Sorted by residual: angle pdb=" C GLY O 142 " pdb=" N ASN O 143 " pdb=" CA ASN O 143 " ideal model delta sigma weight residual 121.70 126.69 -4.99 1.80e+00 3.09e-01 7.67e+00 angle pdb=" C GLY U 142 " pdb=" N ASN U 143 " pdb=" CA ASN U 143 " ideal model delta sigma weight residual 121.70 126.68 -4.98 1.80e+00 3.09e-01 7.65e+00 angle pdb=" C GLY P 142 " pdb=" N ASN P 143 " pdb=" CA ASN P 143 " ideal model delta sigma weight residual 121.70 126.67 -4.97 1.80e+00 3.09e-01 7.62e+00 angle pdb=" C GLY Y 142 " pdb=" N ASN Y 143 " pdb=" CA ASN Y 143 " ideal model delta sigma weight residual 121.70 126.67 -4.97 1.80e+00 3.09e-01 7.61e+00 angle pdb=" C GLY M 142 " pdb=" N ASN M 143 " pdb=" CA ASN M 143 " ideal model delta sigma weight residual 121.70 126.66 -4.96 1.80e+00 3.09e-01 7.61e+00 ... (remaining 5515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.69: 1798 10.69 - 21.37: 314 21.37 - 32.06: 144 32.06 - 42.75: 24 42.75 - 53.43: 48 Dihedral angle restraints: 2328 sinusoidal: 864 harmonic: 1464 Sorted by residual: dihedral pdb=" CA MET C 139 " pdb=" CB MET C 139 " pdb=" CG MET C 139 " pdb=" SD MET C 139 " ideal model delta sinusoidal sigma weight residual 180.00 126.57 53.43 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" CA MET B 139 " pdb=" CB MET B 139 " pdb=" CG MET B 139 " pdb=" SD MET B 139 " ideal model delta sinusoidal sigma weight residual 180.00 126.57 53.43 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" CA MET T 139 " pdb=" CB MET T 139 " pdb=" CG MET T 139 " pdb=" SD MET T 139 " ideal model delta sinusoidal sigma weight residual 180.00 126.58 53.42 3 1.50e+01 4.44e-03 9.20e+00 ... (remaining 2325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 179 0.027 - 0.054: 221 0.054 - 0.080: 43 0.080 - 0.107: 37 0.107 - 0.134: 48 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA ARG U 136 " pdb=" N ARG U 136 " pdb=" C ARG U 136 " pdb=" CB ARG U 136 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ARG P 136 " pdb=" N ARG P 136 " pdb=" C ARG P 136 " pdb=" CB ARG P 136 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ARG C 136 " pdb=" N ARG C 136 " pdb=" C ARG C 136 " pdb=" CB ARG C 136 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 525 not shown) Planarity restraints: 720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA O 120 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C ALA O 120 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA O 120 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL O 121 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA T 120 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C ALA T 120 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA T 120 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL T 121 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 120 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C ALA Q 120 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA Q 120 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL Q 121 " -0.008 2.00e-02 2.50e+03 ... (remaining 717 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 906 2.79 - 3.32: 3097 3.32 - 3.85: 7935 3.85 - 4.37: 9733 4.37 - 4.90: 16254 Nonbonded interactions: 37925 Sorted by model distance: nonbonded pdb=" O HOH M 201 " pdb=" O HOH S 201 " model vdw 2.267 3.040 nonbonded pdb=" O HOH N 201 " pdb=" O HOH T 201 " model vdw 2.272 3.040 nonbonded pdb=" O HOH K 202 " pdb=" O HOH Q 202 " model vdw 2.284 3.040 nonbonded pdb=" O HOH H 201 " pdb=" O HOH N 201 " model vdw 2.297 3.040 nonbonded pdb=" O HOH G 201 " pdb=" O HOH M 201 " model vdw 2.305 3.040 ... (remaining 37920 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' } 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: 1.470 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.030 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.045 4176 Z= 0.423 Angle : 1.059 4.986 5520 Z= 0.572 Chirality : 0.056 0.134 528 Planarity : 0.004 0.014 720 Dihedral : 14.838 53.431 1464 