Starting phenix.real_space_refine on Fri Feb 6 16:42:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9egp_47993/02_2026/9egp_47993.cif Found real_map, /net/cci-nas-00/data/ceres_data/9egp_47993/02_2026/9egp_47993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9egp_47993/02_2026/9egp_47993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9egp_47993/02_2026/9egp_47993.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9egp_47993/02_2026/9egp_47993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9egp_47993/02_2026/9egp_47993.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.033 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: 3 Type Number sf(0) Gaussians C 17016 2.51 5 N 4536 2.21 5 O 5496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27048 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 657 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "D" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 470 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 56} Restraints were copied for chains: E, G, I, K, M, O, Q, S, U, W, Y, B, 0, 2, 4, 6, 8, a, c, e, g, i, k, F, H, J, L, N, P, R, T, V, X, Z, A, 1, 3, 5, 7, 9, b, d, f, h, j, l Time building chain proxies: 2.46, per 1000 atoms: 0.09 Number of scatterers: 27048 At special positions: 0 Unit cell: (77.39, 77.39, 331.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 5496 8.00 N 4536 7.00 C 17016 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: 2.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6624 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 72 sheets defined 34.4% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'B' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER B 37 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 27 Processing helix chain 'A' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA A 41 " --> pdb=" O TYR A 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS A 64 " --> pdb=" O TYR A 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER C 37 " --> pdb=" O GLY C 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 27 Processing helix chain 'D' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU D 63 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS D 64 " --> pdb=" O TYR D 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 38 removed outlier: 3.561A pdb=" N SER E 37 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 27 Processing helix chain 'F' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA F 41 " --> pdb=" O TYR F 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU F 63 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS F 64 " --> pdb=" O TYR F 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER G 37 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 27 Processing helix chain 'H' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER H 62 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS H 64 " --> pdb=" O TYR H 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER I 37 " --> pdb=" O GLY I 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 27 Processing helix chain 'J' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA J 41 " --> pdb=" O TYR J 37 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU J 63 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS J 64 " --> pdb=" O TYR J 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER K 37 " --> pdb=" O GLY K 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 27 Processing helix chain 'L' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA L 41 " --> pdb=" O TYR L 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER L 62 " --> pdb=" O GLU L 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU L 63 " --> pdb=" O SER L 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS L 64 " --> pdb=" O TYR L 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER M 37 " --> pdb=" O GLY M 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 12 through 27 Processing helix chain 'N' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA N 41 " --> pdb=" O TYR N 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER N 62 " --> pdb=" O GLU N 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS N 64 " --> pdb=" O TYR N 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER O 37 " --> pdb=" O GLY O 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 12 through 27 Processing helix chain 'P' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA P 41 " --> pdb=" O TYR P 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER P 62 " --> pdb=" O GLU P 58 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU P 63 " --> pdb=" O SER P 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS P 64 " --> pdb=" O TYR P 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER Q 37 " --> pdb=" O GLY Q 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 27 Processing helix chain 'R' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA R 41 " --> pdb=" O TYR R 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU R 63 " --> pdb=" O SER R 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS R 64 " --> pdb=" O TYR R 60 " (cutoff:3.500A) Processing helix chain 'S' and resid 34 through 38 removed outlier: 3.561A pdb=" N SER S 37 " --> pdb=" O GLY S 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 12 through 27 Processing helix chain 'T' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA T 41 " --> pdb=" O TYR T 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER T 62 " --> pdb=" O GLU T 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU T 63 " --> pdb=" O SER T 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS T 64 " --> pdb=" O TYR T 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER U 37 " --> pdb=" O GLY U 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 12 through 27 Processing helix chain 'V' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA V 41 " --> pdb=" O TYR V 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER V 62 " --> pdb=" O GLU V 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU V 63 " --> pdb=" O SER V 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS V 64 " --> pdb=" O TYR V 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER W 37 " --> pdb=" O GLY W 34 " (cutoff:3.500A) Processing helix chain 'X' and resid 12 through 27 Processing helix chain 'X' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA X 41 " --> pdb=" O TYR X 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER X 62 " --> pdb=" O GLU X 58 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU X 63 " --> pdb=" O SER X 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS X 64 " --> pdb=" O TYR X 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER Y 37 " --> pdb=" O GLY Y 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 27 Processing helix chain 'Z' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA Z 41 " --> pdb=" O TYR Z 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER Z 62 " --> pdb=" O GLU Z 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU Z 63 " --> pdb=" O SER Z 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS Z 64 " --> pdb=" O TYR Z 60 " (cutoff:3.500A) Processing helix chain '0' and resid 34 through 38 removed outlier: 3.561A pdb=" N SER 0 37 " --> pdb=" O GLY 0 34 " (cutoff:3.500A) Processing helix chain '1' and resid 12 through 27 Processing helix chain '1' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA 1 41 " --> pdb=" O TYR 1 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER 1 62 " --> pdb=" O GLU 1 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU 1 63 " --> pdb=" O SER 1 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS 1 64 " --> pdb=" O TYR 1 60 " (cutoff:3.500A) Processing helix chain '2' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER 2 37 " --> pdb=" O GLY 2 34 " (cutoff:3.500A) Processing helix chain '3' and resid 12 through 27 Processing helix chain '3' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA 3 41 " --> pdb=" O TYR 3 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER 3 62 " --> pdb=" O GLU 3 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU 3 63 " --> pdb=" O SER 3 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS 3 64 " --> pdb=" O TYR 3 60 " (cutoff:3.500A) Processing helix chain '4' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER 4 37 " --> pdb=" O GLY 4 34 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 27 Processing helix chain '5' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA 5 41 " --> pdb=" O TYR 5 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER 5 62 " --> pdb=" O GLU 5 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU 5 63 " --> pdb=" O SER 5 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS 5 64 " --> pdb=" O TYR 5 60 " (cutoff:3.500A) Processing helix chain '6' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER 6 37 " --> pdb=" O GLY 6 34 " (cutoff:3.500A) Processing helix chain '7' and resid 12 through 27 Processing helix chain '7' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA 7 41 " --> pdb=" O TYR 7 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER 7 62 " --> pdb=" O GLU 7 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU 7 63 " --> pdb=" O SER 7 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS 7 64 " --> pdb=" O TYR 7 60 " (cutoff:3.500A) Processing helix chain '8' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER 8 37 " --> pdb=" O GLY 8 34 " (cutoff:3.500A) Processing helix chain '9' and resid 12 through 27 Processing helix chain '9' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA 9 41 " --> pdb=" O TYR 9 37 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER 9 62 " --> pdb=" O GLU 9 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU 9 63 " --> pdb=" O SER 9 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS 9 64 " --> pdb=" O TYR 9 60 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER a 37 " --> pdb=" O GLY a 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 12 through 27 Processing helix chain 'b' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA b 41 " --> pdb=" O TYR b 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER b 62 " --> pdb=" O GLU b 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU b 63 " --> pdb=" O SER b 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS b 64 " --> pdb=" O TYR b 60 " (cutoff:3.500A) Processing helix chain 'c' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER c 37 " --> pdb=" O GLY c 34 " (cutoff:3.500A) Processing helix chain 'd' and resid 12 through 27 Processing helix