Starting phenix.real_space_refine on Sat Aug 23 00:25:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8azs_15770/08_2025/8azs_15770.cif Found real_map, /net/cci-nas-00/data/ceres_data/8azs_15770/08_2025/8azs_15770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8azs_15770/08_2025/8azs_15770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8azs_15770/08_2025/8azs_15770.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8azs_15770/08_2025/8azs_15770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8azs_15770/08_2025/8azs_15770.map" } resolution = 2.9 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5868 2.51 5 N 1512 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9036 Number of models: 1 Model: "" Number of chains: 1 Chain: "F" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Restraints were copied for chains: G, I, J, K, L, M, N, O, P, Q, R, H, A, B, C, D, E, S, T, U, V, W, X, Y, Z, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 Time building chain proxies: 0.61, per 1000 atoms: 0.07 Number of scatterers: 9036 At special positions: 0 Unit cell: (73.959, 63.987, 45.705, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1620 8.00 N 1512 7.00 C 5868 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 Links applied TRANS " TYR 0 10 " - " GLY L 9 " " GLU 0 11 " - " TYR L 10 " " VAL 0 12 " - " GLU L 11 " " HIS 0 13 " - " VAL L 12 " " GLN 0 15 " - " HIS C 14 " " LYS 0 16 " - " GLN L 15 " " LEU 0 17 " - " LYS L 16 " " VAL 0 18 " - " LEU L 17 " " PHE 0 19 " - " VAL L 18 " " PHE 0 20 " - " PHE L 19 " " GLU 0 22 " - " ALA L 21 " " ASP 0 23 " - " GLU L 22 " " VAL 0 24 " - " ASP L 23 " " GLY 0 25 " - " VAL L 24 " " SER 0 26 " - " GLY L 25 " " ASN 0 27 " - " SER C 26 " " LYS 0 28 " - " ASN L 27 " " GLY 0 29 " - " LYS C 28 " " ALA 0 30 " - " GLY C 29 " " GLY 0 33 " - " ILE C 32 " " LEU 0 34 " - " GLY L 33 " " MET 0 35 " - " LEU L 34 " " VAL 0 36 " - " MET L 35 " " GLY 0 37 " - " VAL L 36 " " GLY 0 38 " - " GLY L 37 " " VAL 0 39 " - " GLY C 38 " " ILE 0 41 " - " VAL C 40 " " TYR 1 10 " - " GLY E 9 " " GLU 1 11 " - " TYR E 10 " " VAL 1 12 " - " GLU E 11 " " HIS 1 13 " - " VAL E 12 " " GLN 1 15 " - " HIS E 14 " " LYS 1 16 " - " GLN E 15 " " LEU 1 17 " - " LYS E 16 " " VAL 1 18 " - " LEU E 17 " " PHE 1 19 " - " VAL E 18 " " PHE 1 20 " - " PHE E 19 " " ALA 1 21 " - " PHE E 20 " " GLU 1 22 " - " ALA E 21 " " ASP 1 23 " - " GLU E 22 " " VAL 1 24 " - " ASP E 23 " " GLY 1 25 " - " VAL E 24 " " SER 1 26 " - " GLY E 25 " " ASN 1 27 " - " SER E 26 " " LYS 1 28 " - " ASN E 27 " " GLY 1 29 " - " LYS E 28 " " ALA 1 30 " - " GLY E 29 " " ILE 1 31 " - " ALA E 30 " " ILE 1 32 " - " ILE E 31 " " GLY 1 33 " - " ILE E 32 " " LEU 1 34 " - " GLY E 33 " " MET 1 35 " - " LEU E 34 " " VAL 1 36 " - " MET E 35 " " GLY 1 37 " - " VAL E 36 " " GLY 1 38 " - " GLY E 37 " " VAL 1 39 " - " GLY E 38 " " ILE 1 41 " - " VAL E 40 " " TYR 4 10 " - " GLY W 9 " " GLU 4 11 " - " TYR W 10 " " VAL 4 12 " - " GLU W 11 " " HIS 4 13 " - " VAL W 12 " " GLN 4 15 " - " HIS W 14 " " LYS 4 16 " - " GLN W 15 " " LEU 4 17 " - " LYS W 16 " " VAL 4 18 " - " LEU W 17 " " PHE 4 19 " - " VAL W 18 " " PHE 4 20 " - " PHE W 19 " " ALA 4 21 " - " PHE W 20 " " GLU 4 22 " - " ALA W 21 " " ASP 4 23 " - " GLU W 22 " " VAL 4 24 " - " ASP W 23 " " GLY 4 25 " - " VAL W 24 " " SER 4 26 " - " GLY W 25 " " ASN 4 27 " - " SER W 26 " " LYS 4 28 " - " ASN W 27 " " GLY 4 29 " - " LYS W 28 " " ALA 4 30 " - " GLY W 29 " " ILE 4 31 " - " ALA W 30 " " ILE 4 32 " - " ILE W 31 " " GLY 4 33 " - " ILE W 32 " " LEU 4 34 " - " GLY W 33 " " MET 4 35 " - " LEU W 34 " " VAL 4 36 " - " MET W 35 " " GLY 4 37 " - " VAL W 36 " " GLY 4 38 " - " GLY W 37 " " VAL 4 39 " - " GLY W 38 " " ILE 4 41 " - " VAL W 40 " " TYR 5 10 " - " GLY Q 9 " " GLU 5 11 " - " TYR Q 10 " " VAL 5 12 " - " GLU Q 11 " " HIS 5 13 " - " VAL Q 12 " " GLN 5 15 " - " HIS S 14 " " LYS 5 16 " - " GLN Q 15 " " LEU 5 17 " - " LYS Q 16 " " VAL 5 18 " - " LEU Q 17 " " PHE 5 19 " - " VAL Q 18 " " PHE 5 20 " - " PHE Q 19 " " GLU 5 22 " - " ALA Q 21 " " ASP 5 23 " - " GLU Q 22 " " VAL 5 24 " - " ASP Q 23 " " GLY 5 25 " - " VAL Q 24 " " SER 5 26 " - " GLY Q 25 " " ASN 5 27 " - " SER S 26 " " LYS 5 28 " - " ASN Q 27 " " GLY 5 29 " - " LYS S 28 " " ALA 5 30 " - " GLY S 29 " " GLY 5 33 " - " ILE S 32 " " LEU 5 34 " - " GLY Q 33 " " MET 5 35 " - " LEU Q 34 " " VAL 5 36 " - " MET Q 35 " " GLY 5 37 " - " VAL Q 36 " " GLY 5 38 " - " GLY Q 37 " " VAL 5 39 " - " GLY S 38 " " ILE 5 41 " - " VAL S 40 " " TYR 6 10 " - " GLY R 9 " " GLU 6 11 " - " TYR R 10 " " VAL 6 12 " - " GLU R 11 " " HIS 6 13 " - " VAL R 12 " " GLN 6 15 " - " HIS V 14 " " LYS 6 16 " - " GLN R 15 " " LEU 6 17 " - " LYS R 16 " " VAL 6 18 " - " LEU R 17 " " PHE 6 19 " - " VAL R 18 " " PHE 6 20 " - " PHE R 19 " " GLU 6 22 " - " ALA R 21 " " ASP 6 23 " - " GLU R 22 " " VAL 6 24 " - " ASP R 23 " " GLY 6 25 " - " VAL R 24 " " SER 6 26 " - " GLY R 25 " " ASN 6 27 " - " SER V 26 " " LYS 6 28 " - " ASN R 27 " " GLY 6 29 " - " LYS V 28 " " ALA 6 30 " - " GLY V 29 " " GLY 6 33 " - " ILE V 32 " " LEU 6 34 " - " GLY R 33 " " MET 6 35 " - " LEU R 34 " " VAL 6 36 " - " MET R 35 " " GLY 6 37 " - " VAL R 36 " " GLY 6 38 " - " GLY R 37 " " VAL 6 39 " - " GLY V 38 " " ILE 6 41 " - " VAL V 40 " " TYR 7 10 " - " GLY X 9 " " GLU 7 11 " - " TYR X 10 " " VAL 7 12 " - " GLU X 11 " " HIS 7 13 " - " VAL X 12 " " GLN 7 15 " - " HIS X 14 " " LYS 7 16 " - " GLN X 15 " " LEU 7 17 " - " LYS X 16 " " VAL 7 18 " - " LEU X 17 " " PHE 7 19 " - " VAL X 18 " " PHE 7 20 " - " PHE X 19 " " ALA 7 21 " - " PHE X 20 " " GLU 7 22 " - " ALA X 21 " " ASP 7 23 " - " GLU X 22 " " VAL 7 24 " - " ASP X 23 " " GLY 7 25 " - " VAL X 24 " " SER 7 26 " - " GLY X 25 " " ASN 7 27 " - " SER X 26 " " LYS 7 28 " - " ASN X 27 " " GLY 7 29 " - " LYS X 28 " " ALA 7 30 " - " GLY X 29 " " ILE 7 31 " - " ALA X 30 " " ILE 7 32 " - " ILE X 31 " " GLY 7 33 " - " ILE X 32 " " LEU 7 34 " - " GLY X 33 " " MET 7 35 " - " LEU X 34 " " VAL 7 36 " - " MET X 35 " " GLY 7 37 " - " VAL X 36 " " GLY 7 38 " - " GLY X 37 " " VAL 7 39 " - " GLY X 38 " " ILE 7 41 " - " VAL X 40 " " TYR A 10 " - " GLY F 9 " " GLU A 11 " - " TYR F 10 " " VAL A 12 " - " GLU F 11 " " HIS A 13 " - " VAL F 12 " " GLN A 15 " - " HIS F 14 " " LYS A 16 " - " GLN F 15 " " LEU A 17 " - " LYS F 16 " " VAL A 18 " - " LEU F 17 " " PHE A 19 " - " VAL F 18 " " PHE A 20 " - " PHE F 19 " " ALA A 21 " - " PHE F 20 " " GLU A 22 " - " ALA F 21 " " ASP A 23 " - " GLU F 22 " " VAL A 24 " - " ASP F 23 " " GLY A 25 " - " VAL F 24 " " SER A 26 " - " GLY F 25 " " ASN A 27 " - " SER F 26 " " LYS A 28 " - " ASN F 27 " " GLY A 29 " - " LYS F 28 " " ALA A 30 " - " GLY F 29 " " ILE A 31 " - " ALA F 30 " " ILE A 32 " - " ILE F 31 " " GLY A 33 " - " ILE F 32 " " LEU A 34 " - " GLY F 33 " " MET A 35 " - " LEU F 34 " " VAL A 36 " - " MET F 35 " " GLY A 37 " - " VAL F 36 " " GLY A 38 " - " GLY F 37 " " VAL A 39 " - " GLY F 38 " " ILE A 41 " - " VAL F 40 " " TYR B 10 " - " GLY J 9 " " GLU B 11 " - " TYR J 10 " " VAL B 12 " - " GLU J 11 " " HIS B 13 " - " VAL J 12 " " GLN B 15 " - " HIS J 14 " " LYS B 16 " - " GLN J 15 " " LEU B 17 " - " LYS J 16 " " VAL B 18 " - " LEU J 17 " " PHE B 19 " - " VAL J 18 " " PHE B 20 " - " PHE J 19 " " ALA B 21 " - " PHE J 20 " " GLU B 22 " - " ALA J 21 " " ASP B 23 " - " GLU J 22 " " VAL B 24 " - " ASP J 23 " " GLY B 25 " - " VAL J 24 " " SER B 26 " - " GLY J 25 " " ASN B 27 " - " SER J 26 " " LYS B 28 " - " ASN J 27 " " GLY B 29 " - " LYS J 28 " " ALA B 30 " - " GLY J 29 " " ILE B 31 " - " ALA J 30 " " ILE B 32 " - " ILE J 31 " " GLY B 33 " - " ILE J 32 " " LEU B 34 " - " GLY J 33 " " MET B 35 " - " LEU J 34 " " VAL B 36 " - " MET J 35 " " GLY B 37 " - " VAL J 36 " " GLY B 38 " - " GLY J 37 " " VAL B 39 " - " GLY J 38 " " ILE B 41 " - " VAL J 40 " " TYR C 10 " - " GLY 0 9 " " VAL C 12 " - " GLU 0 11 " " HIS C 13 " - " VAL 0 12 " " LEU C 17 " - " LYS 0 16 " " VAL C 18 " - " LEU 0 17 " " PHE C 19 " - " VAL 0 18 " " PHE C 20 " - " PHE 0 19 " " GLY C 25 " - " VAL 0 24 " " ASN C 27 " - " SER L 26 " " ALA C 30 " - " GLY L 29 " " ILE C 32 " - " ILE 0 31 " " LEU C 34 " - " GLY 0 33 " " MET C 35 " - " LEU 0 34 " " VAL C 36 " - " MET 0 35 " " GLY C 37 " - " VAL 0 36 " " GLY C 38 " - " GLY 0 37 " " TYR D 10 " - " GLY Y 9 " " VAL D 12 " - " GLU Y 11 " " HIS D 13 " - " VAL Y 12 " " GLN D 15 " - " HIS Y 14 " " LEU D 17 " - " LYS Y 16 " " VAL D 18 " - " LEU Y 17 " " PHE D 19 " - " VAL Y 18 " " PHE D 20 " - " PHE Y 19 " " ALA D 21 " - " PHE Y 20 " " GLY D 25 " - " VAL Y 24 " " ASN D 27 " - " SER Y 26 " " GLY D 29 " - " LYS Y 28 " " ALA D 30 " - " GLY Y 29 " " ILE D 31 " - " ALA Y 30 " " ILE D 32 " - " ILE Y 31 " " GLY D 33 " - " ILE Y 32 " " LEU D 34 " - " GLY Y 33 " " MET D 35 " - " LEU Y 34 " " VAL D 36 " - " MET Y 35 " " GLY D 37 " - " VAL Y 36 " " GLY D 38 " - " GLY Y 37 " " VAL D 39 " - " GLY Y 38 " " VAL