Starting phenix.real_space_refine on Tue Feb 11 04:55:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yat_33719/02_2025/7yat_33719.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yat_33719/02_2025/7yat_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yat_33719/02_2025/7yat_33719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yat_33719/02_2025/7yat_33719.map" model { file = "/net/cci-nas-00/data/ceres_data/7yat_33719/02_2025/7yat_33719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yat_33719/02_2025/7yat_33719.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, V, Y, X Time building chain proxies: 1.70, per 1000 atoms: 0.41 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: 0.94 Conformation dependent library (CDL) restraints added in 515.5 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: 1.51 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: 1.19 Time building geometry restraints manager: 1.11 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'V' selection = chain 'Y' selection = chain 'X' } 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: 1.390 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.010 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:14.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.200 ------------------------------------------------------------------------------- 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= 0.677 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (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 HIS 0.001 0.000 HIS X 140 PHE 0.005 0.001 PHE I 141 TYR 0.002 0.001 TYR F 128 ARG 0.004 0.002 ARG X 136 *********************** 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 : 0.499 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: 0.7431 (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: 2.0888 time to fit residues: 268.4489 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 : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS F 140 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.115186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.097146 restraints weight = 2786.026| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.35 r_work: 0.3233 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work: 0.2870 rms_B_bonded: 4.89 restraints_weight: 0.1250 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.2090 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= 0.305 Angle : 0.842 5.519 5520 Z= 0.448 Chirality : 0.055 0.159 528 Planarity : 0.004 0.025 720 Dihedral : 5.751 15.651 624 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.34 % Allowed : 20.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (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 HIS 0.002 0.001 HIS C 140 PHE 0.008 0.002 PHE S 141 TYR 0.008 0.001 TYR K 128 ARG 0.004 0.001 ARG T 136 *********************** 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: 9 poor density : 128 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 139 MET cc_start: 0.9300 (mtm) cc_final: 0.8960 (mtm) REVERT: C 136 ARG cc_start: 0.8617 (mtt-85) cc_final: 0.8258 (mtt-85) REVERT: C 138 MET cc_start: 0.8292 (tmt) cc_final: 0.7847 (tmm) REVERT: D 136 ARG cc_start: 0.8659 (mtt-85) cc_final: 0.8330 (mtt-85) REVERT: E 136 ARG cc_start: 0.8347 (mtt-85) cc_final: 0.8115 (mtt-85) REVERT: I 136 ARG cc_start: 0.8651 (mtt-85) cc_final: 0.8296 (mtm180) REVERT: I 138 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7651 (tmt) REVERT: J 136 ARG cc_start: 0.8569 (mtt-85) cc_final: 0.8316 (mtt-85) REVERT: K 138 MET cc_start: 0.8115 (tmt) cc_final: 0.7600 (tmm) REVERT: N 138 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8212 (tmt) REVERT: R 136 ARG cc_start: 0.8716 (mtp-110) cc_final: 0.8391 (mtp-110) REVERT: T 138 MET cc_start: 0.8449 (tmt) cc_final: 0.7572 (mtt) REVERT: X 138 MET cc_start: 0.8348 (tmt) cc_final: 0.7936 (tmt) REVERT: Y 138 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8335 (tmt) outliers start: 9 outliers final: 0 residues processed: 128 average time/residue: 2.0336 time to fit residues: 265.6452 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 : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain Y residue 138 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 41 optimal weight: 0.0670 chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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 = 0.3654 r_free = 0.3654 target = 0.113309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.095379 restraints weight = 2760.082| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.34 r_work: 0.3212 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work: 0.2844 rms_B_bonded: 4.83 restraints_weight: 0.1250 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 4176 Z= 0.418 Angle : 0.905 5.630 5520 Z= 0.485 Chirality : 0.055 0.164 528 Planarity : 0.004 0.028 720 Dihedral : 5.950 17.752 624 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.34 % Allowed : 20.