chain 'd' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA d 41 " --> pdb=" O TYR d 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER d 62 " --> pdb=" O GLU d 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU d 63 " --> pdb=" O SER d 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS d 64 " --> pdb=" O TYR d 60 " (cutoff:3.500A) Processing helix chain 'e' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER e 37 " --> pdb=" O GLY e 34 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 27 Processing helix chain 'f' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA f 41 " --> pdb=" O TYR f 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER f 62 " --> pdb=" O GLU f 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU f 63 " --> pdb=" O SER f 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS f 64 " --> pdb=" O TYR f 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER g 37 " --> pdb=" O GLY g 34 " (cutoff:3.500A) Processing helix chain 'h' and resid 12 through 27 Processing helix chain 'h' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA h 41 " --> pdb=" O TYR h 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER h 62 " --> pdb=" O GLU h 58 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU h 63 " --> pdb=" O SER h 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS h 64 " --> pdb=" O TYR h 60 " (cutoff:3.500A) Processing helix chain 'i' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER i 37 " --> pdb=" O GLY i 34 " (cutoff:3.500A) Processing helix chain 'j' and resid 12 through 27 Processing helix chain 'j' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA j 41 " --> pdb=" O TYR j 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER j 62 " --> pdb=" O GLU j 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU j 63 " --> pdb=" O SER j 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS j 64 " --> pdb=" O TYR j 60 " (cutoff:3.500A) Processing helix chain 'k' and resid 34 through 38 removed outlier: 3.562A pdb=" N SER k 37 " --> pdb=" O GLY k 34 " (cutoff:3.500A) Processing helix chain 'l' and resid 12 through 27 Processing helix chain 'l' and resid 34 through 64 removed outlier: 3.638A pdb=" N ALA l 41 " --> pdb=" O TYR l 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER l 62 " --> pdb=" O GLU l 58 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU l 63 " --> pdb=" O SER l 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS l 64 " --> pdb=" O TYR l 60 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=2, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.716A pdb=" N LEU B 41 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.774A pdb=" N TYR B 85 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN B 111 " --> pdb=" O TYR B 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=3 Processing sheet with id=4, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=5, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.716A pdb=" N LEU C 41 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.774A pdb=" N TYR C 85 " --> pdb=" O ASN C 111 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN C 111 " --> pdb=" O TYR C 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=6 Processing sheet with id=7, first strand: chain 'E' and resid 26 through 27 Processing sheet with id=8, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.716A pdb=" N LEU E 41 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.774A pdb=" N TYR E 85 " --> pdb=" O ASN E 111 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN E 111 " --> pdb=" O TYR E 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=9 Processing sheet with id=10, first strand: chain 'G' and resid 26 through 27 Processing sheet with id=11, first strand: chain 'G' and resid 29 through 32 removed outlier: 3.716A pdb=" N LEU G 41 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'G' and resid 84 through 85 removed outlier: 3.774A pdb=" N TYR G 85 " --> pdb=" O ASN G 111 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASN G 111 " --> pdb=" O TYR G 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=12 Processing sheet with id=13, first strand: chain 'I' and resid 26 through 27 Processing sheet with id=14, first strand: chain 'I' and resid 29 through 32 removed outlier: 3.716A pdb=" N LEU I 41 " --> pdb=" O ILE I 32 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'I' and resid 84 through 85 removed outlier: 3.773A pdb=" N TYR I 85 " --> pdb=" O ASN I 111 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASN I 111 " --> pdb=" O TYR I 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=15 Processing sheet with id=16, first strand: chain 'K' and resid 26 through 27 Processing sheet with id=17, first strand: chain 'K' and resid 29 through 32 removed outlier: 3.716A pdb=" N LEU K 41 " --> pdb=" O ILE K 32 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'K' and resid 84 through 85 removed outlier: 3.774A pdb=" N TYR K 85 " --> pdb=" O ASN K 111 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN K 111 " --> pdb=" O TYR K 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=18 Processing sheet with id=19, first strand: chain 'M' and resid 26 through 27 Processing sheet with id=20, first strand: chain 'M' and resid 29 through 32 removed outlier: 3.716A pdb=" N LEU M 41 " --> pdb=" O ILE M 32 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'M' and resid 84 through 85 removed outlier: 3.773A pdb=" N TYR M 85 " --> pdb=" O ASN M 111 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN M 111 " --> pdb=" O TYR M 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=21 Processing sheet with id=22, first strand: chain 'O' and resid 26 through 27 Processing sheet with id=23, first strand: chain 'O' and resid 29 through 32 removed outlier: 3.716A pdb=" N LEU O 41 " --> pdb=" O ILE O 32 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'O' and resid 84 through 85 removed outlier: 3.773A pdb=" N TYR O 85 " --> pdb=" O ASN O 111 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN O 111 " --> pdb=" O TYR O 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=24 Processing sheet with id=25, first strand: chain 'Q' and resid 26 through 27 Processing sheet with id=26, first strand: chain 'Q' and resid 29 through 32 removed outlier: 3.716A pdb=" N LEU Q 41 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'Q' and resid 84 through 85 removed outlier: 3.774A pdb=" N TYR Q 85 " --> pdb=" O ASN Q 111 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN Q 111 " --> pdb=" O TYR Q 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=27 Processing sheet with id=28, first strand: chain 'S' and resid 26 through 27 Processing sheet with id=29, first strand: chain 'S' and resid 29 through 32 removed outlier: 3.716A pdb=" N LEU S 41 " --> pdb=" O ILE S 32 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'S' and resid 84 through 85 removed outlier: 3.773A pdb=" N TYR S 85 " --> pdb=" O ASN S 111 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN S 111 " --> pdb=" O TYR S 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=30 Processing sheet with id=31, first strand: chain 'U' and resid 26 through 27 Processing sheet with id=32, first strand: chain 'U' and resid 29 through 32 removed outlier: 3.717A pdb=" N LEU U 41 " --> pdb=" O ILE U 32 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'U' and resid 84 through 85 removed outlier: 3.774A pdb=" N TYR U 85 " --> pdb=" O ASN U 111 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASN U 111 " --> pdb=" O TYR U 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=33 Processing sheet with id=34, first strand: chain 'W' and resid 26 through 27 Processing sheet with id=35, first strand: chain 'W' and resid 29 through 32 removed outlier: 3.716A pdb=" N LEU W 41 " --> pdb=" O ILE W 32 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'W' and resid 84 through 85 removed outlier: 3.773A pdb=" N TYR W 85 " --> pdb=" O ASN W 111 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN W 111 " --> pdb=" O TYR W 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=36 Processing sheet with id=37, first strand: chain 'Y' and resid 26 through 27 Processing sheet with id=38, first strand: chain 'Y' and resid 29 through 32 removed outlier: 3.716A pdb=" N LEU Y 41 " --> pdb=" O ILE Y 32 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'Y' and resid 84 through 85 removed outlier: 3.774A pdb=" N TYR Y 85 " --> pdb=" O ASN Y 111 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN Y 111 " --> pdb=" O TYR Y 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=39 Processing sheet with id=40, first strand: chain '0' and resid 26 through 27 Processing sheet with id=41, first strand: chain '0' and resid 29 through 32 removed outlier: 3.715A pdb=" N LEU 0 41 " --> pdb=" O ILE 0 32 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain '0' and resid 84 through 85 removed outlier: 3.773A pdb=" N TYR 0 85 " --> pdb=" O ASN 0 111 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN 0 111 " --> pdb=" O TYR 0 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=42 Processing sheet with id=43, first strand: chain '2' and resid 26 through 27 Processing sheet with id=44, first strand: chain '2' and resid 29 through 32 removed outlier: 3.716A pdb=" N LEU 2 41 " --> pdb=" O ILE 2 32 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain '2' and resid 84 through 85 removed outlier: 3.773A pdb=" N TYR 2 85 " --> pdb=" O ASN 2 111 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN 2 111 " --> pdb=" O TYR 2 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=45 Processing sheet with id=46, first strand: chain '4' and resid 26 through 27 Processing sheet with id=47, first strand: chain '4' and resid 29 through 32 removed outlier: 3.716A pdb=" N LEU 4 41 " --> pdb=" O ILE 4 32 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain '4' and resid 84 through 85 removed outlier: 3.773A pdb=" N TYR 4 85 " --> pdb=" O ASN 4 111 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN 4 111 " --> pdb=" O TYR 4 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=48 Processing sheet with id=49, first strand: chain '6' and resid 26 through 27 Processing sheet with id=50, first strand: chain '6' and resid 29 through 32 removed outlier: 3.715A pdb=" N LEU 6 41 " --> pdb=" O ILE 6 32 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain '6' and resid 84 through 85 removed outlier: 3.774A pdb=" N TYR 6 85 " --> pdb=" O ASN 6 111 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN 6 111 " --> pdb=" O TYR 6 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=51 