Starting phenix.real_space_refine on Thu Jun 19 09:55:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fjs_29246/06_2025/8fjs_29246.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fjs_29246/06_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_29246/06_2025/8fjs_29246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fjs_29246/06_2025/8fjs_29246.map" model { file = "/net/cci-nas-00/data/ceres_data/8fjs_29246/06_2025/8fjs_29246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fjs_29246/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 6.28, per 1000 atoms: 0.28 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: 5.82 Conformation dependent library (CDL) restraints added in 3.4 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: 5.13 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: 10.66 Time building geometry restraints manager: 6.87 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: 6.430 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: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 50.970 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.900 ------------------------------------------------------------------------------- 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 : 2.853 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: 0.5060 time to fit residues: 191.1683 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 : 2.631 ------------------------------------------------------------------------------- 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 = 0.3170 r_free = 0.3170 target = 0.111479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.092146 restraints weight = 26166.943| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.44 r_work: 0.2834 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 0.68443 (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 : 3.538 Fit side-chains REVERT: C 41 VAL cc_start: 0.8646 (m) cc_final: 0.8406 (t) REVERT: D 29 PHE cc_start: 0.8492 (m-10) cc_final: 0.8289 (m-80) REVERT: D 45 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8543 (t) REVERT: D 81 MET cc_start: 0.7815 (mtp) cc_final: 0.7614 (mtt) REVERT: E 45 THR cc_start: 0.8988 (m) cc_final: 0.8694 (m) REVERT: F 89 ASN cc_start: 0.8950 (m110) cc_final: 0.8719 (m110) REVERT: H 89 ASN cc_start: 0.8858 (m110) cc_final: 0.8523 (m-40) REVERT: K 45 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8906 (t) REVERT: K 79 SER cc_start: 0.8261 (t) cc_final: 0.8027 (t) REVERT: L 79 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.7841 (t) REVERT: N 45 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8741 (t) REVERT: O 89 ASN cc_start: 0.8939 (m110) cc_final: 0.8705 (m-40) REVERT: R 45 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8672 (t) REVERT: T 79 SER cc_start: 0.7964 (t) cc_final: 0.7728 (t) REVERT: U 41 VAL cc_start: 0.8649 (m) cc_final: 0.8338 (t) REVERT: U 45 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.8919 (t) REVERT: W 41 VAL cc_start: 0.8616 (m) cc_final: 0.8336 (t) REVERT: W 45 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8928 (t) REVERT: X 41 VAL cc_start: 0.8615 (m) cc_final: 0.8405 (t) outliers start: 45 outliers final: 28 residues processed: 224 average time/residue: 0.6671 time to fit residues: 211.4487 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 : 4.529 ------------------------------------------------------------------------------- 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: 0.6980 chunk 83 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 166 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.3193 r_free = 0.3193 target = 0.113353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.094058 restraints weight = 25936.327| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.43 r_work: 0.2864 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1853 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= 0.168 Angle : 0.576 8.070 31050 Z= 0.308 Chirality : 0.048 0.193 4600 Planarity : 0.002 0.019 3675 Dihedral : 4.632 18.740 3350 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.83 % Allowed : 8.31 % Favored : 88.85 % 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: -0.08 (0.15), residues: 3250 helix: 1.91 (0.17), residues: 1025 sheet: -0.35 (0.15), residues: 1200 loop : -1.66 (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 J 105 Details of bonding type rmsd hydrogen bonds : bond 0.04605 ( 1500) hydrogen bonds : angle 4.14512 ( 4500) covalent geometry : bond 0.00409 (22650) covalent geometry : angle 0.57560 (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 217 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 144 time to evaluate : 2.505 Fit side-chains REVERT: C 41 VAL cc_start: 0.8557 (m) cc_final: 0.8328 (t) REVERT: D 81 MET cc_start: 0.7651 (mtp) cc_final: 0.7424 (mtt) REVERT: E 45 THR cc_start: 0.8915 (m) cc_final: 0.8579 (m) REVERT: F 89 ASN cc_start: 0.8939 (m110) cc_final: 0.8699 (m110) REVERT: H 45 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8651 (m) REVERT: H 89 ASN cc_start: 0.8855 (m110) cc_final: 