Starting phenix.real_space_refine on Thu May 22 03:33:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fjs_29246/05_2025/8fjs_29246.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fjs_29246/05_2025/8fjs_29246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fjs_29246/05_2025/8fjs_29246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fjs_29246/05_2025/8fjs_29246.map" model { file = "/net/cci-nas-00/data/ceres_data/8fjs_29246/05_2025/8fjs_29246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fjs_29246/05_2025/8fjs_29246.cif" } resolution = 3.0 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= 0.003 sd= 0.100 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 25 5.16 5 C 14300 2.51 5 N 3600 2.21 5 O 4625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22550 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} 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, W, V, Y, X Time building chain proxies: 5.35, per 1000 atoms: 0.24 Number of scatterers: 22550 At special positions: 0 Unit cell: (90.72, 91.8, 219.24, 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 25 16.00 O 4625 8.00 N 3600 7.00 C 14300 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: 5.21 Conformation dependent library (CDL) restraints added in 3.3 seconds 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5750 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 50 sheets defined 29.6% alpha, 47.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.71 Creating SS restraints... Processing helix chain 'A' and resid 1 through 34 removed outlier: 3.603A pdb=" N VAL A 5 " --> pdb=" O LEU A 1 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY A 106 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A 108 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.964A pdb=" N GLY B 106 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL B 108 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY C 34 " --> pdb=" O GLY C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY C 106 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL C 108 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY D 106 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL D 108 " --> pdb=" O ARG D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY E 106 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL E 108 " --> pdb=" O ARG E 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY F 34 " --> pdb=" O GLY F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY F 106 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL F 108 " --> pdb=" O ARG F 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY G 34 " --> pdb=" O GLY G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY G 106 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL G 108 " --> pdb=" O ARG G 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY H 34 " --> pdb=" O GLY H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY H 106 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL H 108 " --> pdb=" O ARG H 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY I 34 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 108 removed outlier: 3.964A pdb=" N GLY I 106 " --> pdb=" O THR I 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL I 108 " --> pdb=" O ARG I 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY J 34 " --> pdb=" O GLY J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY J 106 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL J 108 " --> pdb=" O ARG J 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY K 34 " --> pdb=" O GLY K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY K 106 " --> pdb=" O THR K 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL K 108 " --> pdb=" O ARG K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY L 34 " --> pdb=" O GLY L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY L 106 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL L 108 " --> pdb=" O ARG L 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY M 34 " --> pdb=" O GLY M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY M 106 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL M 108 " --> pdb=" O ARG M 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY N 34 " --> pdb=" O GLY N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 108 removed outlier: 3.964A pdb=" N GLY N 106 " --> pdb=" O THR N 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL N 108 " --> pdb=" O ARG N 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY O 34 " --> pdb=" O GLY O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY O 106 " --> pdb=" O THR O 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL O 108 " --> pdb=" O ARG O 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY P 34 " --> pdb=" O GLY P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 108 removed outlier: 3.964A pdb=" N GLY P 106 " --> pdb=" O THR P 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL P 108 " --> pdb=" O ARG P 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY Q 34 " --> pdb=" O GLY Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY Q 106 " --> pdb=" O THR Q 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL Q 108 " --> pdb=" O ARG Q 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY R 34 " --> pdb=" O GLY R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY R 106 " --> pdb=" O THR R 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL R 108 " --> pdb=" O ARG R 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY S 106 " --> pdb=" O THR S 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL S 108 " --> pdb=" O ARG S 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY T 34 " --> pdb=" O GLY T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY T 106 " --> pdb=" O THR T 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL T 108 " --> pdb=" O ARG T 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY U 34 " --> pdb=" O GLY U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY U 106 " --> pdb=" O THR U 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL U 108 " --> pdb=" O ARG U 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY V 34 " --> pdb=" O GLY V 30 " (cutoff:3.500A) Processing helix chain 'V' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY V 106 " --> pdb=" O THR V 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL V 108 " --> pdb=" O ARG V 105 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY W 34 " --> pdb=" O GLY W 30 " (cutoff:3.500A) Processing helix chain 'W' and resid 103 through 108 removed outlier: 3.964A pdb=" N GLY W 106 " --> pdb=" O THR W 