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.89 (0.21), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.16), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 140 PHE 0.007 0.002 PHE Y 141 TYR 0.007 0.001 TYR E 128 ARG 0.005 0.001 ARG V 136 *********************** 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 140 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.470 Fit side-chains REVERT: A 138 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7847 (tmt) REVERT: C 136 ARG cc_start: 0.8585 (mtt-85) cc_final: 0.8196 (mtt-85) REVERT: C 138 MET cc_start: 0.8268 (tmt) cc_final: 0.7818 (tmm) REVERT: D 136 ARG cc_start: 0.8618 (mtt-85) cc_final: 0.8251 (mtt-85) REVERT: F 138 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7834 (tmt) REVERT: H 136 ARG cc_start: 0.8750 (mtt-85) cc_final: 0.8434 (mtm180) REVERT: I 136 ARG cc_start: 0.8667 (mtt-85) cc_final: 0.8359 (mtp85) REVERT: I 138 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.7689 (tmt) REVERT: J 136 ARG cc_start: 0.8562 (mtt-85) cc_final: 0.8330 (mtt-85) REVERT: K 138 MET cc_start: 0.8142 (tmt) cc_final: 0.7622 (tmm) REVERT: L 138 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7453 (tmt) REVERT: N 138 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8170 (tmt) REVERT: Q 143 ASN cc_start: 0.7631 (m-40) cc_final: 0.7368 (m110) REVERT: R 136 ARG cc_start: 0.8772 (mtp-110) cc_final: 0.8503 (mtp-110) REVERT: T 138 MET cc_start: 0.8485 (tmt) cc_final: 0.7580 (mtt) REVERT: X 138 MET cc_start: 0.8441 (tmt) cc_final: 0.7998 (tmt) outliers start: 9 outliers final: 0 residues processed: 131 average time/residue: 1.9044 time to fit residues: 254.6268 Evaluate side-chains 135 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain F 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 0.0770 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 23 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.5940 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.118168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.099798 restraints weight = 2806.010| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.37 r_work: 0.3294 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4176 Z= 0.183 Angle : 0.712 5.427 5520 Z= 0.376 Chirality : 0.053 0.139 528 Planarity : 0.003 0.024 720 Dihedral : 5.160 12.879 624 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.03 (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 HIS 0.001 0.000 HIS X 140 PHE 0.007 0.001 PHE F 141 TYR 0.009 0.001 TYR K 128 ARG 0.004 0.000 ARG T 136 *********************** 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 137 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7239 (tmt) REVERT: A 139 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8551 (mtm) REVERT: C 136 ARG cc_start: 0.8153 (mtt-85) cc_final: 0.7841 (mtt-85) REVERT: C 138 MET cc_start: 0.7794 (tmt) cc_final: 0.7253 (tmm) REVERT: D 136 ARG cc_start: 0.8214 (mtt-85) cc_final: 0.7945 (mtt-85) REVERT: H 139 MET cc_start: 0.9066 (mtm) cc_final: 0.8755 (mpt) REVERT: I 136 ARG cc_start: 0.8277 (mtt-85) cc_final: 0.7966 (mtp85) REVERT: I 138 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7047 (tmt) REVERT: K 138 MET cc_start: 0.7744 (tmt) cc_final: 0.7181 (tmm) REVERT: L 138 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7055 (tmt) REVERT: N 138 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7751 (tmt) REVERT: O 138 MET cc_start: 0.8069 (tmt) cc_final: 0.7666 (tmm) REVERT: R 136 ARG cc_start: 0.8329 (mtp-110) cc_final: 0.8042 (mtp-110) REVERT: T 138 MET cc_start: 0.8027 (tmt) cc_final: 0.7292 (mtt) REVERT: V 139 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8645 (mtm) REVERT: X 138 MET cc_start: 0.8003 (tmt) cc_final: 0.7520 (tmt) outliers start: 10 outliers final: 0 residues processed: 127 average time/residue: 1.9395 time to fit residues: 251.2008 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 : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 139 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 V residue 139 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 28 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 