Starting phenix.real_space_refine on Thu Mar 6 00:22:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yat_33719/03_2025/7yat_33719.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yat_33719/03_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_33719/03_2025/7yat_33719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yat_33719/03_2025/7yat_33719.map" model { file = "/net/cci-nas-00/data/ceres_data/7yat_33719/03_2025/7yat_33719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yat_33719/03_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-5624/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: 2.01, per 1000 atoms: 0.49 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: 0.86 Conformation dependent library (CDL) restraints added in 468.1 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: 0.76 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: 1.00 Time building geometry restraints manager: 1.06 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: 0.04 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: 1.440 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: 13.500 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.430 ------------------------------------------------------------------------------- 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 : 0.455 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: 2.8354 time to fit residues: 362.8303 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 : 0.607 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.115218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.097173 restraints weight = 2785.626| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.35 r_work: 0.3233 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work: 0.2871 rms_B_bonded: 4.89 restraints_weight: 0.1250 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.2087 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= 0.306 Angle : 0.841 5.513 5520 Z= 0.448 Chirality : 0.055 0.160 528 Planarity : 0.004 0.025 720 Dihedral : 5.754 15.686 624 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 10.85 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 0.009 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 : 0.412 Fit side-chains revert: symmetry clash REVERT: A 139 MET cc_start: 0.9304 (mtm) cc_final: 0.8964 (mtm) REVERT: C 136 ARG cc_start: 0.8613 (mtt-85) cc_final: 0.8255 (mtt-85) REVERT: C 138 MET cc_start: 0.8298 (tmt) cc_final: 0.7854 (tmm) REVERT: D 136 ARG cc_start: 0.8652 (mtt-85) cc_final: 0.8322 (mtt-85) REVERT: E 136 ARG cc_start: 0.8361 (mtt-85) cc_final: 0.8131 (mtt-85) REVERT: I 136 ARG cc_start: 0.8647 (mtt-85) cc_final: 0.8286 (mtm180) REVERT: I 138 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7658 (tmt) REVERT: J 136 ARG cc_start: 0.8569 (mtt-85) cc_final: 0.8317 (mtt-85) REVERT: K 138 MET cc_start: 0.8117 (tmt) cc_final: 0.7603 (tmm) REVERT: N 138 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8217 (tmt) REVERT: R 136 ARG cc_start: 0.8713 (mtp-110) cc_final: 0.8390 (mtp-110) REVERT: T 138 MET cc_start: 0.8451 (tmt) cc_final: 0.7585 (mtt) REVERT: X 138 MET cc_start: 0.8350 (tmt) cc_final: 0.7940 (tmt) REVERT: Y 138 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8334 (tmt) outliers start: 9 outliers final: 0 residues processed: 128 average time/residue: 2.1253 time to fit residues: 277.1896 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 : 0.393 ------------------------------------------------------------------------------- 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: 4.9990 chunk 42 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 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: 3.5788 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.111548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.093796 restraints weight = 2760.017| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.32 r_work: 0.3183 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work: 0.2818 rms_B_bonded: 4.72 restraints_weight: 0.1250 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9136 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 4176 Z= 0.619 Angle : 1.044 6.217 5520 Z= 0.562 Chirality : 0.059 0.181 528 Planarity : 0.005 0.030 720 Dihedral : 6.471 19.922 624 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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 (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: -4.87 (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 HIS 