Processing sheet with id=52, first strand: chain '8' and resid 26 through 27 Processing sheet with id=53, first strand: chain '8' and resid 29 through 32 removed outlier: 3.716A pdb=" N LEU 8 41 " --> pdb=" O ILE 8 32 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain '8' and resid 84 through 85 removed outlier: 3.774A pdb=" N TYR 8 85 " --> pdb=" O ASN 8 111 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASN 8 111 " --> pdb=" O TYR 8 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=54 Processing sheet with id=55, first strand: chain 'a' and resid 26 through 27 Processing sheet with id=56, first strand: chain 'a' and resid 29 through 32 removed outlier: 3.716A pdb=" N LEU a 41 " --> pdb=" O ILE a 32 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'a' and resid 84 through 85 removed outlier: 3.774A pdb=" N TYR a 85 " --> pdb=" O ASN a 111 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN a 111 " --> pdb=" O TYR a 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=57 Processing sheet with id=58, first strand: chain 'c' and resid 26 through 27 Processing sheet with id=59, first strand: chain 'c' and resid 29 through 32 removed outlier: 3.717A pdb=" N LEU c 41 " --> pdb=" O ILE c 32 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'c' and resid 84 through 85 removed outlier: 3.774A pdb=" N TYR c 85 " --> pdb=" O ASN c 111 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN c 111 " --> pdb=" O TYR c 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=60 Processing sheet with id=61, first strand: chain 'e' and resid 26 through 27 Processing sheet with id=62, first strand: chain 'e' and resid 29 through 32 removed outlier: 3.717A pdb=" N LEU e 41 " --> pdb=" O ILE e 32 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'e' and resid 84 through 85 removed outlier: 3.774A pdb=" N TYR e 85 " --> pdb=" O ASN e 111 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN e 111 " --> pdb=" O TYR e 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=63 Processing sheet with id=64, first strand: chain 'g' and resid 26 through 27 Processing sheet with id=65, first strand: chain 'g' and resid 29 through 32 removed outlier: 3.716A pdb=" N LEU g 41 " --> pdb=" O ILE g 32 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'g' and resid 84 through 85 removed outlier: 3.774A pdb=" N TYR g 85 " --> pdb=" O ASN g 111 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN g 111 " --> pdb=" O TYR g 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=66 Processing sheet with id=67, first strand: chain 'i' and resid 26 through 27 Processing sheet with id=68, first strand: chain 'i' and resid 29 through 32 removed outlier: 3.717A pdb=" N LEU i 41 " --> pdb=" O ILE i 32 " (cutoff:3.500A) Processing sheet with id=69, first strand: chain 'i' and resid 84 through 85 removed outlier: 3.774A pdb=" N TYR i 85 " --> pdb=" O ASN i 111 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN i 111 " --> pdb=" O TYR i 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=69 Processing sheet with id=70, first strand: chain 'k' and resid 26 through 27 Processing sheet with id=71, first strand: chain 'k' and resid 29 through 32 removed outlier: 3.717A pdb=" N LEU k 41 " --> pdb=" O ILE k 32 " (cutoff:3.500A) Processing sheet with id=72, first strand: chain 'k' and resid 84 through 85 removed outlier: 3.773A pdb=" N TYR k 85 " --> pdb=" O ASN k 111 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN k 111 " --> pdb=" O TYR k 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=72 1224 hydrogen bonds defined for protein. 3456 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: 5.08 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 4512 1.29 - 1.36: 4320 1.36 - 1.42: 2760 1.42 - 1.48: 4320 1.48 - 1.55: 11640 Bond restraints: 27552 Sorted by residual: bond pdb=" CG1 ILE d 14 " pdb=" CD1 ILE d 14 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 9.99e-01 bond pdb=" CG1 ILE T 14 " pdb=" CD1 ILE T 14 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 9.83e-01 bond pdb=" CG1 ILE D 14 " pdb=" CD1 ILE D 14 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 9.82e-01 bond pdb=" CG1 ILE N 14 " pdb=" CD1 ILE N 14 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 9.81e-01 bond pdb=" CG1 ILE f 14 " pdb=" CD1 ILE f 14 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 9.80e-01 ... (remaining 27547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 35137 1.05 - 2.09: 1688 2.09 - 3.14: 519 3.14 - 4.19: 144 4.19 - 5.23: 48 Bond angle restraints: 37536 Sorted by residual: angle pdb=" N ASN 4 88 " pdb=" CA ASN 4 88 " pdb=" C ASN 4 88 " ideal model delta sigma weight residual 114.56 111.26 3.30 1.27e+00 6.20e-01 6.73e+00 angle pdb=" N ASN 8 88 " pdb=" CA ASN 8 88 " pdb=" C ASN 8 88 " ideal model delta sigma weight residual 114.56 111.27 3.29 1.27e+00 6.20e-01 6.72e+00 angle pdb=" N ASN K 88 " pdb=" CA ASN K 88 " pdb=" C ASN K 88 " ideal model delta sigma weight residual 114.56 111.28 3.28 1.27e+00 6.20e-01 6.67e+00 angle pdb=" N ASN 2 88 " pdb=" CA ASN 2 88 " pdb=" C ASN 2 88 " ideal model delta sigma weight residual 114.56 111.29 3.27 1.27e+00 6.20e-01 6.63e+00 angle pdb=" N ASN a 88 " pdb=" CA ASN a 88 " pdb=" C ASN a 88 " ideal model delta sigma weight residual 114.56 111.30 3.26 1.27e+00 6.20e-01 6.60e+00 ... (remaining 37531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.42: 13291 14.42 - 28.83: 2045 28.83 - 43.25: 672 43.25 - 57.66: 96 57.66 - 72.08: 48 Dihedral angle restraints: 16152 sinusoidal: 5736 harmonic: 10416 Sorted by residual: dihedral pdb=" CA ARG h 38 " pdb=" CB ARG h 38 " pdb=" CG ARG h 38 " pdb=" CD ARG h 38 " ideal model delta sinusoidal sigma weight residual 180.00 124.29 55.71 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" CA ARG D 38 " pdb=" CB ARG D 38 " pdb=" CG ARG D 38 " pdb=" CD ARG D 38 " ideal model delta sinusoidal sigma weight residual 180.00 124.29 55.71 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" CA ARG b 38 " pdb=" CB ARG b 38 " pdb=" CG ARG b 38 " pdb=" CD ARG b 38 " ideal model delta sinusoidal sigma weight residual 180.00 124.29 55.71 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 16149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2495 0.025 - 0.049: 1185 0.049 - 0.074: 369 0.074 - 0.098: 223 0.098 - 0.123: 144 Chirality restraints: 4416 Sorted by residual: chirality pdb=" CB VAL a 98 " pdb=" CA VAL a 98 " pdb=" CG1 VAL a 98 " pdb=" CG2 VAL a 98 " both_signs ideal model delta sigma weight residual False -2.63 -2.75 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CB VAL 6 98 " pdb=" CA VAL 6 98 " pdb=" CG1 VAL 6 98 " pdb=" CG2 VAL 6 98 " both_signs ideal model delta sigma weight residual False -2.63 -2.75 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CB VAL G 98 " pdb=" CA VAL G 98 " pdb=" CG1 VAL G 98 " pdb=" CG2 VAL G 98 " both_signs ideal model delta sigma weight residual False -2.63 -2.75 0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 4413 not shown) Planarity restraints: 4800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR I 38 " 0.015 5.00e-02 4.00e+02 2.32e-02 8.61e-01 pdb=" N PRO I 39 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO I 39 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO I 39 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR c 38 " 0.015 5.00e-02 4.00e+02 2.32e-02 8.60e-01 pdb=" N PRO c 39 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO c 39 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO c 39 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR 6 38 " 0.015 5.00e-02 4.00e+02 2.31e-02 8.55e-01 pdb=" N PRO 6 39 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO 6 39 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO 6 39 " 0.013 5.00e-02 4.00e+02 ... (remaining 4797 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1021 2.70 - 3.25: 28362 3.25 - 3.80: 42058 3.80 - 4.35: 51014 4.35 - 4.90: 89400 Nonbonded interactions: 211855 Sorted by model distance: nonbonded pdb=" OE2 GLU N 58 " pdb=" OH TYR N 67 " model vdw 2.150 3.040 nonbonded pdb=" OE2 GLU L 58 " pdb=" OH TYR L 67 " model vdw 2.150 3.040 nonbonded pdb=" OE2 GLU d 58 " pdb=" OH TYR d 67 " model vdw 2.150 3.040 nonbonded pdb=" OE2 GLU T 58 " pdb=" OH TYR T 67 " model vdw 2.150 3.040 nonbonded pdb=" OE2 GLU j 58 " pdb=" OH TYR j 67 " model vdw 2.150 3.040 ... (remaining 211850 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: 0.11 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'B' selection = chain '0' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'A' selection = chain '1' selection = chain '3' selection = chain '5' selection = chain '7' selection = chain '9' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.480 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 : 0.003 0.039 27552 Z= 0.140 Angle : 0.608 5.232 37536 Z= 0.337 Chirality : 0.039 0.123 4416 Planarity : 0.003 0.023 4800 Dihedral : 15.818 72.076 9528 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.00 % Allowed : 27.12 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.15), residues: 3528 helix: 2.29 (0.16), residues: 1104 sheet: -2.70 (0.17), residues: 744 loop : -2.45 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG 1 38 TYR 0.009 0.001 TYR 6 61 PHE 0.005 0.001 PHE d 34 TRP 0.004 0.001 TRP E 109 HIS 0.002 0.001 HIS d 64 Details of bonding type rmsd covalent geometry : bond 0.00326 (27552) covalent geometry : angle 0.60787 (37536) hydrogen bonds : bond 0.16316 ( 1224) hydrogen bonds : angle 7.00592 ( 3456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 533 time to evaluate : 1.042 Fit side-chains REVERT: E 48 GLN cc_start: 0.8342 (pt0) cc_final: 0.8129 (pt0) REVERT: E 69 LYS cc_start: 0.9317 (mtmm) cc_final: 0.8977 (mttp) REVERT: E 87 ASP cc_start: 0.8867 (m-30) cc_final: 0.8614 (m-30) REVERT: H 63 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7608 (mt-10) REVERT: I 87 ASP cc_start: 0.8867 (m-30) cc_final: 0.8600 (m-30) REVERT: M 87 ASP cc_start: 0.8969 (m-30) cc_final: 0.8698 (m-30) REVERT: N 63 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7363 (mt-10) REVERT: Q 87 ASP cc_start: 0.8952 (m-30) cc_final: 0.8663 (m-30) REVERT: R 63 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7248 (mt-10) REVERT: U 47 ASN cc_start: 0.8722 (t0) cc_final: 0.8434 (t0) REVERT: U 87 ASP cc_start: 0.8933 (m-30) cc_final: 0.8598 (m-30) REVERT: 2 87 ASP cc_start: 0.8872 (m-30) cc_final: 0.8608 (m-30) REVERT: 3 63 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7444 (mt-10) REVERT: 4 48 GLN cc_start: 0.8540 (pt0) cc_final: 0.8253 (pt0) REVERT: 8 87 ASP cc_start: 0.8975 (m-30) cc_final: 0.8637 (m-30) REVERT: b 69 ASN cc_start: 0.7552 (t0) cc_final: 0.7343 (t0) REVERT: c 47 ASN cc_start: 0.8737 (t0) cc_final: 0.8479 (t0) REVERT: i 87 ASP cc_start: 0.8906 (m-30) cc_final: 0.8695 (m-30) outliers start: 0 outliers final: 0 residues processed: 533 average time/residue: 0.1451 time to fit residues: 135.2041 Evaluate side-chains 461 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.093362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.078542 restraints weight = 47449.