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL W 108 " --> pdb=" O ARG W 105 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY X 34 " --> pdb=" O GLY X 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY X 106 " --> pdb=" O THR X 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL X 108 " --> pdb=" O ARG X 105 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY Y 34 " --> pdb=" O GLY Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 108 removed outlier: 3.964A pdb=" N GLY Y 106 " --> pdb=" O THR Y 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL Y 108 " --> pdb=" O ARG Y 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.777A pdb=" N THR A 52 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 64 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER A 77 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL A 78 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR A 67 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 64 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR B 52 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 64 " --> pdb=" O ILE B 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 38 through 40 removed outlier: 3.701A pdb=" N SER B 77 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL B 78 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR B 67 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 64 " --> pdb=" O ILE B 84 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 38 through 40 removed outlier: 3.777A pdb=" N THR C 52 " --> pdb=" O SER C 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR C 64 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER C 77 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL C 78 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR C 67 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR C 64 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR D 52 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 64 " --> pdb=" O ILE D 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER D 77 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL D 78 " --> pdb=" O THR D 67 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR D 67 " --> pdb=" O VAL D 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 64 " --> pdb=" O ILE D 84 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 38 through 40 removed outlier: 3.777A pdb=" N THR E 52 " --> pdb=" O SER E 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR E 64 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER E 77 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL E 78 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR E 67 " --> pdb=" O VAL E 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR E 64 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR F 52 " --> pdb=" O SER F 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR F 64 " --> pdb=" O ILE F 84 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER F 77 " --> pdb=" O SER F 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL F 78 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR F 67 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR F 64 " --> pdb=" O ILE F 84 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR G 52 " --> pdb=" O SER G 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR G 64 " --> pdb=" O ILE G 84 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER G 77 " --> pdb=" O SER G 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL G 78 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR G 67 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR G 64 " --> pdb=" O ILE G 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR H 52 " --> pdb=" O SER H 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR H 64 " --> pdb=" O ILE H 84 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER H 77 " --> pdb=" O SER H 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL H 78 " --> pdb=" O THR H 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR H 67 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR H 64 " --> pdb=" O ILE H 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR I 52 " --> pdb=" O SER I 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR I 64 " --> pdb=" O ILE I 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER I 77 " --> pdb=" O SER I 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL I 78 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR I 67 " --> pdb=" O VAL I 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR I 64 " --> pdb=" O ILE I 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR J 52 " --> pdb=" O SER J 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR J 64 " --> pdb=" O ILE J 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER J 77 " --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL J 78 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR J 67 " --> pdb=" O VAL J 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR J 64 " --> pdb=" O ILE J 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 38 through 40 removed outlier: 3.777A pdb=" N THR K 52 " --> pdb=" O SER K 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR K 64 " --> pdb=" O ILE K 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER K 77 " --> pdb=" O SER K 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL K 78 " --> pdb=" O THR K 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR K 67 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR K 64 " --> pdb=" O ILE K 84 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR L 52 " --> pdb=" O SER L 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR L 64 " --> pdb=" O ILE L 84 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER L 77 " --> pdb=" O SER L 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL L 78 " --> pdb=" O THR L 67 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR L 67 " --> pdb=" O VAL L 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR L 64 " --> pdb=" O ILE L 84 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR M 52 " --> pdb=" O SER M 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR M 64 " --> pdb=" O ILE M 84 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER M 77 " --> pdb=" O SER M 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL M 78 " --> pdb=" O THR M 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR M 67 " --> pdb=" O VAL M 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR M 64 " --> pdb=" O ILE M 84 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR N 52 " --> pdb=" O SER N 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR N 64 " --> pdb=" O ILE N 84 