0.8495 (m-40) REVERT: K 45 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8861 (t) REVERT: K 79 SER cc_start: 0.8267 (t) cc_final: 0.8003 (t) REVERT: L 79 SER cc_start: 0.8184 (OUTLIER) cc_final: 0.7713 (t) REVERT: L 81 MET cc_start: 0.7545 (mtp) cc_final: 0.7253 (mtt) REVERT: M 120 ASN cc_start: 0.8820 (p0) cc_final: 0.8593 (p0) REVERT: O 89 ASN cc_start: 0.8939 (m110) cc_final: 0.8705 (m-40) REVERT: O 120 ASN cc_start: 0.8905 (p0) cc_final: 0.8681 (p0) REVERT: Q 45 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8761 (m) REVERT: T 79 SER cc_start: 0.7932 (t) cc_final: 0.7633 (t) REVERT: U 41 VAL cc_start: 0.8506 (m) cc_final: 0.8158 (t) REVERT: W 41 VAL cc_start: 0.8530 (m) cc_final: 0.8297 (t) REVERT: W 45 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8829 (t) REVERT: X 41 VAL cc_start: 0.8525 (m) cc_final: 0.8309 (t) outliers start: 73 outliers final: 54 residues processed: 201 average time/residue: 0.5641 time to fit residues: 154.1740 Evaluate side-chains 189 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 130 time to evaluate : 2.558 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 154 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 241 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 162 optimal weight: 0.2980 chunk 198 optimal weight: 0.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 = 0.3171 r_free = 0.3171 target = 0.111693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.092349 restraints weight = 26334.133| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.44 r_work: 0.2838 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22650 Z= 0.181 Angle : 0.589 8.175 31050 Z= 0.309 Chirality : 0.049 0.188 4600 Planarity : 0.002 0.015 3675 Dihedral : 4.730 21.246 3350 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.81 % Allowed : 10.37 % Favored : 85.83 % 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: -0.13 (0.15), residues: 3250 helix: 1.84 (0.17), residues: 1025 sheet: -0.38 (0.15), residues: 1200 loop : -1.64 (0.17), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.002 PHE M 29 TYR 0.007 0.002 TYR K 91 ARG 0.001 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.04792 ( 1500) hydrogen bonds : angle 4.12260 ( 4500) covalent geometry : bond 0.00446 (22650) covalent geometry : angle 0.58920 (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 226 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 128 time to evaluate : 2.556 Fit side-chains REVERT: C 41 VAL cc_start: 0.8548 (m) cc_final: 0.8343 (t) REVERT: C 79 SER cc_start: 0.7895 (OUTLIER) cc_final: 0.7405 (t) REVERT: D 81 MET cc_start: 0.7853 (mtp) cc_final: 0.7649 (mtt) REVERT: E 45 THR cc_start: 0.8999 (m) cc_final: 0.8653 (m) REVERT: F 89 ASN cc_start: 0.8978 (m110) cc_final: 0.8753 (m110) REVERT: H 45 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8673 (m) REVERT: H 71 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7777 (mt) REVERT: H 89 ASN cc_start: 0.8868 (m110) cc_final: 0.8513 (m-40) REVERT: K 45 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8872 (t) REVERT: K 79 SER cc_start: 0.8293 (t) cc_final: 0.8024 (t) REVERT: L 79 SER cc_start: 0.8147 (OUTLIER) cc_final: 0.7686 (t) REVERT: L 81 MET cc_start: 0.7610 (mtp) cc_final: 0.7367 (mtt) REVERT: N 45 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8733 (t) REVERT: O 71 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7513 (tp) REVERT: O 89 ASN cc_start: 0.8950 (m110) cc_final: 0.8719 (m-40) REVERT: O 120 ASN cc_start: 0.9002 (p0) cc_final: 0.8769 (p0) REVERT: Q 29 PHE cc_start: 0.8363 (m-10) cc_final: 0.8158 (m-10) REVERT: Q 45 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8778 (m) REVERT: T 79 SER cc_start: 0.7939 (t) cc_final: 0.7636 (t) REVERT: U 41 VAL cc_start: 0.8624 (m) cc_final: 0.8328 (t) REVERT: U 71 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7539 (tt) REVERT: W 45 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8825 (t) outliers start: 98 outliers final: 63 residues processed: 211 average time/residue: 0.5252 time to fit residues: 152.6477 Evaluate side-chains 190 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 117 time to evaluate : 2.403 ------------------------------------------------------------------------------- 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 71 ILE 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 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: 5.9990 chunk 220 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 254 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 222 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.3155 r_free = 0.3155 target = 0.110566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.091319 restraints weight = 26410.011| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.43 r_work: 0.2832 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22650 Z= 0.203 Angle : 0.632 8.202 31050 Z= 0.328 Chirality : 0.050 0.188 4600 Planarity : 0.002 0.016 3675 Dihedral : 4.933 23.852 3350 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.46 % Allowed : 10.99 % Favored : 85.55 % 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: -0.18 (0.14), residues: 3250 helix: 1.74 (0.17), residues: 1025 sheet: -0.38 (0.14), residues: 1200 loop : -1.65 (0.17), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.002 PHE M 29 TYR 0.007 0.002 TYR K 91 ARG 0.002 0.001 ARG E 105 Details of bonding type rmsd hydrogen bonds : bond 0.05073 ( 1500) hydrogen bonds : angle 4.15730 ( 4500) covalent geometry : bond 0.00506 (22650) covalent geometry : angle 0.63160 (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 202 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 113 time to evaluate : 2.564 Fit side-chains REVERT: C 79 SER cc_start: 0.7864 (OUTLIER) cc_final: 0.7390 (t) REVERT: D 79 SER cc_start: 0.8490 (OUTLIER) cc_final: 0.7981 (t) REVERT: D 81 MET cc_start: 0.7789 (mtp) cc_final: 0.7571 (mtt) REVERT: E 45 THR cc_start: 0.9027 (m) cc_final: 0.8656 (m) REVERT: F 89 ASN cc_start: 0.8947 (m110) cc_final: 0.8714 (m110) REVERT: H 45 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8674 (m) REVERT: H 71 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7709 (mt) REVERT: H 89 ASN cc_start: 0.8838 (m110) cc_final: 0.8484 (m-40) REVERT: J 65 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8326 (mt0) REVERT: K 45 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8878 (t) REVERT: K 79 SER cc_start: 0.8364 (t) cc_final: 0.8032 (t) REVERT: L 79 SER cc_start: 0.8142 (OUTLIER) cc_final: 0.7689 (t) REVERT: L 81 MET cc_start: 0.7557 (mtp) cc_final: 0.7335 (mtt) REVERT: N 45 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8763 (t) REVERT: O 89 ASN cc_start: 0.8941 (m110) cc_final: 0.8703 (m-40) REVERT: Q 45 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8776 (m) REVERT: T 79 SER cc_start: 0.7890 (t) cc_final: 0.7607 (t) REVERT: U 41 VAL cc_start: 0.8574 (m) cc_final: 0.8293 (t) REVERT: U 71 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7665 (tt) REVERT: V 122 GLU cc_start: 0.8866 (tt0) cc_final: 0.8562 (pt0) REVERT: W 45 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8763 (t) REVERT: Y 65 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.7756 (mp10) REVERT: Y 79 SER cc_start: 0.8040 (OUTLIER) cc_final: 0.7562 (t) outliers start: 89 outliers final: 65 residues processed: 188 average time/residue: 0.5621 time to fit residues: 143.5669 Evaluate side-chains 183 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 105 time to evaluate : 2.291 ------------------------------------------------------------------------------- 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 J residue 65 GLN Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 43 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 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 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 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 R residue 81 MET 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 71 ILE 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 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 103 THR 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: 3.9990 chunk 96 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 244 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 307 optimal weight: 0.9980 chunk 187 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3204 r_free = 0.3204 target = 0.114296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.094984 restraints weight = 25949.053| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.43 r_work: 0.2871 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2018 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= 0.130 Angle : 0.539 7.074 31050 Z= 0.286 Chirality : 0.048 0.178 4600 Planarity : 0.002 0.022 3675 Dihedral : 4.380 21.261 3350 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.02 % Allowed : 13.20 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3250 helix: 2.06 (0.17), residues: 1025 sheet: 0.15 (0.15), residues: 1100 loop : -1.40 (0.16), 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 0.03999 ( 1500) hydrogen bonds : angle 3.89831 ( 4500) covalent geometry : bond 0.00299 (22650) covalent geometry : angle 0.53921 (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: 52 poor density : 137 time to evaluate : 2.363 Fit side-chains REVERT: D 81 MET cc_start: 0.7681 (mtp) cc_final: 0.7474 (mtt) REVERT: E 45 THR cc_start: 0.8943 (m) cc_final: 0.8561 (m) REVERT: F 89 ASN cc_start: 0.8981 (m110) cc_final: 0.8760 (m110) REVERT: H 71 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7711 (mt) REVERT: H 89 ASN cc_start: 0.8843 (m110) cc_final: 0.8471 (m-40) REVERT: L 81 MET cc_start: 0.7574 (mtp) cc_final: 0.7275 (mtt) REVERT: M 120 ASN cc_start: 0.8753 (p0) cc_final: 0.8512 (p0) REVERT: O 89 ASN cc_start: 0.8914 (m110) cc_final: 0.8692 (m-40) REVERT: T 79 SER cc_start: 0.7933 (t) cc_final: 0.7622 (t) REVERT: U 41 VAL cc_start: 0.8561 (m) cc_final: 0.8260 (t) REVERT: U 71 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7478 (tt) REVERT: U 120 ASN cc_start: 0.8722 (p0) cc_final: 0.8466 (p0) REVERT: V 122 GLU cc_start: 0.8850 (tt0) cc_final: 0.8481 (pt0) REVERT: X 45 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8571 (m) REVERT: Y 65 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7683 (mp10) outliers start: 52 outliers final: 43 residues processed: 182 average time/residue: 0.6631 time to fit residues: 157.3328 Evaluate side-chains 169 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 122 time to evaluate : 2.629 ------------------------------------------------------------------------------- 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 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 Q residue 43 THR Chi-restraints excluded: chain R residue 37 THR 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 43 THR Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 71 ILE 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 65 GLN Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 123 THR 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: 3.9990 chunk 65 optimal weight: 0.7980 chunk 202 optimal weight: 9.9990 chunk 142 optimal weight: 8.9990 chunk 192 optimal weight: 3.9990 chunk 269 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 300 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3177 r_free = 0.3177 target = 0.112339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.092992 restraints weight = 26387.637| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.44 r_work: 0.2862 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2082 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= 0.155 Angle : 0.563 7.387 31050 Z= 0.296 Chirality : 0.048 0.179 4600 Planarity : 0.002 0.020 3675 Dihedral : 4.529 20.631 3350 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.80 % Allowed : 13.13 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3250 helix: 1.96 (0.17), residues: 1025 sheet: -0.34 (0.14), residues: 1200 loop : -1.38 (0.17), residues: 1025 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 B 105 Details of bonding type rmsd hydrogen bonds : bond 0.04460 ( 1500) hydrogen bonds : angle 3.96794 ( 4500) covalent geometry : bond 0.00375 (22650) covalent geometry : angle 0.56266 (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 186 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 114 time to evaluate : 2.499 Fit side-chains REVERT: D 81 MET cc_start: 0.7694 (mtp) cc_final: 0.7479 (mtt) REVERT: E 45 THR cc_start: 0.8963 (m) cc_final: 0.8570 (m) REVERT: F 89 ASN cc_start: 0.8985 (m110) cc_final: 0.8770 (m110) REVERT: H 71 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7730 (mt) REVERT: H 89 ASN cc_start: 0.8842 (m110) cc_final: 0.8461 (m-40) REVERT: J 65 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8372 (mt0) REVERT: K 79 SER cc_start: 0.8250 (t) cc_final: 0.7921 (t) REVERT: L 79 SER cc_start: 0.8246 (OUTLIER) cc_final: 0.7713 (t) REVERT: O 89 ASN cc_start: 0.8921 (m110) cc_final: 0.8710 (m-40) REVERT: P 65 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.7927 (mt0) REVERT: Q 65 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8567 (mt0) REVERT: R 65 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7671 (mt0) REVERT: T 79 SER cc_start: 0.7878 (t) cc_final: 0.7546 (t) REVERT: U 41 VAL cc_start: 0.8538 (m) cc_final: 0.8251 (t) REVERT: U 71 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7482 (tt) REVERT: W 45 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8691 (t) REVERT: Y 65 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.7676 (mp10) REVERT: Y 79 SER cc_start: 0.8097 (OUTLIER) cc_final: 0.7588 (t) outliers start: 72 outliers final: 53 residues processed: 178 average time/residue: 0.6192 time to fit residues: 146.2765 Evaluate side-chains 176 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 113 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 43 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 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 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 J residue 65 GLN Chi-restraints excluded: chain K residue 37 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 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 43 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 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 37 THR Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 71 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 291 optimal weight: 2.9990 chunk 316 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 214 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 266 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3185 r_free = 0.3185 target = 0.112751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.093542 restraints weight = 26257.246| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.42 r_work: 0.2838 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2138 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= 0.166 Angle : 0.572 7.662 31050 Z= 0.300 Chirality : 0.049 0.184 4600 Planarity : 0.002 0.017 3675 Dihedral : 4.600 20.913 3350 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.07 % Allowed : 13.28 % Favored : 83.65 % 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: 0.02 (0.15), residues: 3250 helix: 1.92 (0.17), residues: 1025 sheet: -0.34 (0.14), residues: 1200 loop : -1.42 (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 K 91 ARG 0.001 0.001 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.04599 ( 1500) hydrogen bonds : angle 3.98823 ( 4500) covalent geometry : bond 0.00405 (22650) covalent geometry : angle 0.57224 (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 190 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 111 time to evaluate : 2.672 Fit side-chains REVERT: C 79 SER cc_start: 0.7834 (OUTLIER) cc_final: 0.7340 (t) REVERT: D 79 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.7898 (t) REVERT: D 81 MET cc_start: 0.7734 (mtp) cc_final: 0.7512 (mtt) REVERT: E 45 THR cc_start: 0.8992 (m) cc_final: 0.8599 (m) REVERT: F 89 ASN cc_start: 0.9016 (m110) cc_final: 0.8798 (m110) REVERT: H 89 ASN cc_start: 0.8857 (m110) cc_final: 0.8506 (m-40) REVERT: J 65 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8358 (mt0) REVERT: K 79 SER cc_start: 0.8174 (t) cc_final: 0.7840 (t) REVERT: L 79 SER cc_start: 0.8169 (OUTLIER) cc_final: 0.7687 (t) REVERT: N 79 SER cc_start: 0.8107 (t) cc_final: 0.7843 (p) REVERT: P 65 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7992 (mt0) REVERT: Q 45 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8796 (m) REVERT: Q 65 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8606 (mt0) REVERT: R 65 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7781 (mt0) REVERT: T 79 SER cc_start: 0.7864 (t) cc_final: 0.7576 (t) REVERT: U 41 VAL cc_start: 0.8603 (m) cc_final: 0.8338 (t) REVERT: U 71 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7536 (tt) REVERT: V 122 GLU cc_start: 0.8817 (tt0) cc_final: 0.8594 (pt0) REVERT: Y 65 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.7731 (mp10) REVERT: Y 79 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7581 (t) outliers start: 79 outliers final: 62 residues processed: 182 average time/residue: 0.6362 time to fit residues: 154.2098 Evaluate side-chains 180 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 107 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 43 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 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 79 SER 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 K residue 43 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 123 THR Chi-restraints excluded: chain O 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 45 THR Chi-restraints excluded: chain Q residue 65 GLN Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 65 GLN Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 81 MET 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 37 THR Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 71 ILE 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 45 THR Chi-restraints excluded: chain W residue 71 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 238 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 225 optimal weight: 8.9990 chunk 209 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 204 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3221 r_free = 0.3221 target = 0.115715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.096426 restraints weight = 25920.428| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.43 r_work: 0.2920 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22650 Z= 0.114 Angle : 0.510 7.863 31050 Z= 0.272 Chirality : 0.047 0.188 4600 Planarity : 0.002 0.012 3675 Dihedral : 4.173 17.794 3350 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.67 % Allowed : 14.95 % 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: 0.27 (0.14), residues: 3250 helix: 2.21 (0.17), residues: 1025 sheet: -0.13 (0.15), residues: 1050 loop : -1.34 (0.16), residues: 1175 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 M 105 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 1500) hydrogen bonds : angle 3.79632 ( 4500) covalent geometry : bond 0.00255 (22650) covalent geometry : angle 0.50972 (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 185 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 5.012 Fit side-chains REVERT: E 45 THR cc_start: 0.8961 (m) cc_final: 0.8565 (m) REVERT: F 89 ASN cc_start: 0.8975 (m110) cc_final: 0.8761 (m110) REVERT: H 89 ASN cc_start: 0.8841 (m110) cc_final: 0.8449 (m-40) REVERT: Q 65 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8373 (mp-120) REVERT: R 65 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7800 (mt0) REVERT: T 79 SER cc_start: 0.7810 (t) cc_final: 0.7465 (t) REVERT: U 41 VAL cc_start: 0.8493 (m) cc_final: 0.8180 (t) REVERT: U 71 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7453 (tt) REVERT: U 120 ASN cc_start: 0.8629 (p0) cc_final: 0.8419 (p0) REVERT: V 122 GLU cc_start: 0.8789 (tt0) cc_final: 0.8537 (pt0) REVERT: Y 65 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.7646 (mp10) REVERT: Y 79 SER cc_start: 0.8037 (OUTLIER) cc_final: 0.7535 (t) outliers start: 43 outliers final: 33 residues processed: 178 average time/residue: 0.7673 time to fit residues: 174.7715 Evaluate side-chains 167 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 2.422 ------------------------------------------------------------------------------- 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 122 GLU 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 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 37 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 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 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 71 ILE 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 65 GLN Chi-restraints excluded: chain Y residue 79 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 156 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 158 optimal weight: 0.5980 chunk 260 optimal weight: 0.9980 chunk 257 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 283 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3203 r_free = 0.3203 target = 0.114398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.094950 restraints weight = 26240.614| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.44 r_work: 0.2883 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2091 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= 0.127 Angle : 0.530 8.087 31050 Z= 0.280 Chirality : 0.048 0.183 4600 Planarity : 0.002 0.017 3675 Dihedral : 4.195 16.693 3350 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.71 % Allowed : 15.57 % Favored : 82.72 % 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: 0.51 (0.15), residues: 3250 helix: 2.17 (0.17), residues: 1025 sheet: 0.18 (0.15), residues: 1100 loop : -1.20 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 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 0.03983 ( 1500) hydrogen bonds : angle 3.82021 ( 4500) covalent geometry : bond 0.00293 (22650) covalent geometry : angle 0.52968 (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 173 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 129 time to evaluate : 2.652 Fit side-chains REVERT: E 45 THR cc_start: 0.8975 (m) cc_final: 0.8578 (m) REVERT: F 89 ASN cc_start: 0.8998 (m110) cc_final: 0.8779 (m110) REVERT: H 89 ASN cc_start: 0.8867 (m110) cc_final: 0.8490 (m-40) REVERT: K 79 SER cc_start: 0.8169 (t) cc_final: 0.7822 (t) REVERT: Q 65 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8427 (mp10) REVERT: R 65 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: T 79 SER cc_start: 0.7840 (t) cc_final: 0.7507 (t) REVERT: U 41 VAL cc_start: 0.8569 (m) cc_final: 0.8285 (t) REVERT: U 71 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7467 (tt) REVERT: U 120 ASN cc_start: 0.8729 (p0) cc_final: 0.8468 (p0) REVERT: Y 65 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7707 (mp10) REVERT: Y 79 SER cc_start: 0.8090 (OUTLIER) cc_final: 0.7598 (t) outliers start: 44 outliers final: 38 residues processed: 165 average time/residue: 0.7339 time to fit residues: 155.0525 Evaluate side-chains 171 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 2.561 ------------------------------------------------------------------------------- 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 122 GLU 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 K residue 37 THR Chi-restraints excluded: chain K residue 70 LEU 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 N residue 123 THR Chi-restraints excluded: chain O residue 37 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 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 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 71 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 91 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 228 optimal weight: 0.0070 chunk 47 optimal weight: 7.9990 chunk 223 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 308 optimal weight: 0.0970 chunk 155 optimal weight: 5.9990 chunk 279 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 65 GLN X 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.117307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.097943 restraints weight = 25751.140| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.43 r_work: 0.2937 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22650 Z= 0.106 Angle : 0.495 7.870 31050 Z= 0.265 Chirality : 0.047 0.183 4600 Planarity : 0.002 0.018 3675 Dihedral : 3.954 13.657 3350 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.40 % Allowed : 15.88 % Favored : 82.72 % 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: 2.36 (0.17), residues: 1025 sheet: -0.10 (0.15), residues: 1050 loop : -1.17 (0.16), 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 B 105 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 1500) hydrogen bonds : angle 3.71182 ( 4500) covalent geometry : bond 0.00232 (22650) covalent geometry : angle 0.49481 (31050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10072.67 seconds wall clock time: 178 minutes 22.29 seconds (10702.29 seconds total)