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.080854 restraints weight = 27072.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.082381 restraints weight = 17871.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.083435 restraints weight = 13298.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 69)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.084405 restraints weight = 10630.055| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 27552 Z= 0.145 Angle : 0.557 5.819 37536 Z= 0.279 Chirality : 0.040 0.112 4416 Planarity : 0.003 0.023 4800 Dihedral : 4.190 29.232 3864 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 2.79 % Allowed : 27.79 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.15), residues: 3528 helix: 2.50 (0.16), residues: 1104 sheet: -2.22 (0.19), residues: 696 loop : -2.42 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG f 38 TYR 0.018 0.001 TYR S 53 PHE 0.008 0.001 PHE N 34 TRP 0.005 0.002 TRP 0 109 HIS 0.002 0.001 HIS b 64 Details of bonding type rmsd covalent geometry : bond 0.00354 (27552) covalent geometry : angle 0.55655 (37536) hydrogen bonds : bond 0.04480 ( 1224) hydrogen bonds : angle 4.39522 ( 3456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 508 time to evaluate : 1.061 Fit side-chains REVERT: C 77 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8661 (m) REVERT: E 48 GLN cc_start: 0.8400 (pt0) cc_final: 0.8144 (pt0) REVERT: E 69 LYS cc_start: 0.9334 (mtmm) cc_final: 0.8949 (mttp) REVERT: E 87 ASP cc_start: 0.8830 (m-30) cc_final: 0.8627 (m-30) REVERT: I 87 ASP cc_start: 0.8831 (m-30) cc_final: 0.8628 (m-30) REVERT: K 77 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8730 (m) REVERT: M 87 ASP cc_start: 0.8963 (m-30) cc_final: 0.8754 (m-30) REVERT: N 63 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7427 (mt-10) REVERT: O 40 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8611 (ptpt) REVERT: P 60 TYR cc_start: 0.9178 (t80) cc_final: 0.8930 (t80) REVERT: S 77 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8734 (m) REVERT: Y 77 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8828 (m) REVERT: B 77 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8669 (m) REVERT: 2 87 ASP cc_start: 0.8838 (m-30) cc_final: 0.8531 (m-30) REVERT: 3 63 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7391 (mt-10) REVERT: 6 77 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8789 (m) REVERT: a 77 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8776 (m) REVERT: d 60 TYR cc_start: 0.9286 (t80) cc_final: 0.9041 (t80) REVERT: e 77 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8797 (m) REVERT: i 77 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8762 (m) REVERT: l 60 TYR cc_start: 0.9237 (t80) cc_final: 0.9036 (t80) outliers start: 79 outliers final: 51 residues processed: 550 average time/residue: 0.1513 time to fit residues: 144.8962 Evaluate side-chains 529 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 468 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 44 GLN Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain O residue 40 LYS Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain R residue 18 ILE Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain W residue 77 THR Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain Z residue 49 ASP Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain 0 residue 37 SER Chi-restraints excluded: chain 0 residue 49 VAL Chi-restraints excluded: chain 2 residue 77 THR Chi-restraints excluded: chain 3 residue 23 ILE Chi-restraints excluded: chain 5 residue 23 ILE Chi-restraints excluded: chain 5 residue 49 ASP Chi-restraints excluded: chain 6 residue 49 VAL Chi-restraints excluded: chain 6 residue 77 THR Chi-restraints excluded: chain 7 residue 23 ILE Chi-restraints excluded: chain 8 residue 49 VAL Chi-restraints excluded: chain 9 residue 18 ILE Chi-restraints excluded: chain 9 residue 23 ILE Chi-restraints excluded: chain a residue 77 THR Chi-restraints excluded: chain b residue 18 ILE Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain c residue 77 THR Chi-restraints excluded: chain d residue 23 ILE Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 77 THR Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 77 THR Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain i residue 77 THR Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain l residue 22 ILE Chi-restraints excluded: chain l residue 23 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 49 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 214 optimal weight: 5.9990 chunk 183 optimal weight: 0.0000 chunk 55 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 200 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.093085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.075285 restraints weight = 47724.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.078595 restraints weight = 22363.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.080850 restraints weight = 13320.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.082407 restraints weight = 9152.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.083323 restraints weight = 6942.601| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27552 Z= 0.136 Angle : 0.549 5.724 37536 Z= 0.276 Chirality : 0.039 0.119 4416 Planarity : 0.003 0.024 4800 Dihedral : 4.183 32.761 3864 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 4.84 % Allowed : 25.81 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.15), residues: 3528 helix: 2.69 (0.16), residues: 1104 sheet: -2.01 (0.19), residues: 696 loop : -2.35 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG f 38 TYR 0.019 0.001 TYR c 53 PHE 0.006 0.001 PHE A 34 TRP 0.005 0.001 TRP U 109 HIS 0.002 0.000 HIS d 64 Details of bonding type rmsd covalent geometry : bond 0.00330 (27552) covalent geometry : angle 0.54910 (37536) hydrogen bonds : bond 0.04281 ( 1224) hydrogen bonds : angle 4.06827 ( 3456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 509 time to evaluate : 1.072 Fit side-chains REVERT: E 25 ASP cc_start: 0.8970 (p0) cc_final: 0.8754 (p0) REVERT: E 44 GLN cc_start: 0.8250 (mt0) cc_final: 0.8032 (mt0) REVERT: E 48 GLN cc_start: 0.8832 (pt0) cc_final: 0.8596 (pt0) REVERT: E 69 LYS cc_start: 0.9071 (mtmm) cc_final: 0.8823 (mttp) REVERT: H 63 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7778 (mm-30) REVERT: N 63 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7970 (mt-10) REVERT: O 40 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8396 (ptpt) REVERT: P 60 TYR cc_start: 0.8952 (t80) cc_final: 0.8723 (t80) REVERT: Q 31 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8090 (mt-10) REVERT: Z 60 TYR cc_start: 0.8992 (t80) cc_final: 0.8697 (t80) REVERT: 2 25 ASP cc_start: 0.9054 (p0) cc_final: 0.8809 (p0) REVERT: 2 87 ASP cc_start: 0.8864 (m-30) cc_final: 0.8558 (m-30) REVERT: 3 63 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7919 (mt-10) REVERT: 4 25 ASP cc_start: 0.9026 (p0) cc_final: 0.8789 (p0) REVERT: 9 51 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7803 (mmmt) REVERT: 9 60 TYR cc_start: 0.8987 (t80) cc_final: 0.8655 (t80) REVERT: 9 63 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7516 (mm-30) REVERT: a 40 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8467 (ptpt) REVERT: c 25 ASP cc_start: 0.9111 (p0) cc_final: 0.8906 (p0) REVERT: d 60 TYR cc_start: 0.9023 (t80) cc_final: 0.8637 (t80) REVERT: h 60 TYR cc_start: 0.9011 (t80) cc_final: 0.8683 (t80) REVERT: i 25 ASP cc_start: 0.9193 (p0) cc_final: 0.8974 (p0) REVERT: i 46 SER cc_start: 0.8744 (m) cc_final: 0.8366 (t) REVERT: l 38 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7738 (mtt90) outliers start: 137 outliers final: 86 residues processed: 578 average time/residue: 0.1538 time to fit residues: 150.8009 Evaluate side-chains 568 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 478 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 44 GLN Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 49 ASP Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 40 LYS Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain R residue 18 ILE Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 77 THR Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain Y residue 29 SER Chi-restraints excluded: chain Y residue 40 LYS Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain Z residue 49 ASP Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain 0 residue 29 SER Chi-restraints excluded: chain 0 residue 31 GLU Chi-restraints excluded: chain 0 residue 37 SER Chi-restraints excluded: chain 1 residue 23 ILE Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 77 THR Chi-restraints excluded: chain 3 residue 18 ILE Chi-restraints excluded: chain 3 residue 23 ILE Chi-restraints excluded: chain 4 residue 29 SER Chi-restraints excluded: chain 4 residue 49 VAL Chi-restraints excluded: chain 5 residue 23 ILE Chi-restraints excluded: chain 5 residue 49 ASP Chi-restraints excluded: chain 6 residue 29 SER Chi-restraints excluded: chain 6 residue 49 VAL Chi-restraints excluded: chain 7 residue 23 ILE Chi-restraints excluded: chain 8 residue 29 SER Chi-restraints excluded: chain 9 residue 18 ILE Chi-restraints excluded: chain 9 residue 23 ILE Chi-restraints excluded: chain 9 residue 51 LYS Chi-restraints excluded: chain a residue 29 SER Chi-restraints excluded: chain a residue 40 LYS Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain b residue 18 ILE Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain c residue 29 SER Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain d residue 18 ILE Chi-restraints excluded: chain d residue 23 ILE Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain g residue 29 SER Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain h residue 23 ILE Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain k residue 29 SER Chi-restraints excluded: chain k residue 49 VAL Chi-restraints excluded: chain l residue 18 ILE Chi-restraints excluded: chain l residue 22 ILE Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain l residue 38 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 62 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 152 optimal weight: 7.9990 chunk 285 optimal weight: 7.9990 chunk 269 optimal weight: 7.9990 chunk 15 optimal weight: 0.0470 chunk 168 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 255 optimal weight: 8.9990 overall best weight: 3.