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.79 (0.20), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.16), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.002 ARG X 136 TYR 0.002 0.001 TYR F 128 PHE 0.005 0.001 PHE I 141 HIS 0.001 0.000 HIS X 140 Details of bonding type rmsd covalent geometry : bond 0.00906 ( 4176) covalent geometry : angle 1.05902 ( 5520) hydrogen bonds : bond 0.19460 ( 92) hydrogen bonds : angle 10.24478 ( 276) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: C 136 ARG cc_start: 0.7607 (mtt-85) cc_final: 0.7398 (mtt-85) REVERT: D 136 ARG cc_start: 0.7707 (mtt-85) cc_final: 0.7432 (mtt-85) REVERT: G 138 MET cc_start: 0.7241 (tmt) cc_final: 0.6728 (tmm) REVERT: I 136 ARG cc_start: 0.7649 (mtt-85) cc_final: 0.7353 (mtm180) REVERT: J 136 ARG cc_start: 0.7686 (mtt-85) cc_final: 0.7471 (mtt-85) REVERT: O 136 ARG cc_start: 0.7679 (mtt-85) cc_final: 0.7416 (mtt90) REVERT: R 138 MET cc_start: 0.7166 (tmt) cc_final: 0.6291 (tmm) REVERT: U 134 MET cc_start: 0.8962 (ttm) cc_final: 0.8664 (ttm) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.9593 time to fit residues: 123.1835 Evaluate side-chains 125 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.115508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.097397 restraints weight = 2837.641| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.36 r_work: 0.3238 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work: 0.2876 rms_B_bonded: 4.95 restraints_weight: 0.1250 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4176 Z= 0.188 Angle : 0.819 5.669 5520 Z= 0.435 Chirality : 0.055 0.156 528 Planarity : 0.004 0.028 720 Dihedral : 5.679 15.290 624 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.60 % Allowed : 19.53 % Favored : 77.86 % 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: -4.94 (0.21), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.16), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG V 136 TYR 0.009 0.002 TYR K 128 PHE 0.008 0.002 PHE D 141 HIS 0.002 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 4176) covalent geometry : angle 0.81910 ( 5520) hydrogen bonds : bond 0.04924 ( 92) hydrogen bonds : angle 8.49016 ( 276) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 139 MET cc_start: 0.9285 (mtm) cc_final: 0.8951 (mtm) REVERT: C 136 ARG cc_start: 0.8597 (mtt-85) cc_final: 0.8241 (mtt-85) REVERT: C 138 MET cc_start: 0.8290 (tmt) cc_final: 0.7852 (tmm) REVERT: D 136 ARG cc_start: 0.8623 (mtt-85) cc_final: 0.8266 (mtt-85) REVERT: E 136 ARG cc_start: 0.8397 (mtt-85) cc_final: 0.8176 (mtt-85) REVERT: I 136 ARG cc_start: 0.8608 (mtt-85) cc_final: 0.8257 (mtm180) REVERT: I 138 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.7634 (tmt) REVERT: J 136 ARG cc_start: 0.8567 (mtt-85) cc_final: 0.8324 (mtt-85) REVERT: K 138 MET cc_start: 0.8115 (tmt) cc_final: 0.7662 (tmm) REVERT: L 138 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7288 (tmt) REVERT: N 138 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8196 (tmt) REVERT: R 136 ARG cc_start: 0.8699 (mtp-110) cc_final: 0.8341 (mtp-110) REVERT: S 138 MET cc_start: 0.8589 (tmt) cc_final: 0.8360 (tmt) REVERT: T 138 MET cc_start: 0.8439 (tmt) cc_final: 0.7578 (mtt) REVERT: X 138 MET cc_start: 0.8356 (tmt) cc_final: 0.7939 (tmt) outliers start: 10 outliers final: 0 residues processed: 127 average time/residue: 0.9095 time to fit residues: 117.8029 Evaluate side-chains 129 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain N residue 138 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.0170 chunk 43 optimal weight: 6.9990 chunk 27 optimal weight: 0.0170 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.2860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.115390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.097193 restraints weight = 2809.894| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.36 r_work: 0.3244 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work: 0.2876 rms_B_bonded: 4.96 