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER N 77 " --> pdb=" O SER N 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL N 78 " --> pdb=" O THR N 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR N 67 " --> pdb=" O VAL N 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR N 64 " --> pdb=" O ILE N 84 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR O 52 " --> pdb=" O SER O 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR O 64 " --> pdb=" O ILE O 84 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER O 77 " --> pdb=" O SER O 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL O 78 " --> pdb=" O THR O 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR O 67 " --> pdb=" O VAL O 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR O 64 " --> pdb=" O ILE O 84 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR P 52 " --> pdb=" O SER P 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR P 64 " --> pdb=" O ILE P 84 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER P 77 " --> pdb=" O SER P 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL P 78 " --> pdb=" O THR P 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR P 67 " --> pdb=" O VAL P 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR P 64 " --> pdb=" O ILE P 84 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR Q 52 " --> pdb=" O SER Q 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR Q 64 " --> pdb=" O ILE Q 84 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER Q 77 " --> pdb=" O SER Q 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL Q 78 " --> pdb=" O THR Q 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR Q 67 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR Q 64 " --> pdb=" O ILE Q 84 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 38 through 40 removed outlier: 3.777A pdb=" N THR R 52 " --> pdb=" O SER R 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR R 64 " --> pdb=" O ILE R 84 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER R 77 " --> pdb=" O SER R 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL R 78 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR R 67 " --> pdb=" O VAL R 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR R 64 " --> pdb=" O ILE R 84 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'S' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR S 52 " --> pdb=" O SER S 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR S 64 " --> pdb=" O ILE S 84 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER S 77 " --> pdb=" O SER S 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL S 78 " --> pdb=" O THR S 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR S 67 " --> pdb=" O VAL S 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR S 64 " --> pdb=" O ILE S 84 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 38 through 40 removed outlier: 3.777A pdb=" N THR T 52 " --> pdb=" O SER T 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR T 64 " --> pdb=" O ILE T 84 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 38 through 40 removed outlier: 3.701A pdb=" N SER T 77 " --> pdb=" O SER T 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL T 78 " --> pdb=" O THR T 67 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N THR T 67 " --> pdb=" O VAL T 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR T 64 " --> pdb=" O ILE T 84 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'U' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR U 52 " --> pdb=" O SER U 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR U 64 " --> pdb=" O ILE U 84 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'U' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER U 77 " --> pdb=" O SER U 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL U 78 " --> pdb=" O THR U 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR U 67 " --> pdb=" O VAL U 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR U 64 " --> pdb=" O ILE U 84 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR V 52 " --> pdb=" O SER V 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR V 64 " --> pdb=" O ILE V 84 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'V' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER V 77 " --> pdb=" O SER V 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL V 78 " --> pdb=" O THR V 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR V 67 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR V 64 " --> pdb=" O ILE V 84 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'W' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR W 52 " --> pdb=" O SER W 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR W 64 " --> pdb=" O ILE W 84 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'W' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER W 77 " --> pdb=" O SER W 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL W 78 " --> pdb=" O THR W 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR W 67 " --> pdb=" O VAL W 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR W 64 " --> pdb=" O ILE W 84 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR X 52 " --> pdb=" O SER X 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR X 64 " --> pdb=" O ILE X 84 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'X' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER X 77 " --> pdb=" O SER X 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL X 78 " --> pdb=" O THR X 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR X 67 " --> pdb=" O VAL X 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR X 64 " --> pdb=" O ILE X 84 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Y' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR Y 52 " --> pdb=" O SER Y 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR Y 64 " --> pdb=" O ILE Y 84 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER Y 77 " --> pdb=" O SER Y 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL Y 78 " --> pdb=" O THR Y 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR Y 67 " --> pdb=" O VAL Y 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR Y 64 " --> pdb=" O ILE Y 84 " (cutoff:3.500A) 1575 hydrogen bonds defined for protein. 4500 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: 9.95 Time building geometry restraints manager: 5.