Starting phenix.real_space_refine on Mon Sep 23 17:30:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yat_33719/09_2024/7yat_33719.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yat_33719/09_2024/7yat_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yat_33719/09_2024/7yat_33719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yat_33719/09_2024/7yat_33719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yat_33719/09_2024/7yat_33719.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yat_33719/09_2024/7yat_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-5461/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: 1.57, per 1000 atoms: 0.38 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: 0.96 Conformation dependent library (CDL) restraints added in 523.4 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: 0.85 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: 1.05 Time building geometry restraints manager: 1.13 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.290 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.045 4176 Z= 0.677 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 fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.525 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: 1.9286 time to fit residues: 248.0419 Evaluate side-chains 125 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 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 fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 139 MET cc_start: 0.8638 (mtm) cc_final: 0.8260 (mtm) REVERT: C 136 ARG cc_start: 0.7660 (mtt-85) cc_final: 0.7451 (mtt-85) REVERT: C 138 MET cc_start: 0.7158 (tmt) cc_final: 0.6665 (tmm) REVERT: D 136 ARG cc_start: 0.7674 (mtt-85) cc_final: 0.7451 (mtt-85) REVERT: E 136 ARG cc_start: 0.7737 (mtt-85) cc_final: 0.7524 (mtt-85) REVERT: I 136 ARG cc_start: 0.7711 (mtt-85) cc_final: 0.7440 (mtm180) REVERT: I 138 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.6463 (tmt) REVERT: J 136 ARG cc_start: 0.7664 (mtt-85) cc_final: 0.7460 (mtt-85) REVERT: K 138 MET cc_start: 0.7224 (tmt) cc_final: 0.6681 (tmm) REVERT: N 138 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.7038 (tmt) REVERT: R 136 ARG cc_start: 0.7724 (mtp-110) cc_final: 0.7456 (mtp-110) REVERT: S 138 MET cc_start: 0.7321 (tmt) cc_final: 0.7113 (tmt) REVERT: T 138 MET cc_start: 0.7239 (tmt) cc_final: 0.6919 (mtt) REVERT: X 138 MET cc_start: 0.7375 (tmt) cc_final: 0.6908 (tmt) outliers start: 9 outliers final: 0 residues processed: 128 average time/residue: 1.8794 time to fit residues: 245.9801 Evaluate side-chains 128 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain N residue 138 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 0.3980 chunk 36 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4176 Z= 0.259 Angle : 0.779 5.435 5520 Z= 0.415 Chirality : 0.053 0.146 528 Planarity : 0.003 0.024 720 Dihedral : 5.378 14.478 624 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.82 % Allowed : 21.35 % 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: -4.96 (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 A 140 PHE 0.007 0.002 PHE F 141 TYR 0.008 0.001 TYR K 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 134 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 0.479 Fit side-chains REVERT: A 138 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.6670 (tmt) REVERT: C 136 ARG cc_start: 0.7594 (mtt-85) cc_final: 0.7393 (mtt-85) REVERT: C 138 MET cc_start: 0.7140 (tmt) cc_final: 0.6599 (tmm) REVERT: H 136 ARG cc_start: 0.7734 (mtt-85) cc_final: 0.7522 (mtp85) REVERT: I 136 ARG cc_start: 0.7701 (mtt-85) cc_final: 0.7477 (mtm180) REVERT: I 138 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.6452 (tmt) REVERT: K 138 MET cc_start: 0.7270 (tmt) cc_final: 0.6703 (tmm) REVERT: L 138 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6354 (tmt) REVERT: S 138 MET cc_start: 0.7404 (tmt) cc_final: 0.7155 (tmt) REVERT: T 138 MET cc_start: 0.7252 (tmt) cc_final: 0.6906 (mtt) REVERT: X 138 MET cc_start: 0.7415 (tmt) cc_final: 0.6936 (tmt) outliers start: 7 outliers final: 0 residues processed: 127 average time/residue: 1.6410 time to fit residues: 212.7154 Evaluate side-chains 129 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain L residue 138 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4176 Z= 0.406 Angle : 0.892 5.680 5520 Z= 0.478 Chirality : 0.055 0.162 528 Planarity : 0.004 0.030 720 Dihedral : 5.862 16.949 624 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 : 21.61 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.91 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (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 0.008 0.001 TYR K 128 ARG 0.005 0.001 ARG V 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 139 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6762 (tmt) REVERT: C 136 ARG cc_start: 0.7614 (mtt-85) cc_final: 0.7345 (mtt-85) REVERT: C 138 MET cc_start: 0.7225 (tmt) cc_final: 0.6668 (tmm) REVERT: F 138 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6678 (tmt) REVERT: H 138 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6792 (tmt) REVERT: I 136 ARG cc_start: 0.7708 (mtt-85) cc_final: 0.7463 (mtp85) REVERT: I 138 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.6572 (tmt) REVERT: L 138 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6367 (tmt) REVERT: N 138 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.7007 (tmt) REVERT: T 138 MET cc_start: 0.7267 (tmt) cc_final: 0.6987 (mtt) REVERT: X 138 MET cc_start: 0.7485 (tmt) cc_final: 0.6994 (tmt) outliers start: 8 outliers final: 0 residues processed: 131 average time/residue: 