0.005 0.001 HIS F 140 PHE 0.006 0.002 PHE S 141 TYR 0.006 0.002 TYR K 128 ARG 0.006 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 143 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.420 Fit side-chains REVERT: C 136 ARG cc_start: 0.8581 (mtt-85) cc_final: 0.8238 (mtt-85) REVERT: C 138 MET cc_start: 0.8320 (tmt) cc_final: 0.7885 (tmm) REVERT: D 136 ARG cc_start: 0.8625 (mtt-85) cc_final: 0.8291 (mtt-85) REVERT: F 138 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7813 (tmt) REVERT: H 136 ARG cc_start: 0.8706 (mtt-85) cc_final: 0.8459 (mtm180) REVERT: I 136 ARG cc_start: 0.8694 (mtt-85) cc_final: 0.8397 (mtp85) REVERT: I 138 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7761 (tmt) REVERT: J 136 ARG cc_start: 0.8545 (mtt-85) cc_final: 0.8293 (mtt-85) REVERT: L 138 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7403 (tmt) REVERT: N 138 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8187 (tmt) REVERT: N 143 ASN cc_start: 0.7643 (m-40) cc_final: 0.7341 (m-40) REVERT: P 138 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7963 (tmt) REVERT: Q 143 ASN cc_start: 0.7752 (m-40) cc_final: 0.7500 (m110) REVERT: R 136 ARG cc_start: 0.8744 (mtp-110) cc_final: 0.8485 (mtp-110) REVERT: T 138 MET cc_start: 0.8498 (tmt) cc_final: 0.7581 (mtt) REVERT: X 138 MET cc_start: 0.8519 (tmt) cc_final: 0.8012 (tmt) outliers start: 10 outliers final: 0 residues processed: 133 average time/residue: 2.2015 time to fit residues: 297.9595 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 : 0.479 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain P 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: 4.9990 chunk 7 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 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 = 0.3707 r_free = 0.3707 target = 0.115888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.097643 restraints weight = 2802.734| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.35 r_work: 0.3257 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work: 0.2892 rms_B_bonded: 4.92 restraints_weight: 0.1250 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4176 Z= 0.269 Angle : 0.797 5.227 5520 Z= 0.423 Chirality : 0.054 0.150 528 Planarity : 0.004 0.032 720 Dihedral : 5.629 14.320 624 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.60 % Allowed : 20.57 % Favored : 76.82 % 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: -4.98 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.17), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 140 PHE 0.007 0.001 PHE F 141 TYR 0.009 0.001 TYR K 128 ARG 0.004 0.001 ARG U 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 : 0.451 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7658 (tmt) REVERT: C 136 ARG cc_start: 0.8531 (mtt-85) cc_final: 0.8154 (mtt-85) REVERT: C 138 MET cc_start: 0.8257 (tmt) cc_final: 0.7794 (tmm) REVERT: D 136 ARG cc_start: 0.8579 (mtt-85) cc_final: 0.8287 (mtt-85) REVERT: H 138 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8008 (tmt) REVERT: I 136 ARG cc_start: 0.8624 (mtt-85) cc_final: 0.8331 (mtp85) REVERT: I 138 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.7747 (tmt) REVERT: J 136 ARG cc_start: 0.8553 (mtt-85) cc_final: 0.8324 (mtt-85) REVERT: K 138 MET cc_start: 0.8127 (tmt) cc_final: 0.7582 (tmm) REVERT: L 138 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7469 (tmt) REVERT: N 138 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8185 (tmt) REVERT: R 136 ARG cc_start: 0.8694 (mtp-110) cc_final: 0.8480 (mtp-110) REVERT: S 139 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8958 (mtm) REVERT: T 138 MET cc_start: 0.8491 (tmt) cc_final: 0.7585 (mtt) REVERT: X 138 MET cc_start: 0.8399 (tmt) cc_final: 0.7983 (tmt) outliers start: 10 outliers final: 0 residues processed: 127 average time/residue: 1.9914 time to fit residues: 257.8207 Evaluate side-chains 133 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 S 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: 7.9990 chunk 10 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 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 = 0.3643 r_free = 0.3643 target = 0.112364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.094270 restraints weight = 2850.884| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.36 r_work: 0.3193 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work: 0.2828 rms_B_bonded: 4.84 restraints_weight: 0.1250 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 4176 Z= 0.534 