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7125 1.34 - 1.46: 3774 1.46 - 1.57: 11701 1.57 - 1.69: 0 1.69 - 1.80: 50 Bond restraints: 22650 Sorted by residual: bond pdb=" CB ILE U 17 " pdb=" CG2 ILE U 17 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.23e-01 bond pdb=" CB ILE B 17 " pdb=" CG2 ILE B 17 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.18e-01 bond pdb=" CB ILE P 17 " pdb=" CG2 ILE P 17 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.14e-01 bond pdb=" CB ILE Q 17 " pdb=" CG2 ILE Q 17 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.14e-01 bond pdb=" CB ILE O 17 " pdb=" CG2 ILE O 17 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.04e-01 ... (remaining 22645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.71: 28714 0.71 - 1.41: 1770 1.41 - 2.12: 306 2.12 - 2.82: 160 2.82 - 3.53: 100 Bond angle restraints: 31050 Sorted by residual: angle pdb=" N THR C 60 " pdb=" CA THR C 60 " pdb=" C THR C 60 " ideal model delta sigma weight residual 112.59 110.24 2.35 1.22e+00 6.72e-01 3.72e+00 angle pdb=" N THR M 60 " pdb=" CA THR M 60 " pdb=" C THR M 60 " ideal model delta sigma weight residual 112.59 110.24 2.35 1.22e+00 6.72e-01 3.70e+00 angle pdb=" N THR W 60 " pdb=" CA THR W 60 " pdb=" C THR W 60 " ideal model delta sigma weight residual 112.59 110.25 2.34 1.22e+00 6.72e-01 3.69e+00 angle pdb=" N THR N 60 " pdb=" CA THR N 60 " pdb=" C THR N 60 " ideal model delta sigma weight residual 112.59 110.25 2.34 1.22e+00 6.72e-01 3.69e+00 angle pdb=" N THR T 60 " pdb=" CA THR T 60 " pdb=" C THR T 60 " ideal model delta sigma weight residual 112.59 110.25 2.34 1.22e+00 6.72e-01 3.67e+00 ... (remaining 31045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.37: 11400 9.37 - 18.74: 1050 18.74 - 28.12: 300 28.12 - 37.49: 225 37.49 - 46.86: 50 Dihedral angle restraints: 13025 sinusoidal: 3975 harmonic: 9050 Sorted by residual: dihedral pdb=" CA GLN T 65 " pdb=" CB GLN T 65 " pdb=" CG GLN T 65 " pdb=" CD GLN T 65 " ideal model delta sinusoidal sigma weight residual -60.00 -90.33 30.33 3 1.50e+01 4.44e-03 4.82e+00 dihedral pdb=" CA GLN J 65 " pdb=" CB GLN J 65 " pdb=" CG GLN J 65 " pdb=" CD GLN J 65 " ideal model delta sinusoidal sigma weight residual -60.00 -90.32 30.32 3 1.50e+01 4.44e-03 4.82e+00 dihedral pdb=" CA GLN W 65 " pdb=" CB GLN W 65 " pdb=" CG GLN W 65 " pdb=" CD GLN W 65 " ideal model delta sinusoidal sigma weight residual -60.00 -90.31 30.31 3 1.50e+01 4.44e-03 4.82e+00 ... (remaining 13022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2679 0.026 - 0.052: 1039 0.052 - 0.078: 332 0.078 - 0.104: 366 0.104 - 0.130: 184 Chirality restraints: 4600 Sorted by residual: chirality pdb=" CA ILE C 129 " pdb=" N ILE C 129 " pdb=" C ILE C 129 " pdb=" CB ILE C 129 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE K 129 " pdb=" N ILE K 129 " pdb=" C ILE K 129 " pdb=" CB ILE K 129 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE L 129 " pdb=" N ILE L 129 " pdb=" C ILE L 129 " pdb=" CB ILE L 129 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 4597 not shown) Planarity restraints: 3675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE S 29 " -0.006 2.00e-02 2.50e+03 4.67e-03 3.82e-01 pdb=" CG PHE S 29 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE S 29 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE S 29 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE S 29 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE S 29 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE S 29 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE W 29 " -0.006 2.00e-02 2.50e+03 4.66e-03 3.81e-01 pdb=" CG PHE W 29 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE W 29 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE W 29 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE W 29 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE W 29 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE W 29 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 29 " -0.006 2.00e-02 2.50e+03 4.64e-03 3.77e-01 pdb=" CG PHE B 29 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE B 29 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 29 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 29 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 29 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 29 " -0.001 2.00e-02 2.50e+03 ... (remaining 3672 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 8336 2.87 - 3.38: 20122 3.38 - 3.88: 39184 3.88 - 4.39: 40997 4.39 - 4.90: 75447 Nonbonded interactions: 184086 Sorted by model distance: nonbonded pdb=" OD1 ASN T 74 " pdb=" OG SER T 99 " model vdw 2.362 3.040 nonbonded pdb=" OD1 ASN I 74 " pdb=" OG SER I 99 " model vdw 2.362 3.040 nonbonded pdb=" OD1 ASN F 74 " pdb=" OG SER F 99 " model vdw 2.362 3.040 nonbonded pdb=" OD1 ASN B 74 " pdb=" OG SER B 99 " model vdw 2.362 3.040 nonbonded pdb=" OD1 ASN P 74 " pdb=" OG SER P 99 " model vdw 2.362 3.040 ... (remaining 184081 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: 0.23 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 'W' 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: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.860 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 45.680 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.100 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:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.002 0.021 22650 Z= 0.108 Angle : 0.454 3.526 31050 Z= 0.259 Chirality : 0.044 0.130 4600 Planarity : 0.001 0.005 3675 Dihedral : 10.151 46.859 7275 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.15 (0.15), residues: 3250 helix: 2.67 (0.17), residues: 1025 sheet: -0.62 (0.16), residues: 1125 loop : -1.57 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE W 29 TYR 0.002 0.001 TYR G 91 ARG 0.001 0.000 ARG R 105 Details of bonding type rmsd hydrogen bonds : bond 0.15848 ( 1500) hydrogen bonds : angle 5.71406 ( 4500) covalent geometry : bond 0.00222 (22650) covalent geometry : angle 0.45412 (31050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 2.154 Fit side-chains REVERT: B 89 ASN cc_start: 0.8648 (m110) cc_final: 0.8432 (m110) REVERT: E 45 THR cc_start: 0.8707 (m) cc_final: 0.8414 (m) REVERT: E 89 ASN cc_start: 0.8811 (m110) cc_final: 0.8423 (m110) REVERT: F 89 ASN cc_start: 0.8933 (m110) cc_final: 0.8726 (m110) REVERT: H 45 THR cc_start: 0.8755 (m) cc_final: 0.8494 (m) REVERT: H 89 ASN cc_start: 0.8740 (m110) cc_final: 0.8229 (m-40) REVERT: I 89 ASN cc_start: 0.8782 (m110) cc_final: 0.8497 (m110) REVERT: J 89 ASN cc_start: 0.8878 (m110) cc_final: 0.8427 (m110) REVERT: O 89 ASN cc_start: 0.8867 (m110) cc_final: 0.8555 (m-40) REVERT: P 45 THR cc_start: 0.8693 (m) cc_final: 0.8433 (m) REVERT: Q 45 THR cc_start: 0.8842 (m) cc_final: 0.8603 (m) REVERT: S 89 ASN cc_start: 0.8842 (m110) cc_final: 0.8482 (m110) REVERT: T 79 SER cc_start: 