D 40 " - " VAL Y 39 " " ILE D 41 " - " VAL Y 40 " " ALA D 42 " - " ILE Y 41 " " TYR E 10 " - " GLY 1 9 " " VAL E 12 " - " GLU 1 11 " " HIS E 13 " - " VAL 1 12 " " GLN E 15 " - " HIS 1 14 " " LEU E 17 " - " LYS 1 16 " " VAL E 18 " - " LEU 1 17 " " PHE E 19 " - " VAL 1 18 " " PHE E 20 " - " PHE 1 19 " " ALA E 21 " - " PHE 1 20 " " GLY E 25 " - " VAL 1 24 " " ASN E 27 " - " SER 1 26 " " GLY E 29 " - " LYS 1 28 " " ALA E 30 " - " GLY 1 29 " " ILE E 31 " - " ALA 1 30 " " ILE E 32 " - " ILE 1 31 " " GLY E 33 " - " ILE 1 32 " " LEU E 34 " - " GLY 1 33 " " MET E 35 " - " LEU 1 34 " " VAL E 36 " - " MET 1 35 " " GLY E 37 " - " VAL 1 36 " " GLY E 38 " - " GLY 1 37 " " VAL E 39 " - " GLY 1 38 " " VAL E 40 " - " VAL 1 39 " " ILE E 41 " - " VAL 1 40 " " ALA E 42 " - " ILE 1 41 " " TYR F 10 " - " GLY A 9 " " VAL F 12 " - " GLU A 11 " " HIS F 13 " - " VAL A 12 " " GLN F 15 " - " HIS A 14 " " LEU F 17 " - " LYS A 16 " " VAL F 18 " - " LEU A 17 " " PHE F 19 " - " VAL A 18 " " PHE F 20 " - " PHE A 19 " " ALA F 21 " - " PHE A 20 " " GLY F 25 " - " VAL A 24 " " ASN F 27 " - " SER A 26 " " GLY F 29 " - " LYS A 28 " " ALA F 30 " - " GLY A 29 " " ILE F 31 " - " ALA A 30 " " ILE F 32 " - " ILE A 31 " " GLY F 33 " - " ILE A 32 " " LEU F 34 " - " GLY A 33 " " MET F 35 " - " LEU A 34 " " VAL F 36 " - " MET A 35 " " GLY F 37 " - " VAL A 36 " " GLY F 38 " - " GLY A 37 " " VAL F 39 " - " GLY A 38 " " VAL F 40 " - " VAL A 39 " " ILE F 41 " - " VAL A 40 " " ALA F 42 " - " ILE A 41 " " TYR H 10 " - " GLY Z 9 " " VAL H 12 " - " GLU Z 11 " " HIS H 13 " - " VAL Z 12 " " LEU H 17 " - " LYS Z 16 " " VAL H 18 " - " LEU Z 17 " " PHE H 19 " - " VAL Z 18 " " PHE H 20 " - " PHE Z 19 " " GLY H 25 " - " VAL Z 24 " " ASN H 27 " - " SER K 26 " " ALA H 30 " - " GLY K 29 " " ILE H 32 " - " ILE Z 31 " " LEU H 34 " - " GLY Z 33 " " MET H 35 " - " LEU Z 34 " " VAL H 36 " - " MET Z 35 " " GLY H 37 " - " VAL Z 36 " " GLY H 38 " - " GLY Z 37 " " TYR J 10 " - " GLY B 9 " " VAL J 12 " - " GLU B 11 " " HIS J 13 " - " VAL B 12 " " GLN J 15 " - " HIS B 14 " " LEU J 17 " - " LYS B 16 " " VAL J 18 " - " LEU B 17 " " PHE J 19 " - " VAL B 18 " " PHE J 20 " - " PHE B 19 " " ALA J 21 " - " PHE B 20 " " GLY J 25 " - " VAL B 24 " " ASN J 27 " - " SER B 26 " " GLY J 29 " - " LYS B 28 " " ALA J 30 " - " GLY B 29 " " ILE J 31 " - " ALA B 30 " " ILE J 32 " - " ILE B 31 " " GLY J 33 " - " ILE B 32 " " LEU J 34 " - " GLY B 33 " " MET J 35 " - " LEU B 34 " " VAL J 36 " - " MET B 35 " " GLY J 37 " - " VAL B 36 " " GLY J 38 " - " GLY B 37 " " VAL J 39 " - " GLY B 38 " " VAL J 40 " - " VAL B 39 " " ILE J 41 " - " VAL B 40 " " ALA J 42 " - " ILE B 41 " " GLN K 15 " - " HIS Z 14 " " ALA K 21 " - " PHE Z 20 " " GLY K 29 " - " LYS Z 28 " " ILE K 31 " - " ALA Z 30 " " ILE K 32 " - " ILE H 31 " " GLY K 33 " - " ILE Z 32 " " VAL K 39 " - " GLY Z 38 " " VAL K 40 " - " VAL Z 39 " " ILE K 41 " - " VAL Z 40 " " ALA K 42 " - " ILE Z 41 " " GLN L 15 " - " HIS 0 14 " " ALA L 21 " - " PHE 0 20 " " GLY L 29 " - " LYS 0 28 " " ILE L 31 " - " ALA 0 30 " " ILE L 32 " - " ILE C 31 " " GLY L 33 " - " ILE 0 32 " " VAL L 39 " - " GLY 0 38 " " VAL L 40 " - " VAL 0 39 " " ILE L 41 " - " VAL 0 40 " " ALA L 42 " - " ILE 0 41 " " TYR M 10 " - " GLY T 9 " " VAL M 12 " - " GLU T 11 " " HIS M 13 " - " VAL T 12 " " GLN M 15 " - " HIS T 14 " " LEU M 17 " - " LYS T 16 " " VAL M 18 " - " LEU T 17 " " PHE M 19 " - " VAL T 18 " " PHE M 20 " - " PHE T 19 " " ALA M 21 " - " PHE T 20 " " GLY M 25 " - " VAL T 24 " " ASN M 27 " - " SER T 26 " " GLY M 29 " - " LYS T 28 " " ALA M 30 " - " GLY T 29 " " ILE M 31 " - " ALA T 30 " " ILE M 32 " - " ILE T 31 " " GLY M 33 " - " ILE T 32 " " LEU M 34 " - " GLY T 33 " " MET M 35 " - " LEU T 34 " " VAL M 36 " - " MET T 35 " " GLY M 37 " - " VAL T 36 " " GLY M 38 " - " GLY T 37 " " VAL M 39 " - " GLY T 38 " " VAL M 40 " - " VAL T 39 " " ILE M 41 " - " VAL T 40 " " ALA M 42 " - " ILE T 41 " " TYR P 10 " - " GLY U 9 " " VAL P 12 " - " GLU U 11 " " HIS P 13 " - " VAL U 12 " " GLN P 15 " - " HIS U 14 " " LEU P 17 " - " LYS U 16 " " VAL P 18 " - " LEU U 17 " " PHE P 19 " - " VAL U 18 " " PHE P 20 " - " PHE U 19 " " ALA P 21 " - " PHE U 20 " " GLY P 25 " - " VAL U 24 " " ASN P 27 " - " SER U 26 " " GLY P 29 " - " LYS U 28 " " ALA P 30 " - " GLY U 29 " " ILE P 31 " - " ALA U 30 " " ILE P 32 " - " ILE U 31 " " GLY P 33 " - " ILE U 32 " " LEU P 34 " - " GLY U 33 " " MET P 35 " - " LEU U 34 " " VAL P 36 " - " MET U 35 " " GLY P 37 " - " VAL U 36 " " GLY P 38 " - " GLY U 37 " " VAL P 39 " - " GLY U 38 " " VAL P 40 " - " VAL U 39 " " ILE P 41 " - " VAL U 40 " " ALA P 42 " - " ILE U 41 " " GLN Q 15 " - " HIS 5 14 " " ALA Q 21 " - " PHE 5 20 " " GLY Q 29 " - " LYS 5 28 " " ILE Q 31 " - " ALA 5 30 " " ILE Q 32 " - " ILE S 31 " " GLY Q 33 " - " ILE 5 32 " " VAL Q 39 " - " GLY 5 38 " " VAL Q 40 " - " VAL 5 39 " " ILE Q 41 " - " VAL 5 40 " " ALA Q 42 " - " ILE 5 41 " " GLN R 15 " - " HIS 6 14 " " ALA R 21 " - " PHE 6 20 " " GLY R 29 " - " LYS 6 28 " " ILE R 31 " - " ALA 6 30 " " ILE R 32 " - " ILE V 31 " " GLY R 33 " - " ILE 6 32 " " VAL R 39 " - " GLY 6 38 " " VAL R 40 " - " VAL 6 39 " " ILE R 41 " - " VAL 6 40 " " ALA R 42 " - " ILE 6 41 " " TYR S 10 " - " GLY 5 9 " " VAL S 12 " - " GLU 5 11 " " HIS S 13 " - " VAL 5 12 " " LEU S 17 " - " LYS 5 16 " " VAL S 18 " - " LEU 5 17 " " PHE S 19 " - " VAL 5 18 " " PHE S 20 " - " PHE 5 19 " " GLY S 25 " - " VAL 5 24 " " ASN S 27 " - " SER Q 26 " " ALA S 30 " - " GLY Q 29 " " ILE S 32 " - " ILE 5 31 " " LEU S 34 " - " GLY 5 33 " " MET S 35 " - " LEU 5 34 " " VAL S 36 " - " MET 5 35 " " GLY S 37 " - " VAL 5 36 " " GLY S 38 " - " GLY 5 37 " " TYR T 10 " - " GLY M 9 " " GLU T 11 " - " TYR M 10 " " VAL T 12 " - " GLU M 11 " " HIS T 13 " - " VAL M 12 " " GLN T 15 " - " HIS M 14 " " LYS T 16 " - " GLN M 15 " " LEU T 17 " - " LYS M 16 " " VAL T 18 " - " LEU M 17 " " PHE T 19 " - " VAL M 18 " " PHE T 20 " - " PHE M 19 " " ALA T 21 " - " PHE M 20 " " GLU T 22 " - " ALA M 21 " " ASP T 23 " - " GLU M 22 " " VAL T 24 " - " ASP M 23 " " GLY T 25 " - " VAL M 24 " " SER T 26 " - " GLY M 25 " " ASN T 27 " - " SER M 26 " " LYS T 28 " - " ASN M 27 " " GLY T 29 " - " LYS M 28 " " ALA T 30 " - " GLY M 29 " " ILE T 31 " - " ALA M 30 " " ILE T 32 " - " ILE M 31 " " GLY T 33 " - " ILE M 32 " " LEU T 34 " - " GLY M 33 " " MET T 35 " - " LEU M 34 " " VAL T 36 " - " MET M 35 " " GLY T 37 " - " VAL M 36 " " GLY T 38 " - " GLY M 37 " " VAL T 39 " - " GLY M 38 " " ILE T 41 " - " VAL M 40 " " TYR U 10 " - " GLY P 9 " " GLU U 11 " - " TYR P 10 " " VAL U 12 " - " GLU P 11 " " HIS U 13 " - " VAL P 12 " " GLN U 15 " - " HIS P 14 " " LYS U 16 " - " GLN P 15 " " LEU U 17 " - " LYS P 16 " " VAL U 18 " - " LEU P 17 " " PHE U 19 " - " VAL P 18 " " PHE U 20 " - " PHE P 19 " " ALA U 21 " - " PHE P 20 " " GLU U 22 " - " ALA P 21 " " ASP U 23 " - " GLU P 22 " " VAL U 24 " - " ASP P 23 " " GLY U 25 " - " VAL P 24 " " SER U 26 " - " GLY P 25 " " ASN U 27 " - " SER P 26 " " LYS U 28 " - " ASN P 27 " " GLY U 29 " - " LYS P 28 " " ALA U 30 " - " GLY P 29 " " ILE U 31 " - " ALA P 30 " " ILE U 32 " - " ILE P 31 " " GLY U 33 " - " ILE P 32 " " LEU U 34 " - " GLY P 33 " " MET U 35 " - " LEU P 34 " " VAL U 36 " - " MET P 35 " " GLY U 37 " - " VAL P 36 " " GLY U 38 " - " GLY P 37 " " VAL U 39 " - " GLY P 38 " " ILE U 41 " - " VAL P 40 " " TYR V 10 " - " GLY 6 9 " " VAL V 12 " - " GLU 6 11 " " HIS V 13 " - " VAL 6 12 " " LEU V 17 " - " LYS 6 16 " " VAL V 18 " - " LEU 6 17 " " PHE V 19 " - " VAL 6 18 " " PHE V 20 " - " PHE 6 19 " " GLY V 25 " - " VAL 6 24 " " ASN V 27 " - " SER R 26 " " ALA V 30 " - " GLY R 29 " " ILE V 32 " - " ILE 6 31 " " LEU V 34 " - " GLY 6 33 " " MET V 35 " - " LEU 6 34 " " VAL V 36 " - " MET 6 35 " " GLY V 37 " - " VAL 6 36 " " GLY V 38 " - " GLY 6 37 " " TYR W 10 " - " GLY 4 9 " " VAL W 12 " - " GLU 4 11 " " HIS W 13 " - " VAL 4 12 " " GLN W 15 " - " HIS 4 14 " " LEU W 17 " - " LYS 4 16 " " VAL W 18 " - " LEU 4 17 " " PHE W 19 " - " VAL 4 18 " " PHE W 20 " - " PHE 4 19 " " ALA W 21 " - " PHE 4 20 " " GLY W 25 " - " VAL 4 24 " " ASN W 27 " - " SER 4 26 " " GLY W 29 " - " LYS 4 28 " " ALA W 30 " - " GLY 4 29 " " ILE W 31 " - " ALA 4 30 " " ILE W 32 " - " ILE 4 31 " " GLY W 33 " - " ILE 4 32 " " LEU W 34 " - " GLY 4 33 " " MET W 35 " - " LEU 4 34 " " VAL W 36 " - " MET 4 35 " " GLY W 37 " - " VAL 4 36 " " GLY W 38 " - " GLY 4 37 " " VAL W 39 " - " GLY 4 38 " " VAL W 40 " - " VAL 4 39 " " ILE W 41 " - " VAL 4 40 " " ALA W 42 " - " ILE 4 41 " " TYR X 10 " - " GLY 7 9 " " VAL X 12 " - " GLU 7 11 " " HIS X 13 " - " VAL 7 12 " " GLN X 15 " - " HIS 7 14 " " LEU X 17 " - " LYS 7 16 " " VAL X 18 " - " LEU 7 17 " " PHE X 19 " - " VAL 7 18 " " PHE X 20 " - " PHE 7 19 " " ALA X 21 " - " PHE 7 20 " " GLY X 25 " - " VAL 7 24 " " ASN X 27 " - " SER 7 26 " " GLY X 29 " - " LYS 7 28 " " ALA X 30 " - " GLY 7 29 " " ILE X 31 " - " ALA 7 30 " " ILE