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 48 GLN B 44 GLN ** 0 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 48 GLN k 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.096413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.080816 restraints weight = 46569.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.083237 restraints weight = 26662.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.084979 restraints weight = 17611.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.086049 restraints weight = 12896.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 70)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.087035 restraints weight = 10323.592| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 27552 Z= 0.289 Angle : 0.666 7.539 37536 Z= 0.335 Chirality : 0.043 0.188 4416 Planarity : 0.003 0.025 4800 Dihedral : 4.607 34.553 3864 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 6.39 % Allowed : 25.00 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.14), residues: 3528 helix: 2.35 (0.16), residues: 1104 sheet: -1.59 (0.19), residues: 624 loop : -2.79 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG l 38 TYR 0.019 0.002 TYR 6 53 PHE 0.009 0.001 PHE f 11 TRP 0.006 0.002 TRP S 109 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00694 (27552) covalent geometry : angle 0.66587 (37536) hydrogen bonds : bond 0.05881 ( 1224) hydrogen bonds : angle 4.48352 ( 3456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 451 time to evaluate : 1.031 Fit side-chains REVERT: C 25 ASP cc_start: 0.8956 (p0) cc_final: 0.8727 (p0) REVERT: D 58 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8746 (mm-30) REVERT: E 25 ASP cc_start: 0.8884 (p0) cc_final: 0.8657 (p0) REVERT: F 47 GLU cc_start: 0.8299 (tt0) cc_final: 0.8085 (tt0) REVERT: F 51 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8708 (tptp) REVERT: H 51 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8783 (tptm) REVERT: J 51 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8600 (tptm) REVERT: L 51 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8622 (tptp) REVERT: N 51 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8612 (mmmt) REVERT: O 40 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8685 (ptpt) REVERT: P 60 TYR cc_start: 0.9311 (t80) cc_final: 0.9101 (t80) REVERT: R 51 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8588 (tptm) REVERT: T 51 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8609 (tptm) REVERT: Z 51 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8554 (tptm) REVERT: A 51 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8564 (tptm) REVERT: 1 51 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8776 (mmmt) REVERT: 2 87 ASP cc_start: 0.8765 (m-30) cc_final: 0.8469 (m-30) REVERT: 3 63 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7311 (mt-10) REVERT: 7 51 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8679 (tptp) REVERT: 9 51 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8702 (mmmt) REVERT: a 40 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8673 (ptpt) REVERT: d 51 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8723 (tptm) REVERT: d 60 TYR cc_start: 0.9339 (t80) cc_final: 0.9067 (t80) REVERT: f 51 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8530 (tptm) REVERT: i 46 SER cc_start: 0.8807 (m) cc_final: 0.8584 (t) REVERT: j 51 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8472 (tptp) REVERT: l 60 TYR cc_start: 0.9343 (t80) cc_final: 0.9080 (t80) outliers start: 181 outliers final: 115 residues processed: 577 average time/residue: 0.1796 time to fit residues: 167.5228 Evaluate side-chains 564 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 432 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 44 GLN Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 49 ASP Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 103 ILE Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 51 LYS Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 40 LYS Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain R residue 18 ILE Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain R residue 51 LYS Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain T residue 18 ILE Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 41 LEU Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 77 THR Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain Y residue 29 SER Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 103 ILE Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain Z residue 49 ASP Chi-restraints excluded: chain Z residue 51 LYS Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain 0 residue 29 SER Chi-restraints excluded: chain 0 residue 31 GLU Chi-restraints excluded: chain 0 residue 37 SER Chi-restraints excluded: chain 0 residue 49 VAL Chi-restraints excluded: chain 1 residue 51 LYS Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 77 THR Chi-restraints excluded: chain 3 residue 18 ILE Chi-restraints excluded: chain 3 residue 23 ILE Chi-restraints excluded: chain 4 residue 29 SER Chi-restraints excluded: chain 4 residue 49 VAL Chi-restraints excluded: chain 5 residue 18 ILE Chi-restraints excluded: chain 5 residue 23 ILE Chi-restraints excluded: chain 5 residue 49 ASP Chi-restraints excluded: chain 6 residue 29 SER Chi-restraints excluded: chain 6 residue 49 VAL Chi-restraints excluded: chain 7 residue 18 ILE Chi-restraints excluded: chain 7 residue 23 ILE Chi-restraints excluded: chain 7 residue 51 LYS Chi-restraints excluded: chain 8 residue 29 SER Chi-restraints excluded: chain 8 residue 49 VAL Chi-restraints excluded: chain 8 residue 103 ILE Chi-restraints excluded: chain 9 residue 23 ILE Chi-restraints excluded: chain 9 residue 51 LYS Chi-restraints excluded: chain a residue 29 SER Chi-restraints excluded: chain a residue 40 LYS Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain b residue 18 ILE Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain c residue 29 SER Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 77 THR Chi-restraints excluded: chain d residue 18 ILE Chi-restraints excluded: chain d residue 23 ILE Chi-restraints excluded: chain d residue 51 LYS Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 103 ILE Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 51 LYS Chi-restraints excluded: chain g residue 29 SER Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain g residue 77 THR Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 51 LYS Chi-restraints excluded: chain k residue 29 SER Chi-restraints excluded: chain k residue 32 ILE Chi-restraints excluded: chain k residue 49 VAL Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain l residue 18 ILE Chi-restraints excluded: chain l residue 22 ILE Chi-restraints excluded: chain l residue 23 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 195 optimal weight: 0.7980 chunk 241 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.091890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.076976 restraints weight = 47440.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.079323 restraints weight = 27181.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.081015 restraints weight = 17939.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.082231 restraints weight = 13084.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.083014 restraints weight = 10305.601| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27552 Z= 0.152 Angle : 0.583 6.693 37536 Z= 0.292 Chirality : 0.040 0.160 4416 Planarity : 0.003 0.026 4800 Dihedral : 4.481 44.462 3864 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 4.87 % Allowed : 27.40 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.14), residues: 3528 helix: 2.48 (0.15), residues: 1104 sheet: -1.98 (0.19), residues: 696 loop : -2.48 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 38 TYR 0.021 0.001 TYR 6 53 PHE 0.005 0.001 PHE h 66 TRP 0.006 0.002 TRP S 109 HIS 0.002 0.000 HIS d 64 Details of bonding type rmsd covalent geometry : bond 0.00368 (27552) covalent geometry : angle 0.58343 (37536) hydrogen bonds : bond 0.04593 ( 1224) hydrogen bonds : angle 4.08607 ( 3456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 477 time to evaluate : 0.993 Fit side-chains REVERT: C 25 ASP cc_start: 0.8964 (p0) cc_final: 0.8674 (p0) REVERT: E 25 ASP cc_start: 0.8902 (p0) cc_final: 0.8606 (p0) REVERT: E 41 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8721 (pt) REVERT: E 53 TYR cc_start: 0.9003 (t80) cc_final: 0.8510 (t80) REVERT: F 51 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8578 (tptp) REVERT: F 63 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7516 (mm-30) REVERT: N 51 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8355 (mmmt) REVERT: N 63 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7243 (mt-10) REVERT: O 40 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8597 (ptpt) REVERT: O 110 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.8020 (pttm) REVERT: P 51 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8642 (tptp) REVERT: T 51 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8478 (tptm) REVERT: X 60 TYR cc_start: 0.9305 (t80) cc_final: 0.9078 (t80) REVERT: X 63 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7366 (mt-10) REVERT: Z 51 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8469 (tptm) REVERT: A 51 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8523 (tptm) REVERT: 0 41 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8922 (pt) REVERT: 1 51 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8499 (mmmt) REVERT: 2 87 ASP cc_start: 0.8855 (m-30) cc_final: 0.8523 (m-30) REVERT: 7 51 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8462 (tptp) REVERT: 9 51 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8495 (tptm) REVERT: 9 60 TYR cc_start: 0.9263 (t80) cc_final: 0.8990 (t80) REVERT: a 40 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8705 (ptpt) REVERT: c 77 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8906 (m) REVERT: i 46 SER cc_start: 0.8918 (m) cc_final: 0.8681 (t) REVERT: j 51 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8414 (tptp) REVERT: k 77 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8893 (m) outliers start: 138 outliers final: 91 residues processed: 559 average time/residue: 0.1500 time to fit residues: 142.7365 Evaluate side-chains 561 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 453 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 44 GLN Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 49 ASP Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 51 LYS Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 40 LYS Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 110 LYS Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 51 LYS Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain R residue 18 ILE Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 77 THR Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain Y residue 29 SER Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain Z residue 49 ASP Chi-restraints excluded: chain Z residue 51 LYS Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain 0 residue 29 SER Chi-restraints excluded: chain 0 residue 31 GLU Chi-restraints excluded: chain 0 residue 37 SER Chi-restraints excluded: chain 0 residue 41 LEU Chi-restraints excluded: chain 0 residue 49 VAL Chi-restraints excluded: chain 1 residue 23 ILE Chi-restraints excluded: chain 1 residue 51 LYS Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 77 THR Chi-restraints excluded: chain 3 residue 18 ILE Chi-restraints excluded: chain 3 residue 23 ILE Chi-restraints excluded: chain 4 residue 29 SER Chi-restraints excluded: chain 4 residue 49 VAL Chi-restraints excluded: chain 5 residue 18 ILE Chi-restraints excluded: chain 5 residue 23 ILE Chi-restraints excluded: chain 5 residue 49 ASP Chi-restraints excluded: chain 7 residue 23 ILE Chi-restraints excluded: chain 7 residue 51 LYS Chi-restraints excluded: chain 8 residue 29 SER Chi-restraints excluded: chain 8 residue 49 VAL Chi-restraints excluded: chain 8 residue 77 THR Chi-restraints excluded: chain 9 residue 23 ILE Chi-restraints excluded: chain 9 residue 51 LYS Chi-restraints excluded: chain a residue 29 SER Chi-restraints excluded: chain a residue 40 LYS Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain c residue 29 SER Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 77 THR Chi-restraints excluded: chain d residue 18 ILE Chi-restraints excluded: chain d residue 23 ILE Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain g residue 29 SER Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain g residue 77 THR Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 51 LYS Chi-restraints excluded: chain k residue 29 SER Chi-restraints excluded: chain k residue 49 VAL Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain l residue 22 ILE Chi-restraints excluded: chain l residue 23 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 246 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 280 optimal weight: 6.9990 chunk 190 optimal weight: 0.4980 chunk 164 optimal weight: 0.4980 chunk 138 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 297 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 48 GLN ** 0 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.091870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.076696 restraints weight = 48302.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.078949 restraints weight = 28252.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.080599 restraints weight = 18889.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.081764 restraints weight = 13910.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.082471 restraints weight = 11064.836| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 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 0.057 27552 Z= 0.248 Angle : 0.649 7.130 37536 Z= 0.325 Chirality : 0.042 0.157 4416 Planarity : 0.003 0.027 4800 Dihedral : 4.780 61.009 3864 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 6.11 % Allowed : 27.37 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.14), residues: 3528 helix: 2.34 (0.16), residues: 1104 sheet: -1.47 (0.19), residues: 624 loop : -2.82 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 38 TYR 0.025 0.002 TYR d 60 PHE 0.007 0.001 PHE f 11 TRP 0.006 0.002 TRP E 109 HIS 0.002 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00598 (27552) covalent geometry : angle 0.64882 (37536) hydrogen bonds : bond 0.05460 ( 1224) hydrogen bonds : angle 4.31480 ( 3456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 447 time to evaluate : 1.280 Fit side-chains REVERT: C 25 ASP cc_start: 0.9028 (p0) cc_final: 0.8703 (p0) REVERT: E 25 ASP cc_start: 0.8944 (p0) cc_final: 0.8605 (p0) REVERT: E 41 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8742 (pt) REVERT: F 51 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8644 (tptp) REVERT: H 51 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8736 (tptm) REVERT: J 51 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8544 (tptm) REVERT: K 41 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8575 (pt) REVERT: L 51 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8573 (tptp) REVERT: N 51 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8497 (mmmt) REVERT: O 40 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8631 (ptpt) REVERT: P 51 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8592 (tptp) REVERT: R 51 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8548 (tptm) REVERT: T 51 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8530 (tptm) REVERT: Z 51 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8481 (tptm) REVERT: B 53 TYR cc_start: 0.9032 (t80) cc_final: 0.8812 (t80) REVERT: A 51 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8566 (tptm) REVERT: 0 41 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8961 (pt) REVERT: 1 51 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8628 (mmmt) REVERT: 2 87 ASP cc_start: 0.8854 (m-30) cc_final: 0.8545 (m-30) REVERT: 6 41 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8714 (pt) REVERT: 7 51 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8578 (tptp) REVERT: 9 51 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8558 (mmmt) REVERT: a 40 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8711 (ptpt) REVERT: d 51 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8579 (tptp) REVERT: e 46 SER cc_start: 0.9161 (m) cc_final: 0.8764 (t) REVERT: i 46 SER cc_start: 0.8994 (m) cc_final: 0.8766 (t) REVERT: j 51 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8498 (tptp) REVERT: k 77 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8958 (m) outliers start: 173 outliers final: 124 residues processed: 573 average time/residue: 0.1572 time to fit residues: 151.8913 Evaluate side-chains 583 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 437 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain J residue 49 ASP Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 44 GLN Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 49 ASP Chi-restraints excluded: chain L residue 51 LYS Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 51 LYS Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 40 LYS Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 51 LYS Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain R residue 18 ILE Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain R residue 51 LYS Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 41 LEU Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 77 THR Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain Y residue 29 SER Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain Z residue 49 ASP Chi-restraints excluded: chain Z residue 51 LYS Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain 0 residue 27 THR Chi-restraints excluded: chain 0 residue 29 SER Chi-restraints excluded: chain 0 residue 31 GLU Chi-restraints excluded: chain 0 residue 37 SER Chi-restraints excluded: chain 0 residue 41 LEU Chi-restraints excluded: chain 0 residue 49 VAL Chi-restraints excluded: chain 1 residue 23 ILE Chi-restraints excluded: chain 1 residue 51 LYS Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 77 THR Chi-restraints excluded: chain 3 residue 23 ILE Chi-restraints excluded: chain 4 residue 29 SER Chi-restraints excluded: chain 4 residue 49 VAL Chi-restraints excluded: chain 5 residue 14 ILE Chi-restraints excluded: chain 5 residue 18 ILE Chi-restraints excluded: chain 5 residue 23 ILE Chi-restraints excluded: chain 5 residue 49 ASP Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 29 SER Chi-restraints excluded: chain 6 residue 41 LEU Chi-restraints excluded: chain 6 residue 49 VAL Chi-restraints excluded: chain 7 residue 18 ILE Chi-restraints excluded: chain 7 residue 23 ILE Chi-restraints excluded: chain 7 residue 51 LYS Chi-restraints excluded: chain 8 residue 27 THR Chi-restraints excluded: chain 8 residue 29 SER Chi-restraints excluded: chain 8 residue 49 VAL Chi-restraints excluded: chain 8 residue 77 THR Chi-restraints excluded: chain 8 residue 110 LYS Chi-restraints excluded: chain 9 residue 23 ILE Chi-restraints excluded: chain 9 residue 51 LYS Chi-restraints excluded: chain a residue 29 SER Chi-restraints excluded: chain a residue 40 LYS Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain c residue 29 SER Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 77 THR Chi-restraints excluded: chain d residue 18 ILE Chi-restraints excluded: chain d residue 23 ILE Chi-restraints excluded: chain d residue 51 LYS Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain g residue 29 SER Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain g residue 77 THR Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain i residue 27 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 41 LEU Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 51 LYS Chi-restraints excluded: chain k residue 27 THR Chi-restraints excluded: chain k residue 29 SER Chi-restraints excluded: chain k residue 49 VAL Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 103 ILE Chi-restraints excluded: chain l residue 22 ILE Chi-restraints excluded: chain l residue 23 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 165 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 219 optimal weight: 0.7980 chunk 262 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 167 optimal weight: 0.6980 chunk 311 optimal weight: 0.6980 chunk 320 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.103533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.087615 restraints weight = 45029.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.090351 restraints weight = 24667.