0.7676 (t) cc_final: 0.7462 (p) REVERT: T 89 ASN cc_start: 0.8898 (m110) cc_final: 0.8696 (m-40) REVERT: V 89 ASN cc_start: 0.8845 (m110) cc_final: 0.8481 (m110) REVERT: X 45 THR cc_start: 0.8714 (m) cc_final: 0.8416 (m) REVERT: Y 89 ASN cc_start: 0.8848 (m110) cc_final: 0.8298 (m-40) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.4570 time to fit residues: 172.5744 Evaluate side-chains 187 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 274 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 chunk 131 optimal weight: 0.7980 chunk 254 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3178 r_free = 0.3178 target = 0.111983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.092711 restraints weight = 26101.624| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.44 r_work: 0.2836 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 22650 Z= 0.237 Angle : 0.684 9.518 31050 Z= 0.354 Chirality : 0.053 0.296 4600 Planarity : 0.003 0.017 3675 Dihedral : 4.764 15.732 3350 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.75 % Allowed : 5.75 % Favored : 92.50 % 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: -0.17 (0.15), residues: 3250 helix: 1.85 (0.16), residues: 1025 sheet: -0.36 (0.15), residues: 1200 loop : -1.78 (0.17), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE M 29 TYR 0.009 0.003 TYR K 91 ARG 0.002 0.001 ARG J 105 Details of bonding type rmsd hydrogen bonds : bond 0.05603 ( 1500) hydrogen bonds : angle 4.35554 ( 4500) covalent geometry : bond 0.00599 (22650) covalent geometry : angle 0.68442 (31050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 2.341 Fit side-chains REVERT: C 41 VAL cc_start: 0.8644 (m) cc_final: 0.8404 (t) REVERT: D 29 PHE cc_start: 0.8484 (m-10) cc_final: 0.8281 (m-80) REVERT: D 45 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8538 (t) REVERT: D 81 MET cc_start: 0.7810 (mtp) cc_final: 0.7610 (mtt) REVERT: E 45 THR cc_start: 0.8985 (m) cc_final: 0.8690 (m) REVERT: F 89 ASN cc_start: 0.8945 (m110) cc_final: 0.8715 (m110) REVERT: H 89 ASN cc_start: 0.8851 (m110) cc_final: 0.8514 (m-40) REVERT: K 45 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8900 (t) REVERT: K 79 SER cc_start: 0.8259 (t) cc_final: 0.8024 (t) REVERT: L 79 SER cc_start: 0.8365 (OUTLIER) cc_final: 0.7837 (t) REVERT: N 45 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8735 (t) REVERT: O 89 ASN cc_start: 0.8932 (m110) cc_final: 0.8696 (m-40) REVERT: R 45 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8665 (t) REVERT: T 79 SER cc_start: 0.7963 (t) cc_final: 0.7728 (t) REVERT: U 41 VAL cc_start: 0.8647 (m) cc_final: 0.8334 (t) REVERT: U 45 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.8913 (t) REVERT: W 41 VAL cc_start: 0.8614 (m) cc_final: 0.8332 (t) REVERT: W 45 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8923 (t) REVERT: X 41 VAL cc_start: 0.8612 (m) cc_final: 0.8403 (t) outliers start: 45 outliers final: 28 residues processed: 224 average time/residue: 0.4793 time to fit residues: 151.4290 Evaluate side-chains 196 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain N residue 45 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 45 THR Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 103 THR Chi-restraints excluded: chain Y residue 123 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 208 optimal weight: 2.9990 chunk 246 optimal weight: 0.8980 chunk 276 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 166 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3191 r_free = 0.3191 target = 0.113203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.093944 restraints weight = 25956.688| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.42 r_work: 0.2868 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22650 Z= 0.173 Angle : 0.581 8.112 31050 Z= 0.310 Chirality : 0.048 0.196 4600 Planarity : 0.002 0.019 3675 Dihedral : 4.658 19.145 3350 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.80 % Allowed : 8.50 % Favored : 88.70 % 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: -0.09 (0.15), residues: 3250 helix: 1.90 (0.17), residues: 1025 sheet: -0.35 (0.15), residues: 1200 loop : -1.67 (0.17), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.002 PHE M 29 TYR 0.006 0.002 TYR C 91 ARG 0.001 0.001 ARG J 105 Details of bonding type rmsd hydrogen bonds : bond 0.04634 ( 1500) hydrogen bonds : angle 4.15360 ( 4500) covalent geometry : bond 0.00422 (22650) covalent geometry : angle 0.58062 (31050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 146 time to evaluate : 2.263 Fit side-chains REVERT: C 41 VAL cc_start: 0.8561 (m) cc_final: 0.8328 (t) REVERT: D 79 SER cc_start: 0.8452 (OUTLIER) cc_final: 0.7934 (t) REVERT: D 81 MET cc_start: 0.7652 (mtp) cc_final: 0.7420 (mtt) REVERT: E 45 THR cc_start: 0.8917 (m) cc_final: 0.8580 (m) REVERT: F 89 ASN cc_start: 0.8937 (m110) cc_final: 0.8696 (m110) REVERT: H 45 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8646 (m) REVERT: H 89 ASN cc_start: 0.8853 (m110) cc_final: 0.8491 (m-40) REVERT: K 45 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8860 (t) REVERT: K 79 SER cc_start: 0.8260 (t) cc_final: 0.7988 (t) REVERT: L 79 SER cc_start: 0.8182 (OUTLIER) cc_final: 0.7713 (t) REVERT: M 120 ASN cc_start: 0.8821 (p0) cc_final: 0.8594 (p0) REVERT: O 89 ASN cc_start: 0.8938 (m110) cc_final: 0.8702 (m-40) REVERT: O 120 ASN cc_start: 0.8911 (p0) cc_final: 0.8686 (p0) REVERT: Q 45 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8765 (m) REVERT: T 79 SER cc_start: 0.7931 (t) cc_final: 0.7627 (t) REVERT: U 41 VAL cc_start: 0.8521 (m) cc_final: 0.8176 (t) REVERT: W 41 VAL cc_start: 0.8529 (m) cc_final: 0.8298 (t) REVERT: W 45 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8825 (t) REVERT: X 41 VAL cc_start: 0.8492 (m) cc_final: 0.8285 (t) outliers start: 72 outliers final: 52 residues processed: 201 average time/residue: 0.5371 time to fit residues: 146.8281 Evaluate side-chains 189 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 131 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain N residue 45 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 43 THR Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 45 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 74 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 310 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 241 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 198 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3169 r_free = 0.3169 target = 0.111746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.092341 restraints weight = 26416.312| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.44 