Angle : 0.982 5.748 5520 Z= 0.528 Chirality : 0.058 0.171 528 Planarity : 0.005 0.047 720 Dihedral : 6.332 18.779 624 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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 (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: -4.92 (0.21), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.16), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 140 PHE 0.008 0.002 PHE S 141 TYR 0.007 0.002 TYR K 128 ARG 0.007 0.001 ARG U 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 : 0.435 Fit side-chains REVERT: C 136 ARG cc_start: 0.8584 (mtt-85) cc_final: 0.8223 (mtt-85) REVERT: C 138 MET cc_start: 0.8305 (tmt) cc_final: 0.7849 (tmm) REVERT: D 136 ARG cc_start: 0.8618 (mtt-85) cc_final: 0.8269 (mtt-85) REVERT: F 138 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7754 (tmt) REVERT: H 136 ARG cc_start: 0.8686 (mtt-85) cc_final: 0.8474 (mtm180) REVERT: H 138 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8083 (tmt) REVERT: I 136 ARG cc_start: 0.8685 (mtt-85) cc_final: 0.8436 (mtp85) REVERT: I 138 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.7853 (tmt) REVERT: J 136 ARG cc_start: 0.8544 (mtt-85) cc_final: 0.8337 (mtt-85) REVERT: K 138 MET cc_start: 0.8176 (tmt) cc_final: 0.7630 (tmm) REVERT: L 138 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7449 (tmt) REVERT: N 138 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8221 (tmt) REVERT: N 143 ASN cc_start: 0.7662 (m-40) cc_final: 0.7319 (m-40) REVERT: Q 143 ASN cc_start: 0.7700 (m-40) cc_final: 0.7422 (m110) REVERT: T 138 MET cc_start: 0.8504 (tmt) cc_final: 0.7588 (mtt) REVERT: X 138 MET cc_start: 0.8534 (tmt) cc_final: 0.8024 (tmt) outliers start: 8 outliers final: 0 residues processed: 131 average time/residue: 1.9043 time to fit residues: 254.6275 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 : 0.739 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.0050 chunk 25 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.118586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.100167 restraints weight = 2814.080| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.36 r_work: 0.3303 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2396 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= 0.177 Angle : 0.720 5.968 5520 Z= 0.376 Chirality : 0.053 0.144 528 Planarity : 0.003 0.034 720 Dihedral : 5.293 13.288 624 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.34 % Allowed : 20.83 % Favored : 76.82 % 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: -5.05 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (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 0.010 0.002 TYR K 128 ARG 0.005 0.001 ARG U 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 138 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7227 (tmt) REVERT: C 136 ARG cc_start: 0.8165 (mtt-85) cc_final: 0.7805 (mtt-85) REVERT: C 138 MET cc_start: 0.7803 (tmt) cc_final: 0.7206 (tmm) REVERT: D 136 ARG cc_start: 0.8204 (mtt-85) cc_final: 0.7934 (mtt-85) REVERT: H 138 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7493 (tmt) REVERT: I 136 ARG cc_start: 0.8272 (mtt-85) cc_final: 0.7973 (mtp85) REVERT: I 138 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7245 (tmt) REVERT: J 136 ARG cc_start: 0.8213 (mtt-85) cc_final: 0.7998 (mtt-85) REVERT: K 138 MET cc_start: 0.7785 (tmt) cc_final: 0.7225 (tmm) REVERT: L 138 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7120 (tmt) REVERT: N 138 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7766 (tmt) REVERT: R 138 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7306 (tmm) REVERT: S 139 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8620 (mtm) REVERT: T 138 MET cc_start: 0.8061 (tmt) cc_final: 0.7341 (mtt) REVERT: X 138 MET cc_start: 0.7973 (tmt) cc_final: 0.7508 (tmt) outliers start: 9 outliers final: 0 residues processed: 129 average time/residue: 2.8502 time to fit residues: 373.5405 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 : 0.467 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 40 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 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 = 0.3646 r_free = 0.3646 target = 0.112365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.094278 restraints weight = 2809.482| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.35 r_work: 0.3195 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work: 0.2828 rms_B_bonded: 4.82 restraints_weight: 0.1250 