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.092316 restraints weight = 15805.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.093676 restraints weight = 11227.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.094509 restraints weight = 8676.637| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27552 Z= 0.118 Angle : 0.580 6.377 37536 Z= 0.293 Chirality : 0.039 0.144 4416 Planarity : 0.003 0.026 4800 Dihedral : 4.962 88.025 3864 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 3.28 % Allowed : 31.36 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.14), residues: 3528 helix: 2.58 (0.15), residues: 1104 sheet: -1.76 (0.19), residues: 696 loop : -2.44 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 38 TYR 0.026 0.001 TYR H 60 PHE 0.005 0.001 PHE 7 34 TRP 0.008 0.002 TRP M 109 HIS 0.001 0.000 HIS R 64 Details of bonding type rmsd covalent geometry : bond 0.00278 (27552) covalent geometry : angle 0.58011 (37536) hydrogen bonds : bond 0.03872 ( 1224) hydrogen bonds : angle 3.86025 ( 3456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 509 time to evaluate : 0.967 Fit side-chains REVERT: C 25 ASP cc_start: 0.8971 (p0) cc_final: 0.8643 (p0) REVERT: E 25 ASP cc_start: 0.8902 (p0) cc_final: 0.8592 (p0) REVERT: E 46 SER cc_start: 0.9130 (m) cc_final: 0.8853 (t) REVERT: E 53 TYR cc_start: 0.9033 (t80) cc_final: 0.8652 (t80) REVERT: H 51 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8680 (tptm) REVERT: N 51 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8594 (tptp) REVERT: O 40 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8570 (ptpt) REVERT: T 51 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8508 (tptm) REVERT: B 53 TYR cc_start: 0.8974 (t80) cc_final: 0.8742 (t80) REVERT: A 51 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8569 (tptm) REVERT: 0 41 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8868 (pt) REVERT: 1 51 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8386 (mmmt) REVERT: 2 87 ASP cc_start: 0.8859 (m-30) cc_final: 0.8522 (m-30) REVERT: 7 51 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8461 (tptp) REVERT: 9 51 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8436 (tptm) REVERT: e 46 SER cc_start: 0.8968 (m) cc_final: 0.8515 (t) REVERT: i 46 SER cc_start: 0.8881 (m) cc_final: 0.8612 (t) outliers start: 93 outliers final: 64 residues processed: 566 average time/residue: 0.1487 time to fit residues: 143.1838 Evaluate side-chains 547 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 474 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 49 ASP Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain N residue 51 LYS Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 40 LYS Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain R residue 18 ILE Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain Y residue 27 THR Chi-restraints excluded: chain Y residue 29 SER Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain 0 residue 31 GLU Chi-restraints excluded: chain 0 residue 41 LEU Chi-restraints excluded: chain 0 residue 49 VAL Chi-restraints excluded: chain 1 residue 51 LYS Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 4 residue 49 VAL Chi-restraints excluded: chain 5 residue 18 ILE Chi-restraints excluded: chain 5 residue 49 ASP Chi-restraints excluded: chain 6 residue 29 SER Chi-restraints excluded: chain 6 residue 49 VAL Chi-restraints excluded: chain 7 residue 23 ILE Chi-restraints excluded: chain 7 residue 51 LYS Chi-restraints excluded: chain 8 residue 29 SER Chi-restraints excluded: chain 9 residue 51 LYS Chi-restraints excluded: chain a residue 29 SER Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 29 SER Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain g residue 29 SER Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain k residue 27 THR Chi-restraints excluded: chain k residue 29 SER Chi-restraints excluded: chain k residue 49 VAL Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain l residue 22 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 321 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 332 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 1 optimal weight: 0.0020 chunk 49 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.101556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.085406 restraints weight = 45656.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.088183 restraints weight = 24839.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.090100 restraints weight = 15887.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.091331 restraints weight = 11345.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.092412 restraints weight = 8930.021| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27552 Z= 0.149 Angle : 0.597 6.471 37536 Z= 0.301 Chirality : 0.040 0.150 4416 Planarity : 0.003 0.026 4800 Dihedral : 5.260 89.832 3864 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 4.10 % Allowed : 31.14 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.15), residues: 3528 helix: 2.52 (0.15), residues: 1104 sheet: -1.90 (0.18), residues: 744 loop : -2.43 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 38 TYR 0.028 0.001 TYR H 60 PHE 0.004 0.001 PHE Z 11 TRP 0.005 0.002 TRP Y 109 HIS 0.002 0.000 HIS b 64 Details of bonding type rmsd covalent geometry : bond 0.00361 (27552) covalent geometry : angle 0.59712 (37536) hydrogen bonds : bond 0.04325 ( 1224) hydrogen bonds : angle 3.89172 ( 3456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 467 time to evaluate : 1.024 Fit side-chains REVERT: C 25 ASP cc_start: 0.9019 (p0) cc_final: 0.8660 (p0) REVERT: E 25 ASP cc_start: 0.8927 (p0) cc_final: 0.8604 (p0) REVERT: E 46 SER cc_start: 0.9193 (m) cc_final: 0.8872 (t) REVERT: E 53 TYR cc_start: 0.9064 (t80) cc_final: 0.8629 (t80) REVERT: H 51 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8664 (tptm) REVERT: N 51 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8369 (mmmt) REVERT: B 53 TYR cc_start: 0.9037 (t80) cc_final: 0.8806 (t80) REVERT: A 51 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8581 (tptm) REVERT: 0 41 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8857 (pt) REVERT: 1 51 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8404 (mmmt) REVERT: 2 77 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8940 (m) REVERT: 2 87 ASP cc_start: 0.8826 (m-30) cc_final: 0.8488 (m-30) REVERT: 7 51 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8501 (tptp) REVERT: 9 51 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8404 (tptm) REVERT: e 41 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8706 (pt) REVERT: e 46 SER cc_start: 0.9045 (m) cc_final: 0.8579 (t) REVERT: i 46 SER cc_start: 0.8914 (m) cc_final: 0.8637 (t) REVERT: j 51 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8292 (mmmt) outliers start: 116 outliers final: 95 residues processed: 538 average time/residue: 0.1517 time to fit residues: 140.6021 Evaluate side-chains 568 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 463 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain J residue 49 ASP Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 44 GLN Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 49 ASP Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain N residue 51 LYS Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain R residue 18 ILE Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain Y residue 27 THR Chi-restraints excluded: chain Y residue 29 SER Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain 0 residue 29 SER Chi-restraints excluded: chain 0 residue 37 SER Chi-restraints excluded: chain 0 residue 41 LEU Chi-restraints excluded: chain 0 residue 49 VAL Chi-restraints excluded: chain 1 residue 23 ILE Chi-restraints excluded: chain 1 residue 51 LYS Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 77 THR Chi-restraints excluded: chain 4 residue 29 SER Chi-restraints excluded: chain 4 residue 49 VAL Chi-restraints excluded: chain 5 residue 18 ILE Chi-restraints excluded: chain 5 residue 23 ILE Chi-restraints excluded: chain 5 residue 49 ASP Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 29 SER Chi-restraints excluded: chain 6 residue 49 VAL Chi-restraints excluded: chain 7 residue 23 ILE Chi-restraints excluded: chain 7 residue 51 LYS Chi-restraints excluded: chain 8 residue 27 THR Chi-restraints excluded: chain 8 residue 29 SER Chi-restraints excluded: chain 8 residue 49 VAL Chi-restraints excluded: chain 8 residue 65 THR Chi-restraints excluded: chain 9 residue 51 LYS Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain a residue 29 SER Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 29 SER Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain d residue 23 ILE Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain g residue 29 SER Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain h residue 23 ILE Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 51 LYS Chi-restraints excluded: chain k residue 27 THR Chi-restraints excluded: chain k residue 29 SER Chi-restraints excluded: chain k residue 49 VAL Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain l residue 22 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 126 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 332 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 243 optimal weight: 8.9990 chunk 290 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.090476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.072372 restraints weight = 48068.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.075699 restraints weight = 22505.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.078007 restraints weight = 13514.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.079547 restraints weight = 9348.