0.0670 chunk 10 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 0.0030 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 overall best weight: 2.2134 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.113462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.095254 restraints weight = 2848.216| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.37 r_work: 0.3213 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work: 0.2846 rms_B_bonded: 4.90 restraints_weight: 0.1250 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4176 Z= 0.419 Angle : 0.900 5.689 5520 Z= 0.484 Chirality : 0.055 0.161 528 Planarity : 0.004 0.031 720 Dihedral : 5.895 16.699 624 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (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 HIS 0.003 0.001 HIS F 140 PHE 0.007 0.002 PHE Y 141 TYR 0.007 0.001 TYR K 128 ARG 0.006 0.001 ARG V 136 *********************** 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 139 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.446 Fit side-chains REVERT: A 138 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7630 (tmt) REVERT: C 136 ARG cc_start: 0.8598 (mtt-85) cc_final: 0.8192 (mtt-85) REVERT: C 138 MET cc_start: 0.8300 (tmt) cc_final: 0.7807 (tmm) REVERT: D 136 ARG cc_start: 0.8620 (mtt-85) cc_final: 0.8295 (mtt-85) REVERT: H 136 ARG cc_start: 0.8689 (mtt-85) cc_final: 0.8370 (mtm180) REVERT: H 138 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8042 (tmt) REVERT: I 136 ARG cc_start: 0.8634 (mtt-85) cc_final: 0.8388 (mtp85) REVERT: I 138 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7786 (tmt) REVERT: L 138 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7483 (tmt) REVERT: N 138 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8208 (tmt) REVERT: Q 143 ASN cc_start: 0.7664 (m-40) cc_final: 0.7389 (m110) REVERT: R 136 ARG cc_start: 0.8756 (mtp-110) cc_final: 0.8526 (mtp-110) REVERT: T 138 MET cc_start: 0.8497 (tmt) cc_final: 0.7575 (mtt) REVERT: X 138 MET cc_start: 0.8516 (tmt) cc_final: 0.8006 (tmt) outliers start: 8 outliers final: 0 residues processed: 131 average time/residue: 1.9097 time to fit residues: 255.4698 Evaluate side-chains 135 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.117916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.099459 restraints weight = 2812.064| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.37 r_work: 0.3292 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4176 Z= 0.196 Angle : 0.720 5.671 5520 Z= 0.381 Chirality : 0.052 0.142 528 Planarity : 0.003 0.028 720 Dihedral : 5.268 13.719 624 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.03 (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 HIS 0.001 0.000 HIS X 140 PHE 0.007 0.001 PHE F 141 TYR 0.009 0.001 TYR K 128 ARG 0.004 0.001 ARG V 136 *********************** 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 134 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: C 136 ARG cc_start: 0.8156 (mtt-85) cc_final: 0.7786 (mtt-85) REVERT: C 138 MET cc_start: 0.7809 (tmt) cc_final: 0.7229 (tmm) REVERT: D 136 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.7971 (mtt-85) REVERT: H 138 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7476 (tmt) REVERT: I 136 ARG cc_start: 0.8228 (mtt-85) cc_final: 0.7973 (mtp85) REVERT: I 138 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7195 (tmt) REVERT: K 138 MET cc_start: 0.7700 (tmt) cc_final: 0.7115 (tmm) REVERT: L 138 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7089 (tmt) REVERT: N 138 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7791 (tmt) REVERT: R 136 ARG cc_start: 0.8313 (mtp-110) cc_final: 0.8076 (mtp-110) REVERT: R 138 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7302 (tmm) REVERT: T 138 MET cc_start: 0.8078 (tmt) cc_final: 0.7351 (mtt) REVERT: X 138 MET cc_start: 0.7996 (tmt) cc_final: 0.7513 (tmt) outliers start: 7 outliers final: 0 residues processed: 127 average time/residue: 1.9809 time to fit residues: 256.6782 Evaluate side-chains 131 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.112681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.094604 restraints weight = 2808.109| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.35 r_work: 0.3201 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work: 0.2834 rms_B_bonded: 4.83 restraints_weight: 0.1250 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9127 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 : 0.008 0.048 4176 Z= 0.558 Angle : 0.986 5.874 5520 Z= 0.530 Chirality : 