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 4176 Z= 0.558 Angle : 0.997 6.115 5520 Z= 0.535 Chirality : 0.058 0.167 528 Planarity : 0.005 0.058 720 Dihedral : 6.383 18.101 624 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.34 % Allowed : 21.09 % 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: -4.97 (0.21), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.16), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 140 PHE 0.008 0.002 PHE S 141 TYR 0.005 0.002 TYR K 128 ARG 0.008 0.001 ARG V 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 141 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.571 Fit side-chains REVERT: C 136 ARG cc_start: 0.8590 (mtt-85) cc_final: 0.8220 (mtt-85) REVERT: C 138 MET cc_start: 0.8297 (tmt) cc_final: 0.7817 (tmm) REVERT: D 136 ARG cc_start: 0.8663 (mtt-85) cc_final: 0.8300 (mtt-85) REVERT: F 138 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7865 (tmt) REVERT: H 136 ARG cc_start: 0.8716 (mtt-85) cc_final: 0.8435 (mtm180) REVERT: H 138 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8094 (tmt) REVERT: I 136 ARG cc_start: 0.8686 (mtt-85) cc_final: 0.8484 (mtp85) REVERT: I 138 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.7836 (tmt) REVERT: L 138 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7432 (tmt) REVERT: N 138 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8227 (tmt) REVERT: N 143 ASN cc_start: 0.7663 (m-40) cc_final: 0.7269 (m-40) REVERT: Q 143 ASN cc_start: 0.7750 (m-40) cc_final: 0.7442 (m110) REVERT: T 138 MET cc_start: 0.8518 (tmt) cc_final: 0.7600 (mtt) REVERT: X 138 MET cc_start: 0.8551 (tmt) cc_final: 0.8052 (tmt) outliers start: 9 outliers final: 1 residues processed: 132 average time/residue: 2.4563 time to fit residues: 329.8291 Evaluate side-chains 138 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 O 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: 4.9990 chunk 46 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3726 r_free = 0.3726 target = 0.116549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.098276 restraints weight = 2755.036| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.34 r_work: 0.3272 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work: 0.2900 rms_B_bonded: 4.95 restraints_weight: 0.1250 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4176 Z= 0.256 Angle : 0.790 6.189 5520 Z= 0.415 Chirality : 0.053 0.152 528 Planarity : 0.004 0.045 720 Dihedral : 5.682 14.437 624 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.82 % Allowed : 22.66 % 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: -4.98 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.17), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 140 PHE 0.007 0.001 PHE F 141 TYR 0.009 0.001 TYR K 128 ARG 0.007 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 135 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.447 Fit side-chains REVERT: A 138 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7608 (tmt) REVERT: C 136 ARG cc_start: 0.8533 (mtt-85) cc_final: 0.8138 (mtt-85) REVERT: C 138 MET cc_start: 0.8248 (tmt) cc_final: 0.7721 (tmm) REVERT: D 136 ARG cc_start: 0.8619 (mtt-85) cc_final: 0.8320 (mtt-85) REVERT: H 136 ARG cc_start: 0.8684 (mtt-85) cc_final: 0.8461 (mtp85) REVERT: H 138 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7994 (tmt) REVERT: I 136 ARG cc_start: 0.8654 (mtt-85) cc_final: 0.8385 (mtp85) REVERT: I 138 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7706 (tmt) REVERT: K 138 MET cc_start: 0.8150 (tmt) cc_final: 0.7711 (tmm) REVERT: L 138 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7478 (tmt) REVERT: N 138 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8192 (tmt) REVERT: R 136 ARG cc_start: 0.8750 (mtp-110) cc_final: 0.8490 (mtp-110) REVERT: T 138 MET cc_start: 0.8471 (tmt) cc_final: 0.7566 (mtt) REVERT: X 138 MET cc_start: 0.8439 (tmt) cc_final: 0.7939 (tmt) outliers start: 7 outliers final: 0 residues processed: 128 average time/residue: 1.8961 time to fit residues: 247.7150 Evaluate side-chains 133 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 0.1980 chunk 28 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.116639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.098307 restraints weight = 2796.828| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.36 r_work: 0.3275 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work: 0.2904 rms_B_bonded: 4.98 restraints_weight: 0.1250 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4176 