restraints_weight: 0.1250 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4176 Z= 0.186 Angle : 0.795 5.464 5520 Z= 0.424 Chirality : 0.053 0.148 528 Planarity : 0.003 0.026 720 Dihedral : 5.464 15.038 624 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.82 % Allowed : 20.83 % Favored : 77.34 % 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: -4.93 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.17), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG V 136 TYR 0.008 0.001 TYR K 128 PHE 0.007 0.002 PHE F 141 HIS 0.001 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 4176) covalent geometry : angle 0.79521 ( 5520) hydrogen bonds : bond 0.04616 ( 92) hydrogen bonds : angle 8.24782 ( 276) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7643 (tmt) REVERT: C 136 ARG cc_start: 0.8549 (mtt-85) cc_final: 0.8197 (mtt-85) REVERT: C 138 MET cc_start: 0.8245 (tmt) cc_final: 0.7769 (tmm) REVERT: D 136 ARG cc_start: 0.8575 (mtt-85) cc_final: 0.8261 (mtt-85) REVERT: I 136 ARG cc_start: 0.8663 (mtt-85) cc_final: 0.8373 (mtm180) REVERT: I 138 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7673 (tmt) REVERT: K 136 ARG cc_start: 0.8415 (mtp85) cc_final: 0.8213 (mtp85) REVERT: K 138 MET cc_start: 0.8134 (tmt) cc_final: 0.7584 (tmm) REVERT: N 138 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8234 (tmt) REVERT: R 136 ARG cc_start: 0.8745 (mtp-110) cc_final: 0.8434 (mtp-110) REVERT: S 138 MET cc_start: 0.8661 (tmt) cc_final: 0.8431 (tmt) REVERT: T 138 MET cc_start: 0.8453 (tmt) cc_final: 0.7564 (mtt) REVERT: X 138 MET cc_start: 0.8431 (tmt) cc_final: 0.8008 (tmt) outliers start: 7 outliers final: 0 residues processed: 129 average time/residue: 0.8677 time to fit residues: 114.2231 Evaluate side-chains 131 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain N residue 138 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.112255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.094458 restraints weight = 2761.391| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.32 r_work: 0.3198 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work: 0.2832 rms_B_bonded: 4.79 restraints_weight: 0.1250 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 4176 Z= 0.366 Angle : 0.992 5.957 5520 Z= 0.534 Chirality : 0.058 0.176 528 Planarity : 0.005 0.040 720 Dihedral : 6.257 19.292 624 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.08 % Allowed : 20.57 % Favored : 77.34 % 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: -4.88 (0.21), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.16), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG V 136 TYR 0.006 0.002 TYR K 128 PHE 0.007 0.002 PHE Y 141 HIS 0.004 0.001 HIS F 140 Details of bonding type rmsd covalent geometry : bond 0.00763 ( 4176) covalent geometry : angle 0.99186 ( 5520) hydrogen bonds : bond 0.05078 ( 92) hydrogen bonds : angle 8.07793 ( 276) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.157 Fit side-chains REVERT: C 136 ARG cc_start: 0.8570 (mtt-85) cc_final: 0.8221 (mtt-85) REVERT: C 138 MET cc_start: 0.8312 (tmt) cc_final: 0.7855 (tmm) REVERT: D 136 ARG cc_start: 0.8626 (mtt-85) cc_final: 0.8273 (mtt-85) REVERT: F 138 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7747 (tmt) REVERT: H 136 ARG cc_start: 0.8679 (mtt-85) cc_final: 0.8455 (mtm180) REVERT: H 138 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8098 (tmt) REVERT: I 136 ARG cc_start: 0.8660 (mtt-85) cc_final: 0.8367 (mtp85) REVERT: I 138 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.7884 (tmt) REVERT: L 138 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7432 (tmt) REVERT: N 138 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8216 (tmt) REVERT: Q 143 ASN cc_start: 0.7708 (m-40) cc_final: 0.7462 (m110) REVERT: R 136 ARG cc_start: 0.8759 (mtp-110) cc_final: 0.8497 (mtp-110) REVERT: T 138 MET cc_start: 0.8494 (tmt) cc_final: 0.7598 (mtt) REVERT: X 138 MET cc_start: 0.8531 (tmt) cc_final: 0.8031 (tmt) outliers start: 