X 32 " - " ILE 7 31 " " GLY X 33 " - " ILE 7 32 " " LEU X 34 " - " GLY 7 33 " " MET X 35 " - " LEU 7 34 " " VAL X 36 " - " MET 7 35 " " GLY X 37 " - " VAL 7 36 " " GLY X 38 " - " GLY 7 37 " " VAL X 39 " - " GLY 7 38 " " VAL X 40 " - " VAL 7 39 " " ILE X 41 " - " VAL 7 40 " " ALA X 42 " - " ILE 7 41 " " TYR Y 10 " - " GLY D 9 " " GLU Y 11 " - " TYR D 10 " " VAL Y 12 " - " GLU D 11 " " HIS Y 13 " - " VAL D 12 " " GLN Y 15 " - " HIS D 14 " " LYS Y 16 " - " GLN D 15 " " LEU Y 17 " - " LYS D 16 " " VAL Y 18 " - " LEU D 17 " " PHE Y 19 " - " VAL D 18 " " PHE Y 20 " - " PHE D 19 " " ALA Y 21 " - " PHE D 20 " " GLU Y 22 " - " ALA D 21 " " ASP Y 23 " - " GLU D 22 " " VAL Y 24 " - " ASP D 23 " " GLY Y 25 " - " VAL D 24 " " SER Y 26 " - " GLY D 25 " " ASN Y 27 " - " SER D 26 " " LYS Y 28 " - " ASN D 27 " " GLY Y 29 " - " LYS D 28 " " ALA Y 30 " - " GLY D 29 " " ILE Y 31 " - " ALA D 30 " " ILE Y 32 " - " ILE D 31 " " GLY Y 33 " - " ILE D 32 " " LEU Y 34 " - " GLY D 33 " " MET Y 35 " - " LEU D 34 " " VAL Y 36 " - " MET D 35 " " GLY Y 37 " - " VAL D 36 " " GLY Y 38 " - " GLY D 37 " " VAL Y 39 " - " GLY D 38 " " ILE Y 41 " - " VAL D 40 " " TYR Z 10 " - " GLY K 9 " " GLU Z 11 " - " TYR K 10 " " VAL Z 12 " - " GLU K 11 " " HIS Z 13 " - " VAL K 12 " " GLN Z 15 " - " HIS H 14 " " LYS Z 16 " - " GLN K 15 " " LEU Z 17 " - " LYS K 16 " " VAL Z 18 " - " LEU K 17 " " PHE Z 19 " - " VAL K 18 " " PHE Z 20 " - " PHE K 19 " " GLU Z 22 " - " ALA K 21 " " ASP Z 23 " - " GLU K 22 " " VAL Z 24 " - " ASP K 23 " " GLY Z 25 " - " VAL K 24 " " SER Z 26 " - " GLY K 25 " " ASN Z 27 " - " SER H 26 " " LYS Z 28 " - " ASN K 27 " " GLY Z 29 " - " LYS H 28 " " ALA Z 30 " - " GLY H 29 " " GLY Z 33 " - " ILE H 32 " " LEU Z 34 " - " GLY K 33 " " MET Z 35 " - " LEU K 34 " " VAL Z 36 " - " MET K 35 " " GLY Z 37 " - " VAL K 36 " " GLY Z 38 " - " GLY K 37 " " VAL Z 39 " - " GLY H 38 " " ILE Z 41 " - " VAL H 40 " Time building additional restraints: 4.88 Conformation dependent library (CDL) restraints added in 304.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 5.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2250 1.33 - 1.45: 2149 1.45 - 1.57: 4709 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 9180 Sorted by residual: bond pdb=" CE1 HIS G 13 " pdb=" NE2 HIS G 13 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.92e+01 bond pdb=" CE1 HIS N 13 " pdb=" NE2 HIS N 13 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.92e+01 bond pdb=" CE1 HIS 6 13 " pdb=" NE2 HIS 6 13 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.91e+01 bond pdb=" CE1 HIS 0 13 " pdb=" NE2 HIS 0 13 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.91e+01 bond pdb=" CE1 HIS O 13 " pdb=" NE2 HIS O 13 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.91e+01 ... (remaining 9175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 8726 1.41 - 2.82: 2830 2.82 - 4.24: 612 4.24 - 5.65: 108 5.65 - 7.06: 72 Bond angle restraints: 12348 Sorted by residual: angle pdb=" C GLN 5 15 " pdb=" CA GLN 5 15 " pdb=" CB GLN 5 15 " ideal model delta sigma weight residual 109.53 115.42 -5.89 1.69e+00 3.50e-01 1.22e+01 angle pdb=" C GLN Z 15 " pdb=" CA GLN Z 15 " pdb=" CB GLN Z 15 " ideal model delta sigma weight residual 109.53 115.42 -5.89 1.69e+00 3.50e-01 1.22e+01 angle pdb=" C GLN K 15 " pdb=" CA GLN K 15 " pdb=" CB GLN K 15 " ideal model delta sigma weight residual 109.53 115.42 -5.89 1.69e+00 3.50e-01 1.22e+01 angle pdb=" C GLN Q 15 " pdb=" CA GLN Q 15 " pdb=" CB GLN Q 15 " ideal model delta sigma weight residual 109.53 115.42 -5.89 1.69e+00 3.50e-01 1.22e+01 angle pdb=" C GLN 9 15 " pdb=" CA GLN 9 15 " pdb=" CB GLN 9 15 " ideal model delta sigma weight residual 109.53 115.40 -5.87 1.69e+00 3.50e-01 1.21e+01 ... (remaining 12343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 5416 17.38 - 34.75: 696 34.75 - 52.13: 616 52.13 - 69.51: 276 69.51 - 86.89: 64 Dihedral angle restraints: 7068 sinusoidal: 3176 harmonic: 3892 Sorted by residual: dihedral pdb=" CA VAL K 36 " pdb=" C VAL K 36 " pdb=" N GLY Z 37 " pdb=" CA GLY Z 37 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA VAL Q 36 " pdb=" C VAL Q 36 " pdb=" N GLY 5 37 " pdb=" CA GLY 5 37 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA VAL L 36 " pdb=" C VAL L 36 " pdb=" N GLY 0 37 " pdb=" CA GLY 0 37 " ideal model delta harmonic sigma weight residual -180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 7065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 247 0.047 - 0.093: 437 0.093 - 0.139: 351 0.139 - 0.186: 297 0.186 - 0.232: 72 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CB ILE W 31 " pdb=" CA ILE W 31 " pdb=" CG1 ILE W 31 " pdb=" CG2 ILE W 31 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE D 31 " pdb=" CA ILE D 31 " pdb=" CG1 ILE D 31 " pdb=" CG2 ILE D 31 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE I 31 " pdb=" CA ILE I 31 " pdb=" CG1 ILE I 31 " pdb=" CG2 ILE I 31 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1401 not shown) Planarity restraints: 2236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N GLN R 15 " 0.027 2.00e-02 2.50e+03 4.42e-02 1.95e+01 pdb=" CA HIS 6 14 " 0.022 2.00e-02 2.50e+03 pdb=" C HIS 6 14 " -0.077 2.00e-02 2.50e+03 pdb=" O HIS 6 14 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N GLN L 15 " -0.027 2.00e-02 2.50e+03 4.42e-02 1.95e+01 pdb=" CA HIS 0 14 " -0.022 2.00e-02 2.50e+03 pdb=" C HIS 0 14 " 0.077 2.00e-02 2.50e+03 pdb=" O HIS 0 14 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N GLN K 15 " 0.027 2.00e-02 2.50e+03 4.41e-02 1.95e+01 pdb=" CA HIS Z 14 " 0.022 2.00e-02 2.50e+03 pdb=" C HIS Z 14 " -0.076 2.00e-02 2.50e+03 pdb=" O HIS Z 14 " 0.027 2.00e-02 2.50e+03 ... (remaining 2233 not shown) Histogram of nonbonded interaction distances: 0.02 - 0.99: 5060 0.99 - 1.97: 18558 1.97 - 2.95: 65040 2.95 - 3.92: 129811 3.92 - 4.90: 183018 Warning: very small nonbonded interaction distances. Nonbonded interactions: 401487 Sorted by model distance: nonbonded pdb=" CD1 LEU S 34 " pdb=" CD1 LEU 5 34 " model vdw 0.017 3.880 nonbonded pdb=" CD1 LEU K 34 " pdb=" CD1 LEU H 34 " model vdw 0.017 3.880 nonbonded pdb=" CD1 LEU H 34 " pdb=" CD1 LEU Z 34 " model vdw 0.017 3.880 nonbonded pdb=" CD1 LEU Q 34 " pdb=" CD1 LEU S 34 " model vdw 0.017 3.880 nonbonded pdb=" CD2 LEU L 34 " pdb=" CD2 LEU C 34 " model vdw 0.017 3.880 ... (remaining 401482 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: 0.02 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'H' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.470 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4036 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 : 0.018 0.208 9832 Z= 1.244 Angle : 1.762 11.463 14304 Z= 1.099 Chirality : 0.115 0.232 1404 Planarity : 0.008 0.024 1584 Dihedral : 16.095 86.885 3096 Min Nonbonded Distance : 0.017 Molprobity Statistics. All-atom Clashscore : 1346.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.21), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.004 TYR Z 10 PHE 0.031 0.009 PHE Z 19 HIS 0.009 0.005 HIS P 13 Details of bonding type rmsd covalent geometry : bond 0.01119 ( 9180) covalent geometry : angle 1.50231 (12348) link_TRANS : bond 0.05428 ( 652) link_TRANS : angle 2.90937 ( 1956) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 TYR cc_start: 0.6000 (m-80) cc_final: 0.5728 (m-80) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.5773 time to fit residues: 100.8554 Evaluate side-chains 153 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 50.0000 chunk 97 optimal weight: 40.0000 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 40.0000 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 50.0000 chunk 100 optimal weight: 50.0000 chunk 106 optimal weight: 7.9990 chunk 38 optimal weight: 50.0000 overall best weight: 12.