Z= 0.257 Angle : 0.782 6.329 5520 Z= 0.409 Chirality : 0.053 0.152 528 Planarity : 0.004 0.054 720 Dihedral : 5.555 15.224 624 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 11.59 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: -5.02 (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 HIS 0.001 0.000 HIS F 140 PHE 0.007 0.001 PHE F 141 TYR 0.008 0.001 TYR E 128 ARG 0.008 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 133 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: C 136 ARG cc_start: 0.8546 (mtt-85) cc_final: 0.8154 (mtt-85) REVERT: C 138 MET cc_start: 0.8233 (tmt) cc_final: 0.7729 (tmm) REVERT: D 136 ARG cc_start: 0.8630 (mtt-85) cc_final: 0.8338 (mtt-85) REVERT: H 138 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8016 (tmt) REVERT: I 136 ARG cc_start: 0.8655 (mtt-85) cc_final: 0.8385 (mtp85) REVERT: I 138 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.7760 (tmt) REVERT: K 138 MET cc_start: 0.8098 (tmt) cc_final: 0.7592 (tmm) REVERT: L 138 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7517 (tmt) REVERT: N 138 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8224 (tmt) REVERT: T 138 MET cc_start: 0.8476 (tmt) cc_final: 0.7573 (mtt) REVERT: X 138 MET cc_start: 0.8435 (tmt) cc_final: 0.8011 (tmt) outliers start: 7 outliers final: 0 residues processed: 126 average time/residue: 1.8671 time to fit residues: 239.9631 Evaluate side-chains 130 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.116003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.097606 restraints weight = 2791.719| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.36 r_work: 0.3262 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work: 0.2889 rms_B_bonded: 4.96 restraints_weight: 0.1250 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.2417 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= 0.323 Angle : 0.837 6.628 5520 Z= 0.439 Chirality : 0.054 0.167 528 Planarity : 0.004 0.055 720 Dihedral : 5.768 15.903 624 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % 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: -4.98 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (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 0.007 0.001 TYR E 128 ARG 0.009 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 137 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: C 136 ARG cc_start: 0.8558 (mtt-85) cc_final: 0.8190 (mtt-85) REVERT: C 138 MET cc_start: 0.8244 (tmt) cc_final: 0.7745 (tmm) REVERT: D 136 ARG cc_start: 0.8653 (mtt-85) cc_final: 0.8351 (mtt-85) REVERT: H 138 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8012 (tmt) REVERT: I 136 ARG cc_start: 0.8652 (mtt-85) cc_final: 0.8391 (mtp85) REVERT: I 138 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.7703 (tmt) REVERT: K 138 MET cc_start: 0.8132 (tmt) cc_final: 0.7587 (tmm) REVERT: L 138 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7487 (tmt) REVERT: M 136 ARG cc_start: 0.8632 (mtp85) cc_final: 0.8416 (mtp-110) REVERT: N 138 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8210 (tmt) REVERT: T 138 MET cc_start: 0.8497 (tmt) cc_final: 0.7580 (mtt) REVERT: X 138 MET cc_start: 0.8455 (tmt) cc_final: 0.8037 (tmt) outliers start: 6 outliers final: 0 residues processed: 131 average time/residue: 1.9325 time to fit residues: 258.3706 Evaluate side-chains 134 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 0.0000 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.0970 chunk 8 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.4982 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.120185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.101680 restraints weight = 2828.055| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.37 r_work: 0.3335 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2520 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= 0.168 Angle : 0.701 6.639 5520 Z= 0.359 Chirality : 0.052 0.155 528 Planarity : 0.004 0.041 720 Dihedral : 5.090 15.007 624 Min Nonbonded Distance : 2.680 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.56 % Allowed : 22.40 % 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: -5.11 (0.23), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.17), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS X 140 PHE 0.008 0.001 PHE F 141 TYR 0.010 0.002 TYR U 128 ARG 0.008 0.001 ARG U 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5858.70 seconds wall clock time: 101 minutes 54.79 seconds (6114.79 seconds total)