8 outliers final: 0 residues processed: 131 average time/residue: 0.8266 time to fit residues: 110.5394 Evaluate side-chains 136 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain N residue 138 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 chunk 39 optimal weight: 0.0170 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 143 ASN P 143 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.118108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.099720 restraints weight = 2824.767| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.37 r_work: 0.3294 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4176 Z= 0.125 Angle : 0.715 5.198 5520 Z= 0.377 Chirality : 0.053 0.140 528 Planarity : 0.003 0.024 720 Dihedral : 5.251 12.915 624 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.60 % Allowed : 20.31 % Favored : 77.08 % 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: -5.03 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.17), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 136 TYR 0.009 0.001 TYR K 128 PHE 0.008 0.001 PHE F 141 HIS 0.001 0.000 HIS X 140 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 4176) covalent geometry : angle 0.71505 ( 5520) hydrogen bonds : bond 0.03855 ( 92) hydrogen bonds : angle 8.13701 ( 276) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7284 (tmt) REVERT: C 136 ARG cc_start: 0.8158 (mtt-85) cc_final: 0.7806 (mtt-85) REVERT: C 138 MET cc_start: 0.7807 (tmt) cc_final: 0.7250 (tmm) REVERT: D 136 ARG cc_start: 0.8179 (mtt-85) cc_final: 0.7887 (mtt-85) REVERT: H 138 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7514 (tmt) REVERT: I 136 ARG cc_start: 0.8222 (mtt-85) cc_final: 0.7935 (mtm180) REVERT: I 138 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7180 (tmt) REVERT: K 138 MET cc_start: 0.7684 (tmt) cc_final: 0.7106 (tmm) REVERT: L 138 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7065 (tmt) REVERT: N 138 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7754 (tmt) REVERT: R 136 ARG cc_start: 0.8335 (mtp-110) cc_final: 0.8111 (mtp-110) REVERT: R 138 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7298 (tmm) REVERT: S 139 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8688 (mtm) REVERT: T 138 MET cc_start: 0.8035 (tmt) cc_final: 0.7309 (mtt) REVERT: U 134 MET cc_start: 0.9329 (ttm) cc_final: 0.9118 (ttm) REVERT: V 139 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8647 (mtm) REVERT: X 138 MET cc_start: 0.7992 (tmt) cc_final: 0.7528 (tmt) outliers start: 10 outliers final: 0 residues processed: 128 average time/residue: 0.8844 time to fit residues: 115.4500 Evaluate side-chains 133 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain R residue 138 MET Chi-restraints excluded: chain S residue 139 MET Chi-restraints excluded: chain V residue 139 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 35 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.114421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.096176 restraints weight = 2849.883| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.37 r_work: 0.3232 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work: 0.2863 rms_B_bonded: 4.93 restraints_weight: 0.1250 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4176 Z= 0.232 Angle : 0.850 5.726 5520 Z= 0.453 Chirality : 0.054 0.150 528 Planarity : 0.004 0.045 720 Dihedral : 5.729 15.385 624 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.08 % Allowed : 21.61 % Favored : 76.30 % 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: -4.97 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.17), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 136 TYR 0.007 0.001 TYR K 128 PHE 0.007 0.002 PHE Y 141 HIS 0.002 0.001 HIS F 140 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 4176) covalent geometry : angle 0.84969 ( 5520) hydrogen bonds : bond 0.04397 ( 92) hydrogen bonds : angle 7.89342 ( 276) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: C 136 ARG