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6570 r_free = 0.6570 target = 0.583482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.6745 r_free = 0.6745 target = 0.562667 restraints weight = 18145.863| |-----------------------------------------------------------------------------| r_work (start): 0.6555 rms_B_bonded: 0.51 r_work: 0.6716 rms_B_bonded: 0.18 restraints_weight: 0.5000 r_work: 0.6705 rms_B_bonded: 0.37 restraints_weight: 0.2500 r_work: 0.6579 rms_B_bonded: 1.96 restraints_weight: 0.1250 r_work (final): 0.6579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1876 moved from start: 6.7469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.111 1.956 9832 Z= 6.871 Angle : 11.162 75.710 14304 Z= 6.552 Chirality : 0.725 4.642 1404 Planarity : 0.061 0.200 1584 Dihedral : 35.572 100.813 1260 Min Nonbonded Distance : 1.087 Molprobity Statistics. All-atom Clashscore : 1020.24 Ramachandran Plot: Outliers : 40.45 % Allowed : 30.90 % Favored : 28.65 % Rotamer: Outliers : 44.67 % Allowed : 21.00 % Favored : 34.33 % Cbeta Deviations : 62.60 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 40.66 % 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 aren not related in a simple way. whole: -8.79 (0.11), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.70 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.144 0.022 TYR R 10 PHE 0.203 0.034 PHE M 20 HIS 0.099 0.025 HIS M 13 Details of bonding type rmsd covalent geometry : bond 0.10815 ( 9180) covalent geometry : angle 10.22784 (12348) link_TRANS : bond 0.14164 ( 652) link_TRANS : angle 15.83296 ( 1956) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 402 poor density : 143 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 19 PHE cc_start: 0.4278 (OUTLIER) cc_final: 0.3472 (t80) REVERT: N 34 LEU cc_start: 0.3247 (OUTLIER) cc_final: 0.2264 (tp) REVERT: N 41 ILE cc_start: -0.0688 (OUTLIER) cc_final: -0.1192 (tt) REVERT: Q 23 ASP cc_start: 0.0736 (OUTLIER) cc_final: 0.0450 (t70) REVERT: R 32 ILE cc_start: 0.4188 (OUTLIER) cc_final: 0.3861 (mt) REVERT: C 24 VAL cc_start: -0.1948 (OUTLIER) cc_final: -0.2217 (t) REVERT: E 17 LEU cc_start: -0.0180 (OUTLIER) cc_final: -0.0614 (tt) REVERT: T 15 GLN cc_start: 0.3670 (OUTLIER) cc_final: 0.3222 (mm-40) REVERT: X 31 ILE cc_start: -0.0164 (OUTLIER) cc_final: -0.0453 (mm) REVERT: 3 27 ASN cc_start: 0.3542 (OUTLIER) cc_final: 0.2341 (t0) REVERT: 5 32 ILE cc_start: 0.5995 (OUTLIER) cc_final: 0.5761 (mm) REVERT: 7 11 GLU cc_start: 0.5289 (OUTLIER) cc_final: 0.4988 (mt-10) outliers start: 402 outliers final: 244 residues processed: 476 average time/residue: 0.2397 time to fit residues: 131.1862 Evaluate side-chains 388 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 256 poor density : 132 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 13 HIS Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 20 PHE Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 15 GLN Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 13 HIS Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 35 MET Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 35 MET Chi-restraints excluded: chain N residue 41 ILE Chi-restraints excluded: chain O residue 32 ILE Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 35 MET Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 23 ASP Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 41 ILE Chi-restraints excluded: chain R residue 14 HIS Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 22 GLU Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 14 HIS Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain S residue 11 GLU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 22 GLU Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 35 MET Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 13 HIS Chi-restraints excluded: chain T residue 14 HIS Chi-restraints excluded: chain T residue 15 GLN Chi-restraints excluded: chain T residue 19 PHE Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 35 MET Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 15 GLN Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 ASN Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 35 MET Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 13 HIS Chi-restraints excluded: chain V residue 14 HIS Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 20 PHE Chi-restraints excluded: chain V residue 24 VAL Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 14 HIS Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 35 MET Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain X residue 15 GLN Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 19 PHE Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 31 ILE Chi-restraints excluded: chain Y residue 13 HIS Chi-restraints excluded: chain Y residue 14 HIS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 34 LEU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 13 HIS Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 27 ASN Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 41 ILE Chi-restraints excluded: chain 0 residue 12 VAL Chi-restraints excluded: chain 0 residue 13 HIS Chi-restraints excluded: chain 0 residue 14 HIS Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 27 ASN Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 0 residue 32 ILE Chi-restraints excluded: chain 0 residue 34 LEU Chi-restraints excluded: chain 0 residue 39 VAL Chi-restraints excluded: chain 0 residue 40 VAL Chi-restraints excluded: chain 1 residue 13 HIS Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 24 VAL Chi-restraints excluded: chain 1 residue 32 ILE Chi-restraints excluded: chain 1 residue 41 ILE Chi-restraints excluded: chain 2 residue 13 HIS Chi-restraints excluded: chain 2 residue 14 HIS Chi-restraints excluded: chain 2 residue 27 ASN Chi-restraints excluded: chain 2 residue 31 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 41 ILE Chi-restraints excluded: chain 3 residue 13 HIS Chi-restraints excluded: chain 3 residue 22 GLU Chi-restraints excluded: chain 3 residue 27 ASN Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 34 LEU Chi-restraints excluded: chain 3 residue 41 ILE Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 4 residue 13 HIS Chi-restraints excluded: chain 4 residue 17 LEU Chi-restraints excluded: chain 4 residue 36 VAL Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 41 ILE Chi-restraints excluded: chain 5 residue 12 VAL Chi-restraints excluded: chain 5 residue 15 GLN Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 5 residue 32 ILE Chi-restraints excluded: chain 5 residue 36 VAL Chi-restraints excluded: chain 5 residue 39 VAL Chi-restraints excluded: chain 6 residue 12 VAL Chi-restraints excluded: chain 6 residue 13 HIS Chi-restraints excluded: chain 6 residue 14 HIS Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 18 VAL Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 6 residue 34 LEU Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 7 residue 11 GLU Chi-restraints excluded: chain 7 residue 13 HIS Chi-restraints excluded: chain 7 residue 15 GLN Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 24 VAL Chi-restraints excluded: chain 7 residue 34 LEU Chi-restraints excluded: chain 8 residue 13 HIS Chi-restraints excluded: chain 8 residue 14 HIS Chi-restraints excluded: chain 8 residue 27 ASN Chi-restraints excluded: chain 8 residue 32 ILE Chi-restraints excluded: chain 8 residue 34 LEU Chi-restraints excluded: chain 8 residue 35 MET Chi-restraints excluded: chain 8 residue 41 ILE Chi-restraints excluded: chain 9 residue 13 HIS Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 32 ILE Chi-restraints excluded: chain 9 residue 35 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 101 optimal weight: 40.0000 chunk 84 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 HIS ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 15 GLN ** 5 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6730 r_free = 0.6730 target = 0.594052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.6906 r_free = 0.6906 target = 0.573870 restraints weight = 16998.956| |-----------------------------------------------------------------------------| r_work (start): 0.6724 rms_B_bonded: 0.35 r_work: 0.6899 rms_B_bonded: 0.13 restraints_weight: 0.5000 r_work: 0.6893 rms_B_bonded: 0.24 restraints_weight: 0.2500 r_work: 0.6813 rms_B_bonded: 1.18 restraints_weight: 0.1250 r_work (final): 0.6813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1609 moved from start: 7.