1.7661 time to fit residues: 236.4663 Evaluate side-chains 136 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 11 optimal weight: 0.0010 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.1980 chunk 27 optimal weight: 0.0770 overall best weight: 0.3744 ------------------------------------------------------------------------------- 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 Q 143 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4176 Z= 0.150 Angle : 0.671 5.433 5520 Z= 0.352 Chirality : 0.052 0.136 528 Planarity : 0.003 0.023 720 Dihedral : 4.893 12.280 624 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.34 % Allowed : 21.35 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.09 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.17), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS X 140 PHE 0.007 0.001 PHE F 141 TYR 0.009 0.001 TYR K 128 ARG 0.006 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 138 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6629 (tmt) REVERT: C 138 MET cc_start: 0.7167 (tmt) cc_final: 0.6569 (tmm) REVERT: H 138 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6786 (tmt) REVERT: H 139 MET cc_start: 0.8635 (mtm) cc_final: 0.8310 (mpt) REVERT: I 136 ARG cc_start: 0.7630 (mtt-85) cc_final: 0.7377 (mtm180) REVERT: I 138 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.6506 (tmt) REVERT: K 138 MET cc_start: 0.7095 (tmt) cc_final: 0.6492 (tmm) REVERT: L 138 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6432 (tmt) REVERT: N 138 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.7048 (tmt) REVERT: R 138 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6585 (tmm) REVERT: T 138 MET cc_start: 0.7253 (tmt) cc_final: 0.6974 (mtt) REVERT: V 139 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8274 (mtm) REVERT: X 138 MET cc_start: 0.7320 (tmt) cc_final: 0.6820 (tmt) outliers start: 9 outliers final: 0 residues processed: 129 average time/residue: 1.8035 time to fit residues: 237.5800 Evaluate side-chains 134 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 V residue 139 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.2980 chunk 46 optimal weight: 8.9990 chunk 38 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4176 Z= 0.209 Angle : 0.718 6.053 5520 Z= 0.378 Chirality : 0.052 0.143 528 Planarity : 0.003 0.038 720 Dihedral : 4.976 13.773 624 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.08 % Allowed : 22.66 % 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: -5.05 (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 H 140 PHE 0.008 0.001 PHE F 141 TYR 0.008 0.001 TYR K 128 ARG 0.008 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 136 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 138 MET cc_start: 0.7180 (tmt) cc_final: 0.6565 (tmm) REVERT: F 138 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6633 (tmt) REVERT: H 138 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6750 (tmt) REVERT: H 139 MET cc_start: 0.8628 (mtm) cc_final: 0.8296 (mpt) REVERT: I 136 ARG cc_start: 0.7646 (mtt-85) cc_final: 0.7419 (mtm180) REVERT: K 138 MET cc_start: 0.7198 (tmt) cc_final: 0.6611 (tmm) REVERT: L 138 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6450 (tmt) REVERT: N 138 MET cc_start: 0.7271 (OUTLIER) cc_final: 0.7043 (tmt) REVERT: R 138 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6581 (tmm) REVERT: T 138 MET cc_start: 0.7275 (tmt) cc_final: 0.6947 (mtt) REVERT: V 139 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8264 (mtm) REVERT: X 138 MET cc_start: 0.7356 (tmt) cc_final: 0.6856 (tmt) outliers start: 8 outliers final: 0 residues processed: 128 average time/residue: 1.8688 time to fit residues: 244.2284 Evaluate side-chains 134 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain H 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 V residue 139 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 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 : 0.004 0.030 4176 Z= 0.281 Angle : 0.776 5.985 5520 Z= 0.411 Chirality : 0.052 0.152 528 Planarity : 0.004 0.039 720 Dihedral : 5.327 15.028 624 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.82 % Allowed : 23.44 % Favored : 74.74 % 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: -4.96 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (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 K 128 ARG 0.010 0.001 ARG U 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 134 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: C 136 ARG cc_start: 0.7659 (mtp85) cc_final: 0.7380 (mtt-85) REVERT: C 138 MET cc_start: 0.7187 (tmt) cc_final: 0.6540 (tmm) REVERT: F 138 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6700 (tmt) REVERT: H 138 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6776 (tmt) REVERT: I 136 ARG cc_start: 0.7659 (mtt-85) cc_final: 0.7437 (mtp85) REVERT: K 138 MET cc_start: 0.7273 (tmt) cc_final: 0.6669 (tmm) REVERT: L 138 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6448 (tmt) REVERT: N 138 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.7040 (tmt) REVERT: T 138 MET cc_start: 0.7312 (tmt) cc_final: 0.7008 (mtt) REVERT: X 138 MET cc_start: 0.7421 (tmt) cc_final: 0.6925 (tmt) outliers start: 7 outliers final: 0 residues processed: 127 average time/residue: 1.9040 time to fit residues: 246.6992 Evaluate side-chains 131 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain H 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 29 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4176 Z= 0.276 Angle : 0.783 6.144 5520 Z= 0.414 Chirality : 0.052 0.155 528 Planarity : 0.005 0.046 720 Dihedral : 