cc_start: 0.8571 (mtt-85) cc_final: 0.8169 (mtt-85) REVERT: C 138 MET cc_start: 0.8300 (tmt) cc_final: 0.7758 (tmm) REVERT: D 136 ARG cc_start: 0.8597 (mtt-85) cc_final: 0.8216 (mtt-85) REVERT: F 138 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7963 (tmt) REVERT: H 138 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8059 (tmt) REVERT: I 136 ARG cc_start: 0.8646 (mtt-85) cc_final: 0.8350 (mtp85) REVERT: I 138 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.7798 (tmt) REVERT: K 138 MET cc_start: 0.8119 (tmt) cc_final: 0.7578 (tmm) REVERT: L 138 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7468 (tmt) REVERT: N 138 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8217 (tmt) REVERT: Q 143 ASN cc_start: 0.7628 (m-40) cc_final: 0.7328 (m110) REVERT: R 136 ARG cc_start: 0.8766 (mtp-110) cc_final: 0.8534 (mtp-110) REVERT: S 139 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8920 (mtm) REVERT: T 138 MET cc_start: 0.8463 (tmt) cc_final: 0.7557 (mtt) REVERT: X 138 MET cc_start: 0.8485 (tmt) cc_final: 0.8069 (tmt) outliers start: 8 outliers final: 0 residues processed: 131 average time/residue: 0.8987 time to fit residues: 120.0847 Evaluate side-chains 137 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain S residue 139 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 10 optimal weight: 6.9990 chunk 7 optimal weight: 0.4980 chunk 33 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 42 optimal weight: 0.0870 chunk 24 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 0.0980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.117508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.099039 restraints weight = 2869.427| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.38 r_work: 0.3282 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4176 Z= 0.145 Angle : 0.739 5.834 5520 Z= 0.388 Chirality : 0.052 0.142 528 Planarity : 0.004 0.051 720 Dihedral : 5.316 14.025 624 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.82 % Allowed : 22.14 % Favored : 76.04 % 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: -5.02 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.17), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 136 TYR 0.009 0.001 TYR K 128 PHE 0.007 0.001 PHE F 141 HIS 0.001 0.000 HIS F 140 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 4176) covalent geometry : angle 0.73931 ( 5520) hydrogen bonds : bond 0.03820 ( 92) hydrogen bonds : angle 7.89203 ( 276) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: C 136 ARG cc_start: 0.8154 (mtt-85) cc_final: 0.7788 (mtt-85) REVERT: C 138 MET cc_start: 0.7843 (tmt) cc_final: 0.7269 (tmm) REVERT: D 136 ARG cc_start: 0.8199 (mtt-85) cc_final: 0.7904 (mtt-85) REVERT: H 138 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7538 (tmt) REVERT: I 136 ARG cc_start: 0.8266 (mtt-85) cc_final: 0.8010 (mtp85) REVERT: I 138 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7217 (tmt) REVERT: K 138 MET cc_start: 0.7757 (tmt) cc_final: 0.7193 (tmm) REVERT: L 138 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7070 (tmt) REVERT: N 138 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7735 (tmt) REVERT: R 138 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7205 (tmm) REVERT: S 139 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8683 (mtm) REVERT: T 138 MET cc_start: 0.8090 (tmt) cc_final: 0.7357 (mtt) REVERT: X 138 MET cc_start: 0.8015 (tmt) cc_final: 0.7539 (tmt) outliers start: 7 outliers final: 0 residues processed: 126 average time/residue: 0.9407 time to fit residues: 120.8114 Evaluate side-chains 132 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain R residue 138 MET Chi-restraints excluded: chain S residue 139 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 0.0670 chunk 24 optimal weight: 8.9990 overall best weight: 1.2520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.116346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.098081 restraints weight = 