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.092 1.824 9832 Z= 5.762 Angle : 9.724 69.503 14304 Z= 5.774 Chirality : 0.590 4.765 1404 Planarity : 0.061 0.204 1584 Dihedral : 37.811 117.776 1260 Min Nonbonded Distance : 1.037 Molprobity Statistics. All-atom Clashscore : 875.06 Ramachandran Plot: Outliers : 38.02 % Allowed : 37.59 % Favored : 24.39 % Rotamer: Outliers : 44.00 % Allowed : 20.11 % Favored : 35.89 % Cbeta Deviations : 50.89 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 42.26 % 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 aren not related in a simple way. whole: -9.11 (0.10), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.94 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.187 0.018 TYR R 10 PHE 0.199 0.027 PHE A 19 HIS 0.080 0.018 HIS V 14 Details of bonding type rmsd covalent geometry : bond 0.08928 ( 9180) covalent geometry : angle 8.75976 (12348) link_TRANS : bond 0.12811 ( 652) link_TRANS : angle 14.38789 ( 1956) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 396 poor density : 129 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 11 GLU cc_start: 0.4432 (OUTLIER) cc_final: 0.4190 (mt-10) REVERT: L 20 PHE cc_start: 0.2635 (OUTLIER) cc_final: 0.1878 (m-10) REVERT: M 19 PHE cc_start: 0.2323 (OUTLIER) cc_final: 0.2122 (t80) REVERT: N 23 ASP cc_start: 0.0694 (OUTLIER) cc_final: 0.0394 (p0) REVERT: N 34 LEU cc_start: 0.0339 (OUTLIER) cc_final: -0.0098 (tp) REVERT: Q 35 MET cc_start: 0.5277 (OUTLIER) cc_final: 0.5071 (ptt) REVERT: H 20 PHE cc_start: 0.0834 (OUTLIER) cc_final: 0.0413 (m-80) REVERT: A 31 ILE cc_start: 0.1996 (OUTLIER) cc_final: 0.1535 (mt) REVERT: B 15 GLN cc_start: 0.1739 (OUTLIER) cc_final: 0.1141 (tt0) REVERT: E 17 LEU cc_start: 0.2462 (OUTLIER) cc_final: 0.2098 (tp) REVERT: V 34 LEU cc_start: 0.2533 (OUTLIER) cc_final: 0.2001 (mt) REVERT: 4 35 MET cc_start: 0.0615 (OUTLIER) cc_final: 0.0316 (mpp) REVERT: 6 41 ILE cc_start: 0.1476 (OUTLIER) cc_final: 0.1257 (mm) outliers start: 396 outliers final: 239 residues processed: 456 average time/residue: 0.2433 time to fit residues: 126.8387 Evaluate side-chains 375 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 252 poor density : 123 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 20 PHE Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 19 PHE Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 20 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 13 HIS Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 20 PHE Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 15 GLN Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain M residue 20 PHE Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 35 MET Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 41 ILE Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 13 HIS Chi-restraints excluded: chain O residue 14 HIS Chi-restraints excluded: chain O residue 22 GLU Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 20 PHE Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 35 MET Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 35 MET Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 14 HIS Chi-restraints excluded: chain R residue 20 PHE Chi-restraints excluded: chain R residue 22 GLU Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 14 HIS Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain S residue 11 GLU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain S residue 23 ASP Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 35 MET Chi-restraints excluded: chain T residue 14 HIS Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain T residue 22 GLU Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 35 MET Chi-restraints excluded: chain U residue 15 GLN Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 28 LYS Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 14 HIS Chi-restraints excluded: chain V residue 31 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 35 MET Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain W residue 10 TYR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 15 GLN Chi-restraints excluded: chain W residue 19 PHE Chi-restraints excluded: chain W residue 20 PHE Chi-restraints excluded: chain W residue 24 VAL Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 35 MET Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 14 HIS Chi-restraints excluded: chain X residue 15 GLN Chi-restraints excluded: chain X residue 34 LEU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 14 HIS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 32 ILE Chi-restraints excluded: chain Y residue 35 MET Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 41 ILE Chi-restraints excluded: chain Z residue 11 GLU Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain 0 residue 12 VAL Chi-restraints excluded: chain 0 residue 13 HIS Chi-restraints excluded: chain 0 residue 14 HIS Chi-restraints excluded: chain 0 residue 15 GLN Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 40 VAL Chi-restraints excluded: chain 1 residue 13 HIS Chi-restraints excluded: chain 1 residue 14 HIS Chi-restraints excluded: chain 1 residue 15 GLN Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 24 VAL Chi-restraints excluded: chain 1 residue 35 MET Chi-restraints excluded: chain 1 residue 41 ILE Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 20 PHE Chi-restraints excluded: chain 2 residue 22 GLU Chi-restraints excluded: chain 2 residue 27 ASN Chi-restraints excluded: chain 2 residue 31 ILE Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 4 residue 11 GLU Chi-restraints excluded: chain 4 residue 13 HIS Chi-restraints excluded: chain 4 residue 14 HIS Chi-restraints excluded: chain 4 residue 24 VAL Chi-restraints excluded: chain 4 residue 35 MET Chi-restraints excluded: chain 4 residue 36 VAL Chi-restraints excluded: chain 4 residue 41 ILE Chi-restraints excluded: chain 5 residue 12 VAL Chi-restraints excluded: chain 5 residue 15 GLN Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 5 residue 32 ILE Chi-restraints excluded: chain 5 residue 41 ILE Chi-restraints excluded: chain 6 residue 12 VAL Chi-restraints excluded: chain 6 residue 13 HIS Chi-restraints excluded: chain 6 residue 18 VAL Chi-restraints excluded: chain 6 residue 23 ASP Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 40 VAL Chi-restraints excluded: chain 6 residue 41 ILE Chi-restraints excluded: chain 7 residue 13 HIS Chi-restraints excluded: chain 7 residue 14 HIS Chi-restraints excluded: chain 7 residue 15 GLN Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 7 residue 34 LEU Chi-restraints excluded: chain 7 residue 35 MET Chi-restraints excluded: chain 7 residue 41 ILE Chi-restraints excluded: chain 8 residue 10 TYR Chi-restraints excluded: chain 8 residue 13 HIS Chi-restraints excluded: chain 8 residue 14 HIS Chi-restraints excluded: chain 8 residue 20 PHE Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 8 residue 34 LEU Chi-restraints excluded: chain 8 residue 40 VAL Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 32 ILE Chi-restraints excluded: chain 9 residue 35 MET Chi-restraints excluded: chain 9 residue 39 VAL Chi-restraints excluded: chain 9 residue 40 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 65 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 11 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 13 HIS ** 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 = 0.6737 r_free = 0.6737 target = 0.588729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.6848 r_free = 0.6848 target = 0.565237 restraints weight = 22258.611| |-----------------------------------------------------------------------------| r_work (start): 0.6724 rms_B_bonded: 0.94 r_work: 0.6828 rms_B_bonded: 0.25 restraints_weight: 0.5000 r_work: 0.6820 rms_B_bonded: 0.48 restraints_weight: 0.2500 r_work: 0.6682 rms_B_bonded: 2.97 restraints_weight: 0.1250 r_work (final): 0.6682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1691 moved from start: 7.7389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.086 1.824 9832 Z= 5.370 Angle : 9.151 72.585 14304 Z= 5.476 Chirality : 0.502 4.627 1404 Planarity : 0.062 0.204 1584 Dihedral : 38.728 115.756 1260 Min Nonbonded Distance : 1.125 Molprobity Statistics. All-atom Clashscore : 774.66 Ramachandran Plot: Outliers : 36.89 % Allowed : 38.63 % Favored : 24.48 % Rotamer: Outliers : 42.67 % Allowed : 22.67 % Favored : 34.67 % Cbeta Deviations : 46.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 45.62 % 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 aren not related in a simple way. whole: -9.10 (0.10), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.93 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.186 0.015 TYR R 10 PHE 0.167 0.026 PHE P 20 HIS 0.071 0.017 HIS H 14 Details of bonding type rmsd covalent geometry : bond 0.08266 ( 9180) covalent geometry : angle 8.17236 (12348) link_TRANS : bond 0.12079 ( 652) link_TRANS : angle 13.81210 ( 1956) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 384 poor density : 117 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 19 PHE cc_start: 0.3875 (OUTLIER) cc_final: 0.2497 (m-80) REVERT: G 23 ASP cc_start: 0.0131 (OUTLIER) cc_final: -0.1867 (t70) REVERT: G 24 VAL cc_start: 0.0885 (OUTLIER) cc_final: 0.0480 (t) REVERT: I 36 VAL cc_start: 0.2581 (OUTLIER) cc_final: 0.2182 (p) REVERT: J 16 LYS cc_start: 0.1953 (tttt) cc_final: 0.1751 (mmmt) REVERT: N 23 ASP cc_start: 0.0094 (OUTLIER) cc_final: -0.0118 (m-30) REVERT: A 31 ILE cc_start: 0.1693 (OUTLIER) cc_final: 0.1427 (mt) REVERT: B 20 PHE cc_start: 0.0008 (OUTLIER) cc_final: -0.0266 (m-80) REVERT: B 32 ILE cc_start: 0.0258 (OUTLIER) cc_final: -0.0078 (mt) REVERT: C 15 GLN cc_start: -0.0359 (OUTLIER) cc_final: -0.0787 (mm-40) REVERT: E 10 TYR cc_start: 0.5446 (OUTLIER) cc_final: 0.4209 (p90) REVERT: S 15 GLN cc_start: 0.4999 (OUTLIER) cc_final: 0.4393 (mt0) REVERT: U 15 GLN cc_start: 0.0759 (OUTLIER) cc_final: -0.0471 (tp40) REVERT: V 14 HIS cc_start: 0.3722 (t70) cc_final: 0.3466 (t70) REVERT: V 35 MET cc_start: 0.4587 (OUTLIER) cc_final: 0.4353 (mtt) REVERT: W 19 PHE cc_start: 0.1230 (OUTLIER) cc_final: 0.0353 (m-80) REVERT: 3 19 PHE cc_start: 0.3248 (m-10) cc_final: 0.3042 (m-80) REVERT: 8 10 TYR cc_start: 0.1059 (OUTLIER) cc_final: -0.0718 (m-10) REVERT: 8 27 ASN cc_start: 0.4234 (OUTLIER) cc_final: 0.2388 (p0) outliers start: 384 outliers final: 203 residues processed: 446 average time/residue: 0.2523 time to fit residues: 127.6493 Evaluate side-chains 320 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 101 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 15 GLN Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 35 MET Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 11 GLU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 20 PHE Chi-restraints excluded: chain N residue 19 PHE Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 35 MET Chi-restraints excluded: chain O residue 13 HIS Chi-restraints excluded: chain O residue 14 HIS Chi-restraints excluded: chain O residue 22 GLU Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 20 PHE Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain P residue 35 MET Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain Q residue 14 HIS Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 41 ILE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 22 GLU Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 14 HIS Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain S residue 23 ASP Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 14 HIS Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 35 MET Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 13 HIS Chi-restraints excluded: chain U residue 15 GLN Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 27 ASN Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 31 ILE Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 35 MET Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain W residue 10 TYR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 13 HIS Chi-restraints excluded: chain W residue 15 GLN Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain W residue 19 PHE Chi-restraints excluded: chain W residue 20 PHE Chi-restraints excluded: chain W residue 23 ASP Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 19 PHE Chi-restraints excluded: chain X residue 34 LEU Chi-restraints excluded: chain Y residue 11 GLU Chi-restraints excluded: chain Y residue 14 HIS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 19 PHE Chi-restraints excluded: chain Y residue 35 MET Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 41 ILE Chi-restraints excluded: chain Z residue 13 HIS Chi-restraints excluded: chain Z residue 19 PHE Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain 0 residue 13 HIS Chi-restraints excluded: chain 0 residue 15 GLN Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 23 ASP Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 0 residue 40 VAL Chi-restraints excluded: chain 1 residue 15 GLN Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 24 VAL Chi-restraints excluded: chain 1 residue 35 MET Chi-restraints excluded: chain 1 residue 39 VAL Chi-restraints excluded: chain 1 residue 41 ILE Chi-restraints excluded: chain 2 residue 10 TYR Chi-restraints excluded: chain 2 residue 11 GLU Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 27 ASN Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 3 residue 10 TYR Chi-restraints excluded: chain 3 residue 15 GLN Chi-restraints excluded: chain 3 residue 39 VAL Chi-restraints excluded: chain 4 residue 14 HIS Chi-restraints excluded: chain 4 residue 19 PHE Chi-restraints excluded: chain 4 residue 24 VAL Chi-restraints excluded: chain 4 residue 27 ASN Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 41 ILE Chi-restraints excluded: chain 5 residue 12 VAL Chi-restraints excluded: chain 5 residue 13 HIS Chi-restraints excluded: chain 5 residue 15 GLN Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 19 PHE Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 36 VAL Chi-restraints excluded: chain 5 residue 41 ILE Chi-restraints excluded: chain 6 residue 11 GLU Chi-restraints excluded: chain 6 residue 12 VAL Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 18 VAL Chi-restraints excluded: chain 6 residue 19 PHE Chi-restraints excluded: chain 6 residue 23 ASP Chi-restraints excluded: chain 6 residue 32 ILE Chi-restraints excluded: chain 6 residue 40 VAL Chi-restraints excluded: chain 7 residue 13 HIS Chi-restraints excluded: chain 7 residue 14 HIS Chi-restraints excluded: chain 7 residue 15 GLN Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 27 ASN Chi-restraints excluded: chain 7 residue 28 LYS Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 7 residue 35 MET Chi-restraints excluded: chain 8 residue 10 TYR Chi-restraints excluded: chain 8 residue 13 HIS Chi-restraints excluded: chain 8 residue 14 HIS Chi-restraints excluded: chain 8 residue 15 GLN Chi-restraints excluded: chain 8 residue 27 ASN Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 8 residue 41 ILE Chi-restraints excluded: chain 9 residue 15 GLN Chi-restraints excluded: chain 9 residue 22 GLU Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 40 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 46 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 15 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 = 0.6763 r_free = 0.6763 target = 0.597335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.6916 r_free = 0.6916 target = 0.576951 restraints weight = 18435.110| |-----------------------------------------------------------------------------| r_work (start): 0.6798 rms_B_bonded: 0.49 r_work: 0.6932 rms_B_bonded: 0.19 restraints_weight: 0.5000 r_work: 0.6926 rms_B_bonded: 0.35 restraints_weight: 0.2500 r_work: 0.6846 rms_B_bonded: 1.63 restraints_weight: 0.1250 r_work (final): 0.6846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1601 moved from start: 7.9356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 1.895 9832 Z= 5.169 Angle : 8.887 74.052 14304 Z= 5.322 Chirality : 0.467 4.452 1404 Planarity : 0.062 0.200 1584 Dihedral : 39.060 119.209 1260 Min Nonbonded Distance : 1.158 Molprobity Statistics. All-atom Clashscore : 733.17 Ramachandran Plot: Outliers : 36.55 % Allowed : 35.68 % Favored : 27.78 % Rotamer: Outliers : 39.56 % Allowed : 24.67 % Favored : 35.78 % Cbeta Deviations : 44.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 45.45 % 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 aren not related in a simple way. whole: -9.09 (0.10), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.93 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.180 0.015 TYR R 10 PHE 0.180 0.027 PHE P 20 HIS 0.078 0.016 HIS H 14 Details of bonding type rmsd covalent geometry : bond 0.07865 ( 9180) covalent geometry : angle 7.90066 (12348) link_TRANS : bond 0.11947 ( 652) link_TRANS : angle 13.54595 ( 1956) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 356 poor density : 106 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 28 LYS cc_start: 0.4145 (pptt) cc_final: 0.3798 (pttp) REVERT: J 27 ASN cc_start: -0.0256 (OUTLIER) cc_final: -0.0582 (m110) REVERT: J 31 ILE cc_start: 0.1589 (OUTLIER) cc_final: 0.1199 (mm) REVERT: K 19 PHE cc_start: 0.5067 (m-10) cc_final: 0.4581 (m-80) REVERT: L 27 ASN cc_start: -0.0226 (OUTLIER) cc_final: -0.0511 (m110) REVERT: L 39 VAL cc_start: -0.3744 (OUTLIER) cc_final: -0.3974 (m) REVERT: C 15 GLN cc_start: -0.0427 (OUTLIER) cc_final: -0.1347 (mm-40) REVERT: D 20 PHE cc_start: 0.0598 (OUTLIER) cc_final: 0.0384 (p90) REVERT: S 17 LEU cc_start: 0.0998 (OUTLIER) cc_final: 0.0790 (mt) REVERT: V 32 ILE cc_start: 0.4096 (OUTLIER) cc_final: 0.3595 (mp) REVERT: W 16 LYS cc_start: 0.2377 (tttt) cc_final: 0.2168 (mmmt) REVERT: W 19 PHE cc_start: 0.0204 (OUTLIER) cc_final: -0.1036 (m-80) REVERT: 1 17 LEU cc_start: 0.0764 (OUTLIER) cc_final: -0.0275 (mp) REVERT: 1 27 ASN cc_start: 0.0296 (OUTLIER) cc_final: -0.0140 (p0) REVERT: 9 13 HIS cc_start: 0.2930 (OUTLIER) cc_final: 0.2634 (p90) REVERT: 9 15 GLN cc_start: -0.1074 (OUTLIER) cc_final: -0.2297 (tp-100) outliers start: 356 outliers final: 225 residues processed: 409 average time/residue: 0.2628 time to fit residues: 122.5717 Evaluate side-chains 332 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 94 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain J residue 15 GLN Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 20 PHE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 19 PHE Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 35 MET Chi-restraints excluded: chain O residue 13 HIS Chi-restraints excluded: chain O residue 14 HIS Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain P residue 35 MET Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 41 ILE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 