r_work: 0.2837 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22650 Z= 0.172 Angle : 0.578 8.037 31050 Z= 0.304 Chirality : 0.048 0.184 4600 Planarity : 0.002 0.015 3675 Dihedral : 4.664 20.869 3350 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.81 % Allowed : 10.45 % Favored : 85.75 % 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: -0.09 (0.15), residues: 3250 helix: 1.88 (0.17), residues: 1025 sheet: -0.37 (0.15), residues: 1200 loop : -1.60 (0.17), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.002 PHE M 29 TYR 0.006 0.002 TYR K 91 ARG 0.001 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.04668 ( 1500) hydrogen bonds : angle 4.09304 ( 4500) covalent geometry : bond 0.00422 (22650) covalent geometry : angle 0.57814 (31050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 131 time to evaluate : 2.398 Fit side-chains REVERT: C 41 VAL cc_start: 0.8536 (m) cc_final: 0.8328 (t) REVERT: D 81 MET cc_start: 0.7693 (mtp) cc_final: 0.7487 (mtt) REVERT: E 45 THR cc_start: 0.8968 (m) cc_final: 0.8615 (m) REVERT: F 89 ASN cc_start: 0.8958 (m110) cc_final: 0.8735 (m110) REVERT: H 45 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8650 (m) REVERT: H 71 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7756 (mt) REVERT: H 89 ASN cc_start: 0.8840 (m110) cc_final: 0.8484 (m-40) REVERT: K 45 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8851 (t) REVERT: K 79 SER cc_start: 0.8291 (t) cc_final: 0.8023 (t) REVERT: L 79 SER cc_start: 0.8132 (OUTLIER) cc_final: 0.7662 (t) REVERT: M 120 ASN cc_start: 0.8870 (p0) cc_final: 0.8633 (p0) REVERT: N 45 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8705 (t) REVERT: N 79 SER cc_start: 0.8079 (t) cc_final: 0.7786 (p) REVERT: O 71 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7463 (tp) REVERT: O 89 ASN cc_start: 0.8925 (m110) cc_final: 0.8685 (m-40) REVERT: O 120 ASN cc_start: 0.8965 (p0) cc_final: 0.8736 (p0) REVERT: Q 45 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8765 (m) REVERT: T 79 SER cc_start: 0.7927 (t) cc_final: 0.7634 (t) REVERT: U 41 VAL cc_start: 0.8607 (m) cc_final: 0.8304 (t) REVERT: W 45 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8809 (t) outliers start: 98 outliers final: 65 residues processed: 215 average time/residue: 0.5003 time to fit residues: 148.2074 Evaluate side-chains 194 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 121 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain N residue 45 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 71 ILE Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 43 THR Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 45 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 87 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 254 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 222 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3215 r_free = 0.3215 target = 0.115019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.095329 restraints weight = 25986.350| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.47 r_work: 0.2883 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22650 Z= 0.133 Angle : 0.542 7.207 31050 Z= 0.288 Chirality : 0.048 0.179 4600 Planarity : 0.002 0.017 3675 Dihedral : 4.321 19.419 3350 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.06 % Allowed : 12.58 % Favored : 85.36 % 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: 0.38 (0.15), residues: 3250 helix: 2.09 (0.17), residues: 1025 sheet: 0.15 (0.15), residues: 1100 loop : -1.37 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.002 PHE M 29 TYR 0.005 0.001 TYR K 91 ARG 0.001 0.000 ARG U 105 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 1500) hydrogen bonds : angle 3.92468 ( 4500) covalent geometry : bond 0.00310 (22650) covalent geometry : angle 0.54249 (31050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 133 time to evaluate : 2.359 Fit side-chains REVERT: E 45 THR cc_start: 0.8990 (m) cc_final: 0.8638 (m) REVERT: F 89 ASN cc_start: 0.9002 (m110) cc_final: 0.8777 (m110) REVERT: H 71 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7677 (mt) REVERT: H 89 ASN cc_start: 0.8883 (m110) cc_final: 0.8515 (m-40) REVERT: L 79 SER cc_start: 0.8242 (OUTLIER) cc_final: 0.7703 (t) REVERT: M 120 ASN cc_start: 0.8764 (p0) cc_final: 0.8527 (p0) REVERT: O 89 ASN cc_start: 0.8944 (m110) cc_final: 0.8734 (m-40) REVERT: Q 29 PHE cc_start: 0.8114 (m-10) cc_final: 0.7899 (m-10) REVERT: T 79 SER cc_start: 0.7906 (t) cc_final: 0.7594 (t) REVERT: U 41 VAL cc_start: 0.8526 (m) cc_final: 0.8205 (t) REVERT: U 120 ASN cc_start: 0.8743 (p0) cc_final: 0.8504 (p0) REVERT: V 122 GLU cc_start: 0.8828 (tt0) cc_final: 0.8514 (pt0) REVERT: W 45 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8736 (t) REVERT: X 45 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8675 (m) REVERT: Y 65 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7769 (mp10) outliers start: 53 outliers final: 40 residues processed: 177 average time/residue: 0.6188 time to fit residues: 148.2645 Evaluate side-chains 168 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 123 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 43 THR Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 65 GLN Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 250 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 128 optimal weight: 0.5980 chunk 244 optimal weight: 0.0370 chunk 63 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 307 optimal weight: 0.4980 chunk 187 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 291 optimal weight: 1.9990 overall best weight: 0.8262 ------------------------------------------------------------------------------- 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 = 0.3241 r_free = 0.3241 target = 0.117176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.097726 restraints weight = 25683.365| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.44 r_work: 0.2910 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22650 Z= 0.111 Angle : 0.509 7.099 31050 Z= 0.271 Chirality : 0.047 0.183 4600 Planarity : 0.002 0.023 3675 Dihedral : 4.025 16.379 3350 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.28 % Allowed : 13.75 % Favored : 84.97 % 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: 0.58 (0.15), residues: 3250 helix: 2.27 (0.17), residues: 1025 sheet: 0.17 (0.15), residues: 1100 loop : -1.16 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.001 PHE H 29 TYR 0.003 0.001 TYR K 91 ARG 0.001 0.000 ARG U 105 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 1500) hydrogen bonds : angle 3.77805 ( 