2790.086| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.36 r_work: 0.3267 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work: 0.2896 rms_B_bonded: 4.95 restraints_weight: 0.1250 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4176 Z= 0.180 Angle : 0.785 6.208 5520 Z= 0.413 Chirality : 0.053 0.146 528 Planarity : 0.004 0.042 720 Dihedral : 5.470 15.214 624 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.08 % Allowed : 22.40 % Favored : 75.52 % 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: -5.01 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.17), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 136 TYR 0.007 0.001 TYR K 128 PHE 0.007 0.001 PHE F 141 HIS 0.002 0.000 HIS F 140 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 4176) covalent geometry : angle 0.78502 ( 5520) hydrogen bonds : bond 0.03983 ( 92) hydrogen bonds : angle 7.75026 ( 276) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: C 136 ARG cc_start: 0.8557 (mtt-85) cc_final: 0.8153 (mtt-85) REVERT: C 138 MET cc_start: 0.8268 (tmt) cc_final: 0.7721 (tmm) REVERT: D 136 ARG cc_start: 0.8566 (mtt-85) cc_final: 0.8238 (mtt-85) REVERT: F 138 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7897 (tmt) REVERT: H 138 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8059 (tmt) REVERT: I 136 ARG cc_start: 0.8640 (mtt-85) cc_final: 0.8352 (mtp85) REVERT: I 138 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7764 (tmt) REVERT: K 138 MET cc_start: 0.8179 (tmt) cc_final: 0.7644 (tmm) REVERT: L 138 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7485 (tmt) REVERT: N 138 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8226 (tmt) REVERT: R 138 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7713 (tmm) REVERT: S 139 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8913 (mtm) REVERT: T 138 MET cc_start: 0.8470 (tmt) cc_final: 0.7555 (mtt) REVERT: X 138 MET cc_start: 0.8433 (tmt) cc_final: 0.8013 (tmt) outliers start: 8 outliers final: 0 residues processed: 129 average time/residue: 0.9392 time to fit residues: 123.5959 Evaluate side-chains 135 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain R residue 138 MET Chi-restraints excluded: chain S residue 139 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 45 optimal weight: 0.0470 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 8.9990 chunk 47 optimal weight: 0.0270 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 0.0980 chunk 16 optimal weight: 4.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 143 ASN H 143 ASN Q 143 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.122124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.103664 restraints weight = 2851.312| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.37 r_work: 0.3366 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4176 Z= 0.097 Angle : 0.660 6.333 5520 Z= 0.337 Chirality : 0.051 0.151 528 Planarity : 0.004 0.044 720 Dihedral : 4.724 14.038 624 Min Nonbonded Distance : 2.676 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.82 % Allowed : 23.18 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.17 (0.23), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.17), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG U 136 TYR 0.010 0.002 TYR U 128 PHE 0.007 0.001 PHE F 141 HIS 0.001 0.000 HIS I 140 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 4176) covalent geometry : angle 0.65985 ( 5520) hydrogen bonds : bond 0.03159 ( 92) hydrogen bonds : angle 7.80344 ( 276) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: C 136 ARG cc_start: 0.8164 (mtt-85) cc_final: 0.7810 (mtt-85) REVERT: C 138 MET cc_start: 0.7829 (tmt) cc_final: 0.7271 (tmm) REVERT: D 136 ARG cc_start: 0.8138 (mtt-85) cc_final: 0.7833 (mtt-85) REVERT: I 136 ARG cc_start: 0.8186 (mtt-85) cc_final: 0.7895 (mtm180) REVERT: I 138 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7212 (tmt) REVERT: K 138 MET cc_start: 0.7607 (tmt) cc_final: 0.7040 (tmm) REVERT: L 138 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7135 (tmt) REVERT: N 138 MET cc_start: 0.8040 (tmt) cc_final: 0.7769 (tmt) REVERT: P 136 ARG cc_start: 0.8096 (mtp-110) cc_final: 0.7847 (mtt-85) REVERT: S 139 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8674 (mtm) REVERT: T 138 MET cc_start: 0.8061 (tmt) cc_final: 0.7342 (mtt) REVERT: X 138 MET cc_start: 0.7895 (tmt) cc_final: 0.7415 (tmt) outliers start: 7 outliers final: 0 residues processed: 133 average time/residue: 0.9105 time to fit residues: 123.5223 Evaluate side-chains 130 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain S residue 139 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.112495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.094371 restraints weight = 2812.538| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.35 r_work: 0.3199 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work: 0.2835 rms_B_bonded: 4.83 restraints_weight: 0.1250 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 4176 Z= 0.401 Angle : 1.039 7.529 5520 Z= 0.555 Chirality : 0.058 0.220 528 Planarity : 0.006 0.054 720 Dihedral : 6.391 17.596 624 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.04 % Allowed : 23.18 % Favored : 75.78 % 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: -4.95 (0.21), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.16), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG U 136 TYR 0.011 0.002 TYR T 128 PHE 0.007 0.002 PHE S 141 HIS 0.004 0.001 HIS F 140 Details of bonding type rmsd covalent geometry : bond 0.00827 ( 4176) covalent geometry : angle 1.03934 ( 5520) hydrogen bonds : bond 0.04611 ( 92) hydrogen bonds : angle 7.75140 ( 276) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 133 time to evaluate : 0.184 Fit side-chains REVERT: C 136 ARG cc_start: 0.8584 (mtt-85) cc_final: 0.8223 (mtt-85) REVERT: D 136 ARG cc_start: 0.8616 (mtt-85) cc_final: 0.8220 (mtt-85) REVERT: F 138 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8177 (tmt) REVERT: I 136 ARG cc_start: 0.8664 (mtt-85) cc_final: 0.8393 (mtp85) REVERT: I 138 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.7754 (tmt) REVERT: L 138 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7396 (tmt) REVERT: M 136 ARG cc_start: 0.8460 (mtp85) cc_final: 0.8207 (mtt180) REVERT: Q 143 ASN cc_start: 0.7766 (m-40) cc_final: 0.7500 (m110) REVERT: R 136 ARG cc_start: 0.8841 (mtp-110) cc_final: 0.8569 (mtp-110) REVERT: T 138 MET cc_start: 0.8546 (tmt) cc_final: 0.7587 (mtt) REVERT: X 138 MET cc_start: 0.8561 (tmt) cc_final: 0.8048 (tmt) outliers start: 4 outliers final: 0 residues processed: 133 average time/residue: 0.9443 time to fit residues: 128.0928 Evaluate side-chains 135 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain L residue 138 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 42 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 0.0270 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.118067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.099649 restraints weight = 2834.016| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.37 r_work: 0.3295 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4176 Z= 0.138 Angle : 0.755 6.976 5520 Z= 0.389 Chirality : 0.053 0.155 528 Planarity : 0.004 0.048 720 Dihedral : 5.419 15.066 624 Min Nonbonded Distance : 2.673 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.04 % Allowed : 23.96 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.01 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.17), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG U 136 TYR 0.009 0.001 TYR K 128 PHE 0.008 0.001 PHE F 141 HIS 0.001 0.000 HIS F 140 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4176) covalent geometry : angle 0.75492 ( 5520) hydrogen bonds : bond 0.03677 ( 92) hydrogen bonds : angle 7.83861 ( 276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2570.81 seconds wall clock time: 44 minutes 13.71 seconds (2653.71 seconds total)