14 HIS Chi-restraints excluded: chain R residue 22 GLU Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 14 HIS Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 23 ASP Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 14 HIS Chi-restraints excluded: chain T residue 19 PHE Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain U residue 13 HIS Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 ASN Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 31 ILE Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain W residue 10 TYR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 13 HIS Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain W residue 19 PHE Chi-restraints excluded: chain W residue 20 PHE Chi-restraints excluded: chain W residue 24 VAL Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 13 HIS Chi-restraints excluded: chain Y residue 14 HIS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 19 PHE Chi-restraints excluded: chain Y residue 35 MET Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 41 ILE Chi-restraints excluded: chain Z residue 13 HIS Chi-restraints excluded: chain Z residue 19 PHE Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain 0 residue 12 VAL Chi-restraints excluded: chain 0 residue 15 GLN Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 23 ASP Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 0 residue 40 VAL Chi-restraints excluded: chain 1 residue 11 GLU Chi-restraints excluded: chain 1 residue 13 HIS Chi-restraints excluded: chain 1 residue 15 GLN Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 27 ASN Chi-restraints excluded: chain 1 residue 32 ILE Chi-restraints excluded: chain 1 residue 34 LEU Chi-restraints excluded: chain 1 residue 35 MET Chi-restraints excluded: chain 1 residue 39 VAL Chi-restraints excluded: chain 1 residue 41 ILE Chi-restraints excluded: chain 2 residue 10 TYR Chi-restraints excluded: chain 2 residue 14 HIS Chi-restraints excluded: chain 2 residue 15 GLN Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 27 ASN Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 35 MET Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 2 residue 40 VAL Chi-restraints excluded: chain 3 residue 10 TYR Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 27 ASN Chi-restraints excluded: chain 3 residue 34 LEU Chi-restraints excluded: chain 3 residue 39 VAL Chi-restraints excluded: chain 4 residue 13 HIS Chi-restraints excluded: chain 4 residue 14 HIS Chi-restraints excluded: chain 4 residue 19 PHE Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 35 MET Chi-restraints excluded: chain 4 residue 36 VAL Chi-restraints excluded: chain 5 residue 11 GLU Chi-restraints excluded: chain 5 residue 15 GLN Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 19 PHE Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 5 residue 34 LEU Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 36 VAL Chi-restraints excluded: chain 5 residue 40 VAL Chi-restraints excluded: chain 5 residue 41 ILE Chi-restraints excluded: chain 6 residue 11 GLU Chi-restraints excluded: chain 6 residue 19 PHE Chi-restraints excluded: chain 6 residue 23 ASP Chi-restraints excluded: chain 6 residue 24 VAL Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 7 residue 13 HIS Chi-restraints excluded: chain 7 residue 14 HIS Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 28 LYS Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 7 residue 34 LEU Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 7 residue 41 ILE Chi-restraints excluded: chain 8 residue 10 TYR Chi-restraints excluded: chain 8 residue 13 HIS Chi-restraints excluded: chain 8 residue 27 ASN Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 8 residue 39 VAL Chi-restraints excluded: chain 8 residue 41 ILE Chi-restraints excluded: chain 9 residue 13 HIS Chi-restraints excluded: chain 9 residue 15 GLN Chi-restraints excluded: chain 9 residue 20 PHE Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 35 MET Chi-restraints excluded: chain 9 residue 40 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 94 optimal weight: 20.0000 chunk 96 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 83 optimal weight: 40.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 15 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 = 0.6811 r_free = 0.6811 target = 0.597680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.6931 r_free = 0.6931 target = 0.579475 restraints weight = 20710.569| |-----------------------------------------------------------------------------| r_work (start): 0.6798 rms_B_bonded: 0.64 r_work: 0.6930 rms_B_bonded: 0.22 restraints_weight: 0.5000 r_work: 0.6921 rms_B_bonded: 0.42 restraints_weight: 0.2500 r_work: 0.6809 rms_B_bonded: 2.33 restraints_weight: 0.1250 r_work (final): 0.6809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1583 moved from start: 7.9590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 1.875 9832 Z= 5.148 Angle : 8.879 71.862 14304 Z= 5.301 Chirality : 0.456 4.434 1404 Planarity : 0.062 0.204 1584 Dihedral : 39.146 121.455 1260 Min Nonbonded Distance : 1.143 Molprobity Statistics. All-atom Clashscore : 732.05 Ramachandran Plot: Outliers : 35.33 % Allowed : 37.76 % Favored : 26.91 % Rotamer: Outliers : 38.11 % Allowed : 25.11 % Favored : 36.78 % Cbeta Deviations : 41.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 45.45 % 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 aren not related in a simple way. whole: -9.09 (0.10), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.92 (0.07), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.183 0.013 TYR R 10 PHE 0.184 0.026 PHE J 20 HIS 0.075 0.015 HIS H 14 Details of bonding type rmsd covalent geometry : bond 0.07854 ( 9180) covalent geometry : angle 7.89830 (12348) link_TRANS : bond 0.11844 ( 652) link_TRANS : angle 13.51644 ( 1956) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 343 poor density : 97 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 27 ASN cc_start: -0.0307 (OUTLIER) cc_final: -0.0697 (m110) REVERT: J 31 ILE cc_start: 0.2066 (OUTLIER) cc_final: 0.1616 (mm) REVERT: K 19 PHE cc_start: 0.5278 (m-10) cc_final: 0.4734 (m-80) REVERT: L 27 ASN cc_start: -0.0103 (OUTLIER) cc_final: -0.0505 (m110) REVERT: M 11 GLU cc_start: 0.3677 (OUTLIER) cc_final: 0.3383 (tt0) REVERT: R 16 LYS cc_start: 0.2028 (OUTLIER) cc_final: 0.1691 (ttmm) REVERT: B 14 HIS cc_start: 0.5585 (OUTLIER) cc_final: 0.5357 (m170) REVERT: C 15 GLN cc_start: -0.0242 (OUTLIER) cc_final: -0.1249 (mm110) REVERT: E 10 TYR cc_start: 0.4429 (OUTLIER) cc_final: 0.3511 (p90) REVERT: S 17 LEU cc_start: 0.1012 (OUTLIER) cc_final: 0.0754 (mt) REVERT: U 27 ASN cc_start: 0.1728 (OUTLIER) cc_final: 0.1375 (p0) REVERT: V 22 GLU cc_start: 0.3943 (OUTLIER) cc_final: 0.3735 (mm-30) REVERT: W 19 PHE cc_start: 0.0108 (OUTLIER) cc_final: -0.1104 (m-80) REVERT: Y 16 LYS cc_start: -0.2888 (OUTLIER) cc_final: -0.3106 (pmtt) REVERT: Y 17 LEU cc_start: -0.1930 (OUTLIER) cc_final: -0.2524 (mt) REVERT: 1 13 HIS cc_start: 0.0116 (OUTLIER) cc_final: -0.0307 (m90) REVERT: 1 17 LEU cc_start: 0.0825 (OUTLIER) cc_final: -0.0201 (mp) REVERT: 8 14 HIS cc_start: -0.0229 (m90) cc_final: -0.0562 (m90) REVERT: 8 28 LYS cc_start: 0.3747 (tptp) cc_final: 0.3497 (tmtt) REVERT: 9 15 GLN cc_start: -0.1239 (OUTLIER) cc_final: -0.2326 (tp-100) outliers start: 343 outliers final: 232 residues processed: 399 average time/residue: 0.2718 time to fit residues: 124.3385 Evaluate side-chains 341 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 92 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain J residue 15 GLN Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 11 GLU Chi-restraints excluded: chain M residue 20 PHE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 14 HIS Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 19 PHE Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 35 MET Chi-restraints excluded: chain O residue 13 HIS Chi-restraints excluded: chain O residue 14 HIS Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 41 ILE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 14 HIS Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 22 GLU Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 14 HIS Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 14 HIS Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 23 ASP Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 14 HIS Chi-restraints excluded: chain T residue 19 PHE Chi-restraints excluded: chain T residue 22 GLU Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain U residue 13 HIS Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 ASN Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 22 GLU Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain W residue 10 