0.057 0.174 528 Planarity : 0.005 0.035 720 Dihedral : 6.219 17.839 624 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.82 % Allowed : 21.61 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (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 HIS 0.004 0.001 HIS F 140 PHE 0.007 0.002 PHE Y 141 TYR 0.006 0.002 TYR T 128 ARG 0.006 0.001 ARG M 136 *********************** 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 139 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.468 Fit side-chains REVERT: C 136 ARG cc_start: 0.8587 (mtt-85) cc_final: 0.8185 (mtt-85) REVERT: C 138 MET cc_start: 0.8306 (tmt) cc_final: 0.7795 (tmm) REVERT: D 136 ARG cc_start: 0.8626 (mtt-85) cc_final: 0.8240 (mtt-85) REVERT: F 138 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7971 (tmt) REVERT: H 136 ARG cc_start: 0.8718 (mtt-85) cc_final: 0.8506 (mtm180) REVERT: H 138 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8090 (tmt) REVERT: I 136 ARG cc_start: 0.8636 (mtt-85) cc_final: 0.8411 (mtp85) REVERT: I 138 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.7842 (tmt) REVERT: K 138 MET cc_start: 0.8138 (tmt) cc_final: 0.7592 (tmm) REVERT: L 138 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7469 (tmt) REVERT: N 138 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8214 (tmt) REVERT: Q 143 ASN cc_start: 0.7755 (m-40) cc_final: 0.7487 (m110) REVERT: R 136 ARG cc_start: 0.8751 (mtp-110) cc_final: 0.8512 (mtp-110) REVERT: T 138 MET cc_start: 0.8517 (tmt) cc_final: 0.7597 (mtt) REVERT: X 138 MET cc_start: 0.8546 (tmt) cc_final: 0.8041 (tmt) outliers start: 7 outliers final: 0 residues processed: 132 average time/residue: 1.9291 time to fit residues: 259.9079 Evaluate side-chains 137 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.116021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.097812 restraints weight = 2743.363| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.34 r_work: 0.3264 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work: 0.2891 rms_B_bonded: 4.93 restraints_weight: 0.1250 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4176 Z= 0.291 Angle : 0.804 5.803 5520 Z= 0.426 Chirality : 0.054 0.153 528 Planarity : 0.004 0.034 720 Dihedral : 5.706 14.892 624 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.56 % Allowed : 22.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (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 HIS 0.002 0.001 HIS F 140 PHE 0.007 0.001 PHE F 141 TYR 0.008 0.001 TYR K 128 ARG 0.004 0.001 ARG U 136 *********************** 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: 6 poor density : 131 time to evaluate : 0.471 Fit side-chains REVERT: C 136 ARG cc_start: 0.8537 (mtt-85) cc_final: 0.8141 (mtt-85) REVERT: C 138 MET cc_start: 0.8261 (tmt) cc_final: 0.7742 (tmm) REVERT: D 136 ARG cc_start: 0.8584 (mtt-85) cc_final: 0.8207 (mtt-85) REVERT: H 136 ARG cc_start: 0.8681 (mtt-85) cc_final: 0.8450 (mtp85) REVERT: H 138 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8002 (tmt) REVERT: I 136 ARG cc_start: 0.8633 (mtt-85) cc_final: 0.8353 (mtp85) REVERT: I 138 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7714 (tmt) REVERT: K 138 MET cc_start: 0.8110 (tmt) cc_final: 0.7584 (tmm) REVERT: L 138 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7466 (tmt) REVERT: N 138 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8218 (tmt) REVERT: R 136 ARG cc_start: 0.8721 (mtp-110) cc_final: 0.8507 (mtp-110) REVERT: T 138 MET cc_start: 0.8473 (tmt) cc_final: 0.7560 (mtt) REVERT: X 138 MET cc_start: 0.8451 (tmt) cc_final: 0.8025 (tmt) outliers start: 6 outliers final: 0 residues processed: 131 average time/residue: 1.8746 time to fit residues: 250.7770 Evaluate side-chains 135 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 chunk 28 optimal weight: 4.9990 chunk 47 optimal weight: 0.0060 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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** N 143 ASN Q 143 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.118436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.100078 restraints weight = 2792.854| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.36 r_work: 0.3303 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4176 Z= 0.196 Angle : 0.722 6.434 5520 Z= 0.377 Chirality : 0.052 0.145 528 Planarity : 0.003 0.031 720 Dihedral : 5.211 14.604 624 Min Nonbonded Distance : 2.671 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.08 % Allowed : 22.