5.409 15.334 624 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.56 % Allowed : 24.22 % Favored : 74.22 % 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: -4.95 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (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 K 128 ARG 0.011 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 134 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: C 138 MET cc_start: 0.7196 (tmt) cc_final: 0.6587 (tmm) REVERT: F 138 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6715 (tmt) REVERT: H 138 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6765 (tmt) REVERT: I 136 ARG cc_start: 0.7665 (mtt-85) cc_final: 0.7419 (mtp85) REVERT: I 138 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.6594 (tmt) REVERT: K 138 MET cc_start: 0.7291 (tmt) cc_final: 0.6691 (tmm) REVERT: L 138 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6404 (tmt) REVERT: N 138 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.7034 (tmt) REVERT: R 138 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6553 (tmm) REVERT: T 138 MET cc_start: 0.7326 (tmt) cc_final: 0.7020 (mtt) REVERT: X 138 MET cc_start: 0.7435 (tmt) cc_final: 0.6949 (tmt) outliers start: 6 outliers final: 0 residues processed: 128 average time/residue: 1.8857 time to fit residues: 246.3460 Evaluate side-chains 134 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain R residue 138 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 0.0370 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 143 ASN Q 143 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4176 Z= 0.192 Angle : 0.706 6.362 5520 Z= 0.369 Chirality : 0.051 0.153 528 Planarity : 0.004 0.049 720 Dihedral : 5.034 14.876 624 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.56 % Allowed : 23.96 % Favored : 74.48 % 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 (0.23), 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 A 140 PHE 0.007 0.001 PHE F 141 TYR 0.008 0.001 TYR K 128 ARG 0.011 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 fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: C 136 ARG cc_start: 0.7616 (mtp85) cc_final: 0.7360 (mtt-85) REVERT: C 138 MET cc_start: 0.7153 (tmt) cc_final: 0.6524 (tmm) REVERT: H 139 MET cc_start: 0.8628 (mtm) cc_final: 0.8297 (mpt) REVERT: I 136 ARG cc_start: 0.7611 (mtt-85) cc_final: 0.7400 (mtm180) REVERT: K 138 MET cc_start: 0.7205 (tmt) cc_final: 0.6607 (tmm) REVERT: L 138 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.6450 (tmt) REVERT: N 138 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.7035 (tmt) REVERT: R 138 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6531 (tmm) REVERT: T 138 MET cc_start: 0.7292 (tmt) cc_final: 0.6979 (mtt) REVERT: X 138 MET cc_start: 0.7299 (tmt) cc_final: 0.6795 (tmt) outliers start: 6 outliers final: 0 residues processed: 128 average time/residue: 1.8554 time to fit residues: 242.3717 Evaluate side-chains 129 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 44 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 0.0470 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2457 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= 0.265 Angle : 0.779 6.679 5520 Z= 0.407 Chirality : 0.052 0.162 528 Planarity : 0.004 0.056 720 Dihedral : 5.322 15.524 624 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.30 % Allowed : 23.96 % Favored : 74.74 % 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: -4.99 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (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 0.007 0.001 TYR K 128 ARG 0.013 0.001 ARG V 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 133 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: C 136 ARG cc_start: 0.7645 (mtp85) cc_final: 0.7407 (mtt-85) REVERT: C 138 MET cc_start: 0.7176 (tmt) cc_final: 0.6536 (tmm) REVERT: I 136 ARG cc_start: 0.7679 (mtt-85) cc_final: 0.7457 (mtp85) REVERT: I 138 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.6544 (tmt) REVERT: K 138 MET cc_start: 0.7294 (tmt) cc_final: 0.6697 (tmm) REVERT: L 138 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6450 (tmt) REVERT: N 138 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.7048 (tmt) REVERT: R 138 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6570 (tmm) REVERT: T 138 MET cc_start: 0.7310 (tmt) cc_final: 0.7034 (mtt) REVERT: X 138 MET cc_start: 0.7386 (tmt) cc_final: 0.6897 (tmt) outliers start: 5 outliers final: 0 residues processed: 128 average time/residue: 2.0500 time to fit residues: 267.7558 Evaluate side-chains 132 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain N residue 138 MET 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 38 optimal weight: 0.0670 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 0.0470 chunk 32 optimal weight: 6.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.121897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.103467 restraints weight = 2782.052| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.36 r_work: 0.3366 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4176 Z= 0.153 Angle : 0.673 6.721 5520 Z= 0.344 Chirality : 0.051 0.149 528 Planarity : 0.004 0.049 720 Dihedral : 4.733 14.729 624 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.26 % Allowed : 25.26 % Favored : 74.48 % 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: -5.12 (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 0.001 HIS X 140 PHE 0.007 0.001 PHE F 141 TYR 0.009 0.001 TYR M 128 ARG 0.013 0.001 ARG V 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3637.41 seconds wall clock time: 65 minutes 0.57 seconds (3900.57 seconds total)