4500) covalent geometry : bond 0.00247 (22650) covalent geometry : angle 0.50897 (31050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 2.217 Fit side-chains REVERT: E 45 THR cc_start: 0.8950 (m) cc_final: 0.8579 (m) REVERT: F 89 ASN cc_start: 0.8966 (m110) cc_final: 0.8743 (m110) REVERT: H 89 ASN cc_start: 0.8835 (m110) cc_final: 0.8454 (m-40) REVERT: J 65 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8374 (mt0) REVERT: O 89 ASN cc_start: 0.8980 (m110) cc_final: 0.8721 (m-40) REVERT: Q 29 PHE cc_start: 0.8015 (m-10) cc_final: 0.7774 (m-10) REVERT: T 79 SER cc_start: 0.7878 (t) cc_final: 0.7556 (t) REVERT: U 41 VAL cc_start: 0.8543 (m) cc_final: 0.8220 (t) REVERT: U 120 ASN cc_start: 0.8638 (p0) cc_final: 0.8431 (p0) REVERT: V 122 GLU cc_start: 0.8804 (tt0) cc_final: 0.8453 (pt0) REVERT: Y 65 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7724 (mp10) outliers start: 33 outliers final: 23 residues processed: 183 average time/residue: 0.6898 time to fit residues: 161.1621 Evaluate side-chains 161 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain Y residue 65 GLN Chi-restraints excluded: chain Y residue 79 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 248 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 269 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 300 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.113271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.093791 restraints weight = 26257.406| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.44 r_work: 0.2876 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22650 Z= 0.148 Angle : 0.559 7.760 31050 Z= 0.295 Chirality : 0.048 0.181 4600 Planarity : 0.002 0.019 3675 Dihedral : 4.308 16.939 3350 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.21 % Allowed : 13.94 % Favored : 83.84 % 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: 0.45 (0.15), residues: 3250 helix: 2.09 (0.17), residues: 1025 sheet: 0.16 (0.15), residues: 1100 loop : -1.22 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.002 PHE M 29 TYR 0.005 0.002 TYR K 91 ARG 0.001 0.000 ARG U 105 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 1500) hydrogen bonds : angle 3.91917 ( 4500) covalent geometry : bond 0.00355 (22650) covalent geometry : angle 0.55886 (31050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 127 time to evaluate : 2.179 Fit side-chains REVERT: E 45 THR cc_start: 0.9003 (m) cc_final: 0.8639 (m) REVERT: F 89 ASN cc_start: 0.8986 (m110) cc_final: 0.8772 (m110) REVERT: H 89 ASN cc_start: 0.8844 (m110) cc_final: 0.8466 (m-40) REVERT: J 65 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8374 (mt0) REVERT: L 79 SER cc_start: 0.8238 (OUTLIER) cc_final: 0.7694 (t) REVERT: L 81 MET cc_start: 0.7453 (mtp) cc_final: 0.7246 (mtt) REVERT: M 79 SER cc_start: 0.8218 (p) cc_final: 0.7698 (t) REVERT: P 65 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7943 (mt0) REVERT: Q 29 PHE cc_start: 0.8150 (m-10) cc_final: 0.7921 (m-10) REVERT: Q 65 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8297 (mp10) REVERT: R 65 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7648 (mt0) REVERT: T 79 SER cc_start: 0.7914 (t) cc_final: 0.7597 (t) REVERT: U 41 VAL cc_start: 0.8527 (m) cc_final: 0.8240 (t) REVERT: V 122 GLU cc_start: 0.8842 (tt0) cc_final: 0.8454 (pt0) REVERT: Y 65 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7734 (mp10) REVERT: Y 79 SER cc_start: 0.8087 (OUTLIER) cc_final: 0.7590 (t) outliers start: 57 outliers final: 43 residues processed: 176 average time/residue: 0.6283 time to fit residues: 143.9636 Evaluate side-chains 172 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 122 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 65 GLN Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 65 GLN Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 65 GLN Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 43 THR Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 45 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 65 GLN Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 291 optimal weight: 1.9990 chunk 316 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 214 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 175 optimal weight: 0.0870 chunk 80 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 266 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- 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 = 0.3232 r_free = 0.3232 target = 0.116454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.097086 restraints weight = 25911.014| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.44 r_work: 0.2898 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22650 Z= 0.118 Angle : 0.517 7.797 31050 Z= 0.275 Chirality : 0.047 0.187 4600 Planarity : 0.002 0.014 3675 Dihedral : 4.052 15.460 3350 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.86 % Allowed : 14.76 % Favored : 83.38 % 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: 0.63 (0.15), residues: 3250 helix: 2.26 (0.17), residues: 1025 sheet: 0.18 (0.15), residues: 1100 loop : -1.06 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.001 PHE M 29 TYR 0.004 0.001 TYR K 91 ARG 0.001 0.000 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 1500) hydrogen bonds : angle 3.79254 ( 4500) covalent geometry : bond 0.00267 (22650) covalent geometry : angle 0.51654 (31050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 134 time to evaluate : 2.442 Fit side-chains REVERT: E 45 THR cc_start: 0.8949 (m) cc_final: 0.8569 (m) REVERT: F 89 ASN cc_start: 0.8991 (m110) cc_final: 0.8769 (m110) REVERT: H 89 ASN cc_start: 0.8870 (m110) cc_final: 0.8499 (m-40) REVERT: J 65 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8397 (mt0) REVERT: M 79 SER cc_start: 0.8217 (p) cc_final: 0.7679 (t) REVERT: Q 29 PHE cc_start: 0.8089 (m-10) cc_final: 0.7865 (m-10) REVERT: Q 65 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8323 (mp10) REVERT: R 65 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.7755 (mt0) REVERT: T 79 SER cc_start: 0.7878 (t) cc_final: 0.7553 (t) REVERT: U 41 VAL cc_start: 0.8535 (m) cc_final: 0.8236 (t) REVERT: U 120 ASN cc_start: 0.8701 (p0) cc_final: 0.8470 (p0) REVERT: V 122 GLU cc_start: 0.8817 (tt0) cc_final: 0.8424 (pt0) REVERT: Y 65 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7725 (mp10) outliers start: 48 outliers final: 38 residues processed: 178 average time/residue: 0.6772 time to fit residues: 155.4460 Evaluate side-chains 169 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 65 GLN Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 65 GLN Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 