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.080676 restraints weight = 7132.219| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27552 Z= 0.183 Angle : 0.626 6.754 37536 Z= 0.316 Chirality : 0.041 0.151 4416 Planarity : 0.003 0.027 4800 Dihedral : 5.347 80.211 3864 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 4.91 % Allowed : 30.61 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.14), residues: 3528 helix: 2.41 (0.16), residues: 1104 sheet: -1.14 (0.20), residues: 624 loop : -2.75 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 38 TYR 0.030 0.001 TYR 3 60 PHE 0.006 0.001 PHE f 11 TRP 0.005 0.002 TRP a 109 HIS 0.002 0.000 HIS R 64 Details of bonding type rmsd covalent geometry : bond 0.00441 (27552) covalent geometry : angle 0.62553 (37536) hydrogen bonds : bond 0.04807 ( 1224) hydrogen bonds : angle 4.03141 ( 3456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 451 time to evaluate : 1.080 Fit side-chains REVERT: C 25 ASP cc_start: 0.9109 (p0) cc_final: 0.8687 (p0) REVERT: E 25 ASP cc_start: 0.9082 (p0) cc_final: 0.8670 (p0) REVERT: E 41 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7987 (pt) REVERT: E 46 SER cc_start: 0.9164 (m) cc_final: 0.8751 (t) REVERT: E 53 TYR cc_start: 0.8994 (t80) cc_final: 0.8541 (t80) REVERT: M 41 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7912 (pt) REVERT: N 51 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7827 (mmmt) REVERT: O 40 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8395 (ptpt) REVERT: P 51 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8049 (tptp) REVERT: R 51 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8120 (tptm) REVERT: B 41 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8011 (pt) REVERT: 0 41 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8114 (pt) REVERT: 1 51 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7978 (mmmt) REVERT: 2 87 ASP cc_start: 0.8817 (m-30) cc_final: 0.8534 (m-30) REVERT: 7 51 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.8026 (tptp) REVERT: 9 51 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7887 (mmmt) REVERT: e 41 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8039 (pt) REVERT: e 46 SER cc_start: 0.9059 (m) cc_final: 0.8583 (t) REVERT: i 46 SER cc_start: 0.8774 (m) cc_final: 0.8399 (t) REVERT: j 51 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7808 (tptp) outliers start: 139 outliers final: 111 residues processed: 542 average time/residue: 0.1486 time to fit residues: 138.3665 Evaluate side-chains 568 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 444 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain J residue 49 ASP Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 44 GLN Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain L residue 49 ASP Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 51 LYS Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 40 LYS Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain P residue 51 LYS Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain R residue 18 ILE Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain R residue 51 LYS Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain Y residue 27 THR Chi-restraints excluded: chain Y residue 29 SER Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain 0 residue 27 THR Chi-restraints excluded: chain 0 residue 29 SER Chi-restraints excluded: chain 0 residue 37 SER Chi-restraints excluded: chain 0 residue 41 LEU Chi-restraints excluded: chain 0 residue 49 VAL Chi-restraints excluded: chain 1 residue 23 ILE Chi-restraints excluded: chain 1 residue 51 LYS Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 4 residue 29 SER Chi-restraints excluded: chain 4 residue 49 VAL Chi-restraints excluded: chain 5 residue 18 ILE Chi-restraints excluded: chain 5 residue 23 ILE Chi-restraints excluded: chain 5 residue 49 ASP Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 29 SER Chi-restraints excluded: chain 6 residue 49 VAL Chi-restraints excluded: chain 7 residue 18 ILE Chi-restraints excluded: chain 7 residue 23 ILE Chi-restraints excluded: chain 7 residue 51 LYS Chi-restraints excluded: chain 8 residue 27 THR Chi-restraints excluded: chain 8 residue 29 SER Chi-restraints excluded: chain 8 residue 49 VAL Chi-restraints excluded: chain 8 residue 65 THR Chi-restraints excluded: chain 9 residue 23 ILE Chi-restraints excluded: chain 9 residue 51 LYS Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain a residue 29 SER Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 29 SER Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain d residue 23 ILE Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain g residue 29 SER Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain h residue 23 ILE Chi-restraints excluded: chain h residue 59 SER Chi-restraints excluded: chain i residue 27 THR Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 51 LYS Chi-restraints excluded: chain j residue 59 SER Chi-restraints excluded: chain k residue 27 THR Chi-restraints excluded: chain k residue 29 SER Chi-restraints excluded: chain k residue 49 VAL Chi-restraints excluded: chain k residue 65 THR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain l residue 22 ILE Chi-restraints excluded: chain l residue 23 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 303 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 133 optimal weight: 0.4980 chunk 274 optimal weight: 4.9990 chunk 204 optimal weight: 0.0970 chunk 80 optimal weight: 1.9990 chunk 281 optimal weight: 0.0020 chunk 272 optimal weight: 4.9990 chunk 302 optimal weight: 0.3980 chunk 325 optimal weight: 7.9990 chunk 40 optimal weight: 0.3980 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.080531 restraints weight = 46584.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.084059 restraints weight = 21571.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.086483 restraints weight = 12727.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.088110 restraints weight = 8641.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.089202 restraints weight = 6525.266| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27552 Z= 0.111 Angle : 0.588 6.806 37536 Z= 0.301 Chirality : 0.039 0.151 4416 Planarity : 0.003 0.026 4800 Dihedral : 5.156 84.357 3864 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 1.94 % Allowed : 33.62 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.15), residues: 3528 helix: 2.58 (0.16), residues: 1104 sheet: -1.45 (0.20), residues: 696 loop : -2.32 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG j 38 TYR 0.030 0.001 TYR X 60 PHE 0.008 0.001 PHE L 42 TRP 0.007 0.002 TRP c 109 HIS 0.001 0.000 HIS L 64 Details of bonding type rmsd covalent geometry : bond 0.00252 (27552) covalent geometry : angle 0.58816 (37536) hydrogen bonds : bond 0.03400 ( 1224) hydrogen bonds : angle 3.64941 ( 3456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 530 time to evaluate : 1.060 Fit side-chains REVERT: C 25 ASP cc_start: 0.9071 (p0) cc_final: 0.8648 (p0) REVERT: E 25 ASP cc_start: 0.9052 (p0) cc_final: 0.8659 (p0) REVERT: E 41 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7860 (pt) REVERT: E 46 SER cc_start: 0.9123 (m) cc_final: 0.8687 (t) REVERT: E 53 TYR cc_start: 0.8892 (t80) cc_final: 0.8651 (t80) REVERT: M 41 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8042 (pt) REVERT: O 84 TYR cc_start: 0.8416 (m-80) cc_final: 0.8153 (m-80) REVERT: Q 31 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7832 (mt-10) REVERT: Q 46 SER cc_start: 0.8871 (m) cc_final: 0.8382 (t) REVERT: U 46 SER cc_start: 0.8895 (m) cc_final: 0.8430 (t) REVERT: 2 84 TYR cc_start: 0.8319 (m-80) cc_final: 0.8008 (m-80) REVERT: 2 87 ASP cc_start: 0.8816 (m-30) cc_final: 0.8521 (m-30) REVERT: 5 63 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7968 (mm-30) REVERT: 7 51 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7992 (tptp) REVERT: 7 53 THR cc_start: 0.8669 (m) cc_final: 0.8422 (m) REVERT: 7 69 ASN cc_start: 0.7332 (t0) cc_final: 0.7087 (t0) REVERT: e 41 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7934 (pt) REVERT: e 46 SER cc_start: 0.8936 (m) cc_final: 0.8391 (t) REVERT: i 46 SER cc_start: 0.8655 (m) cc_final: 0.8286 (t) outliers start: 55 outliers final: 45 residues processed: 556 average time/residue: 0.1366 time to fit residues: 132.5293 Evaluate side-chains 524 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 475 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain Y residue 29 SER Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain 0 residue 29 SER Chi-restraints excluded: chain 0 residue 49 VAL Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 4 residue 29 SER Chi-restraints excluded: chain 4 residue 49 VAL Chi-restraints excluded: chain 5 residue 49 ASP Chi-restraints excluded: chain 7 residue 51 LYS Chi-restraints excluded: chain 8 residue 27 THR Chi-restraints excluded: chain 8 residue 29 SER Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain a residue 29 SER Chi-restraints excluded: chain c residue 29 SER Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 29 SER Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain g residue 29 SER Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain i residue 29 SER Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain k residue 27 THR Chi-restraints excluded: chain k residue 29 SER Chi-restraints excluded: chain k residue 65 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 10 optimal weight: 50.0000 chunk 98 optimal weight: 6.9990 chunk 23 optimal weight: 50.0000 chunk 36 optimal weight: 2.9990 chunk 238 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 236 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 306 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN K 48 GLN ** O 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 GLN ** 0 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 48 GLN c 48 GLN g 48 GLN l 56 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.087551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.072505 restraints weight = 48892.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.074606 restraints weight = 29229.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.076017 restraints weight = 19843.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.077169 restraints weight = 14935.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.077968 restraints weight = 12012.708| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.083 27552 Z= 0.405 Angle : 0.806 8.494 37536 Z= 0.409 Chirality : 0.047 0.183 4416 Planarity : 0.004 0.028 4800 Dihedral : 5.686 75.084 3864 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 4.06 % Allowed : 32.42 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.14), residues: 3528 helix: 1.94 (0.16), residues: 1104 sheet: -1.12 (0.20), residues: 600 loop : -2.89 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 1 38 TYR 0.044 0.002 TYR 5 60 PHE 0.011 0.002 PHE f 11 TRP 0.008 0.003 TRP G 109 HIS 0.004 0.001 HIS J 64 Details of bonding type rmsd covalent geometry : bond 0.00969 (27552) covalent geometry : angle 0.80583 (37536) hydrogen bonds : bond 0.06546 ( 1224) hydrogen bonds : angle 4.70532 ( 3456) =============================================================================== Job complete usr+sys time: 4619.12 seconds wall clock time: 81 minutes 18.85 seconds (4878.85 seconds total)