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.06 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.17), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 140 PHE 0.007 0.001 PHE F 141 TYR 0.009 0.002 TYR C 128 ARG 0.005 0.001 ARG U 136 *********************** 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 134 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7478 (tmt) REVERT: C 136 ARG cc_start: 0.8146 (mtt-85) cc_final: 0.7790 (mtt-85) REVERT: C 138 MET cc_start: 0.7843 (tmt) cc_final: 0.7269 (tmm) REVERT: D 136 ARG cc_start: 0.8222 (mtt-85) cc_final: 0.7955 (mtt-85) REVERT: F 138 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7585 (tmm) REVERT: H 138 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7566 (tmt) REVERT: I 136 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.8035 (mtm180) REVERT: I 138 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7235 (tmt) REVERT: K 138 MET cc_start: 0.7706 (tmt) cc_final: 0.7157 (tmm) REVERT: L 138 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7118 (tmt) REVERT: N 138 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7773 (tmt) REVERT: R 136 ARG cc_start: 0.8322 (mtp-110) cc_final: 0.8102 (mtp-110) REVERT: R 138 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7334 (tmm) REVERT: T 138 MET cc_start: 0.8018 (tmt) cc_final: 0.7323 (mtt) REVERT: X 138 MET cc_start: 0.7975 (tmt) cc_final: 0.7496 (tmt) outliers start: 8 outliers final: 0 residues processed: 126 average time/residue: 1.9608 time to fit residues: 252.0935 Evaluate side-chains 132 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 7.9990 chunk 25 optimal weight: 0.0670 chunk 2 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 19 optimal weight: 0.0770 chunk 33 optimal weight: 0.1980 chunk 26 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.121589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.103182 restraints weight = 2802.831| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.36 r_work: 0.3359 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4176 Z= 0.154 Angle : 0.677 6.960 5520 Z= 0.346 Chirality : 0.051 0.141 528 Planarity : 0.003 0.028 720 Dihedral : 4.739 14.990 624 Min Nonbonded Distance : 2.680 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.82 % Allowed : 22.92 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.15 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.17), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS I 140 PHE 0.007 0.001 PHE F 141 TYR 0.011 0.002 TYR C 128 ARG 0.011 0.001 ARG U 136 ********************** 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 141 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: C 136 ARG cc_start: 0.8154 (mtt-85) cc_final: 0.7808 (mtt-85) REVERT: C 138 MET cc_start: 0.7839 (tmt) cc_final: 0.7284 (tmm) REVERT: D 136 ARG cc_start: 0.8208 (mtt-85) cc_final: 0.7903 (mtt-85) REVERT: H 138 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7543 (tmt) REVERT: I 136 ARG cc_start: 0.8227 (mtt-85) cc_final: 0.7945 (mtm180) REVERT: K 138 MET cc_start: 0.7585 (tmt) cc_final: 0.7027 (tmm) REVERT: N 138 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7763 (tmt) REVERT: R 138 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7284 (tmm) REVERT: T 138 MET cc_start: 0.8053 (tmt) cc_final: 0.7342 (mtt) REVERT: X 138 MET cc_start: 0.7839 (tmt) cc_final: 0.7349 (tmt) outliers start: 7 outliers final: 0 residues processed: 134 average time/residue: 1.9099 time to fit residues: 261.3161 Evaluate side-chains 132 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain R residue 138 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 0.0470 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.0270 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.0070 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.121005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.102570 restraints weight = 2842.887| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.38 r_work: 0.3349 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2571 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= 0.172 Angle : 0.708 7.052 5520 Z= 0.357 Chirality : 0.051 0.145 528 Planarity : 0.004 0.048 720 Dihedral : 4.774 15.861 624 Min Nonbonded Distance : 2.684 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.15 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.17), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS X 140 PHE 0.007 0.001 PHE F 141 TYR 0.009 0.002 TYR C 128 ARG 0.014 0.001 ARG U 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5028.91 seconds wall clock time: 88 minutes 57.39 seconds (5337.39 seconds total)