43 THR Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 65 GLN Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 238 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.113584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.094149 restraints weight = 26050.661| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.43 r_work: 0.2870 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22650 Z= 0.141 Angle : 0.550 7.564 31050 Z= 0.290 Chirality : 0.048 0.188 4600 Planarity : 0.002 0.017 3675 Dihedral : 4.232 15.918 3350 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.17 % Allowed : 14.83 % Favored : 82.99 % 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: 0.50 (0.15), residues: 3250 helix: 2.14 (0.17), residues: 1025 sheet: 0.17 (0.15), residues: 1100 loop : -1.18 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.002 PHE M 29 TYR 0.005 0.001 TYR K 91 ARG 0.001 0.000 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 1500) hydrogen bonds : angle 3.88677 ( 4500) covalent geometry : bond 0.00336 (22650) covalent geometry : angle 0.55023 (31050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 128 time to evaluate : 2.261 Fit side-chains REVERT: E 45 THR cc_start: 0.8973 (m) cc_final: 0.8595 (m) REVERT: F 89 ASN cc_start: 0.9005 (m110) cc_final: 0.8782 (m110) REVERT: H 89 ASN cc_start: 0.8868 (m110) cc_final: 0.8491 (m-40) REVERT: H 122 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8955 (tt0) REVERT: J 65 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8386 (mt0) REVERT: M 79 SER cc_start: 0.8230 (OUTLIER) cc_final: 0.7692 (t) REVERT: Q 29 PHE cc_start: 0.8208 (m-10) cc_final: 0.7937 (m-10) REVERT: Q 65 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8325 (mp10) REVERT: R 65 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7793 (mt0) REVERT: T 79 SER cc_start: 0.7864 (t) cc_final: 0.7536 (t) REVERT: U 41 VAL cc_start: 0.8550 (m) cc_final: 0.8263 (t) REVERT: X 65 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8278 (mt0) REVERT: Y 65 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.7729 (mp10) REVERT: Y 79 SER cc_start: 0.8080 (OUTLIER) cc_final: 0.7602 (t) outliers start: 56 outliers final: 44 residues processed: 175 average time/residue: 0.6750 time to fit residues: 151.2911 Evaluate side-chains 178 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 126 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain N residue 81 MET Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 65 GLN Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 65 GLN Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 43 THR Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 65 GLN Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 156 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 260 optimal weight: 0.8980 chunk 257 optimal weight: 0.0370 chunk 26 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.117652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.098350 restraints weight = 25929.611| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.43 r_work: 0.2934 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22650 Z= 0.106 Angle : 0.503 7.310 31050 Z= 0.268 Chirality : 0.047 0.183 4600 Planarity : 0.002 0.015 3675 Dihedral : 3.923 13.764 3350 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.48 % Allowed : 15.65 % Favored : 82.87 % 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: 0.48 (0.15), residues: 3250 helix: 2.38 (0.17), residues: 1025 sheet: -0.11 (0.15), residues: 1050 loop : -1.11 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.001 PHE M 29 TYR 0.003 0.001 TYR K 91 ARG 0.001 0.000 ARG C 105 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 1500) hydrogen bonds : angle 3.73533 ( 4500) covalent geometry : bond 0.00229 (22650) covalent geometry : angle 0.50267 (31050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 2.365 Fit side-chains REVERT: E 45 THR cc_start: 0.8938 (m) cc_final: 0.8553 (m) REVERT: F 89 ASN cc_start: 0.8983 (m110) cc_final: 0.8759 (m110) REVERT: H 89 ASN cc_start: 0.8860 (m110) cc_final: 0.8479 (m-40) REVERT: J 65 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8371 (mt0) REVERT: J 120 ASN cc_start: 0.8472 (p0) cc_final: 0.8214 (p0) REVERT: M 79 SER cc_start: 0.8198 (p) cc_final: 0.7644 (t) REVERT: Q 29 PHE cc_start: 0.8051 (m-10) cc_final: 0.7813 (m-10) REVERT: Q 65 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8360 (mp-120) REVERT: R 65 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7780 (mt0) REVERT: T 79 SER cc_start: 0.7847 (t) cc_final: 0.7509 (t) REVERT: U 41 VAL cc_start: 0.8486 (m) cc_final: 0.8163 (t) REVERT: Y 65 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7708 (mp10) REVERT: Y 79 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7544 (t) outliers start: 38 outliers final: 30 residues processed: 172 average time/residue: 0.6854 time to fit residues: 151.4673 Evaluate side-chains 164 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 65 GLN Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 65 GLN Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 43 THR Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 65 GLN Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 91 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 228 optimal weight: 0.2980 chunk 47 optimal weight: 8.9990 chunk 223 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 308 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 279 optimal weight: 0.2980 chunk 243 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3234 r_free = 0.3234 target = 0.116653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.096967 restraints weight = 25676.311| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.47 r_work: 0.2884 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22650 Z= 0.120 Angle : 0.521 7.449 31050 Z= 0.276 Chirality : 0.048 0.185 4600 Planarity : 0.002 0.016 3675 Dihedral : 3.995 13.421 3350 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.67 % Allowed : 15.92 % Favored : 82.41 % 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: 0.68 (0.15), residues: 3250 helix: 2.32 (0.17), residues: 1025 sheet: 0.20 (0.15), residues: 1100 loop : -1.03 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.001 PHE M 29 TYR 0.004 0.001 TYR K 91 ARG 0.001 0.000 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 1500) hydrogen bonds : angle 3.77689 ( 4500) covalent geometry : bond 0.00274 (22650) covalent geometry : angle 0.52084 (31050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9712.88 seconds wall clock time: 170 minutes 2.43 seconds (10202.43 seconds total)