TYR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain W residue 19 PHE Chi-restraints excluded: chain W residue 20 PHE Chi-restraints excluded: chain W residue 24 VAL Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 34 LEU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 13 HIS Chi-restraints excluded: chain Y residue 14 HIS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 16 LYS Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 19 PHE Chi-restraints excluded: chain Y residue 35 MET Chi-restraints excluded: chain Y residue 41 ILE Chi-restraints excluded: chain Z residue 13 HIS Chi-restraints excluded: chain Z residue 19 PHE Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain 0 residue 12 VAL Chi-restraints excluded: chain 0 residue 14 HIS Chi-restraints excluded: chain 0 residue 15 GLN Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 23 ASP Chi-restraints excluded: chain 0 residue 35 MET Chi-restraints excluded: chain 0 residue 40 VAL Chi-restraints excluded: chain 1 residue 13 HIS Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 28 LYS Chi-restraints excluded: chain 1 residue 32 ILE Chi-restraints excluded: chain 1 residue 39 VAL Chi-restraints excluded: chain 1 residue 41 ILE Chi-restraints excluded: chain 2 residue 10 TYR Chi-restraints excluded: chain 2 residue 14 HIS Chi-restraints excluded: chain 2 residue 15 GLN Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 2 residue 27 ASN Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 35 MET Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 2 residue 40 VAL Chi-restraints excluded: chain 3 residue 10 TYR Chi-restraints excluded: chain 3 residue 13 HIS Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 27 ASN Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 36 VAL Chi-restraints excluded: chain 3 residue 39 VAL Chi-restraints excluded: chain 4 residue 11 GLU Chi-restraints excluded: chain 4 residue 13 HIS Chi-restraints excluded: chain 4 residue 14 HIS Chi-restraints excluded: chain 4 residue 19 PHE Chi-restraints excluded: chain 4 residue 22 GLU Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 35 MET Chi-restraints excluded: chain 4 residue 36 VAL Chi-restraints excluded: chain 4 residue 40 VAL Chi-restraints excluded: chain 5 residue 11 GLU Chi-restraints excluded: chain 5 residue 13 HIS Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 19 PHE Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 5 residue 34 LEU Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 36 VAL Chi-restraints excluded: chain 5 residue 40 VAL Chi-restraints excluded: chain 5 residue 41 ILE Chi-restraints excluded: chain 6 residue 19 PHE Chi-restraints excluded: chain 6 residue 23 ASP Chi-restraints excluded: chain 6 residue 24 VAL Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 7 residue 13 HIS Chi-restraints excluded: chain 7 residue 14 HIS Chi-restraints excluded: chain 7 residue 15 GLN Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 22 GLU Chi-restraints excluded: chain 7 residue 28 LYS Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 7 residue 34 LEU Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 7 residue 41 ILE Chi-restraints excluded: chain 8 residue 13 HIS Chi-restraints excluded: chain 8 residue 27 ASN Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 8 residue 39 VAL Chi-restraints excluded: chain 8 residue 41 ILE Chi-restraints excluded: chain 9 residue 15 GLN Chi-restraints excluded: chain 9 residue 20 PHE Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 35 MET Chi-restraints excluded: chain 9 residue 40 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 30.0000 chunk 14 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6700 r_free = 0.6700 target = 0.587733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 137)---------------| | r_work = 0.6816 r_free = 0.6816 target = 0.565561 restraints weight = 19046.121| |-----------------------------------------------------------------------------| r_work (start): 0.6724 rms_B_bonded: 0.73 r_work: 0.6807 rms_B_bonded: 0.42 restraints_weight: 0.5000 r_work: 0.6789 rms_B_bonded: 0.81 restraints_weight: 0.2500 r_work: 0.6628 rms_B_bonded: 3.78 restraints_weight: 0.1250 r_work (final): 0.6628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1791 moved from start: 8.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 1.620 9832 Z= 4.955 Angle : 8.721 81.457 14304 Z= 5.219 Chirality : 0.425 3.838 1404 Planarity : 0.062 0.202 1584 Dihedral : 39.598 126.386 1260 Min Nonbonded Distance : 1.142 Molprobity Statistics. All-atom Clashscore : 678.36 Ramachandran Plot: Outliers : 35.68 % Allowed : 38.37 % Favored : 25.95 % Rotamer: Outliers : 36.33 % Allowed : 24.78 % Favored : 38.89 % Cbeta Deviations : 40.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 45.03 % 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 aren not related in a simple way. whole: -9.01 (0.10), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.86 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.167 0.014 TYR R 10 PHE 0.201 0.026 PHE J 20 HIS 0.072 0.016 HIS H 14 Details of bonding type rmsd covalent geometry : bond 0.07518 ( 9180) covalent geometry : angle 7.71589 (12348) link_TRANS : bond 0.11594 ( 652) link_TRANS : angle 13.42832 ( 1956) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 327 poor density : 99 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 11 GLU cc_start: -0.0023 (OUTLIER) cc_final: -0.0412 (pp20) REVERT: I 36 VAL cc_start: 0.3236 (OUTLIER) cc_final: 0.2300 (p) REVERT: L 27 ASN cc_start: 0.0263 (OUTLIER) cc_final: -0.0512 (m110) REVERT: O 23 ASP cc_start: 0.0683 (OUTLIER) cc_final: 0.0278 (t70) REVERT: O 34 LEU cc_start: 0.1180 (OUTLIER) cc_final: 0.0628 (mp) REVERT: P 14 HIS cc_start: 0.0522 (t70) cc_final: 0.0252 (t70) REVERT: P 41 ILE cc_start: 0.0596 (OUTLIER) cc_final: 0.0077 (mt) REVERT: R 10 TYR cc_start: -0.1879 (OUTLIER) cc_final: -0.3276 (m-10) REVERT: C 15 GLN cc_start: -0.0366 (OUTLIER) cc_final: -0.1503 (mm110) REVERT: T 35 MET cc_start: 0.3504 (OUTLIER) cc_final: 0.3128 (mtt) REVERT: W 15 GLN cc_start: 0.0671 (OUTLIER) cc_final: -0.0174 (pt0) REVERT: W 19 PHE cc_start: -0.1929 (OUTLIER) cc_final: -0.3266 (m-10) REVERT: 2 14 HIS cc_start: 0.3887 (OUTLIER) cc_final: 0.0926 (t70) REVERT: 4 15 GLN cc_start: 0.1232 (tt0) cc_final: 0.0936 (tt0) outliers start: 327 outliers final: 207 residues processed: 383 average time/residue: 0.2730 time to fit residues: 118.7681 Evaluate side-chains 314 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 95 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain J residue 15 GLN Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 11 GLU Chi-restraints excluded: chain M residue 20 PHE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 14 HIS Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 19 PHE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 35 MET Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 13 HIS Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 23 ASP Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 41 ILE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 14 HIS Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 14 HIS Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 23 ASP Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 14 HIS Chi-restraints excluded: chain T residue 19 PHE Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 35 MET Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 20 PHE Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain W residue 10 TYR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 15 GLN Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain W residue 19 PHE Chi-restraints excluded: chain W residue 20 PHE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 34 LEU Chi-restraints excluded: chain Y residue 13 HIS Chi-restraints excluded: chain Y residue 14 HIS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 19 PHE Chi-restraints excluded: chain Y residue 35 MET Chi-restraints excluded: chain Y residue 40 VAL Chi-restraints excluded: chain Y residue 41 ILE Chi-restraints excluded: chain Z residue 13 HIS Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 19 PHE Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain 0 residue 12 VAL Chi-restraints excluded: chain 0 residue 15 GLN Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 23 ASP Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 0 residue 35 MET Chi-restraints excluded: chain 1 residue 11 GLU Chi-restraints excluded: chain 1 residue 15 GLN Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 32 ILE Chi-restraints excluded: chain 1 residue 39 VAL Chi-restraints excluded: chain 1 residue 41 ILE Chi-restraints excluded: chain 2 residue 10 TYR Chi-restraints excluded: chain 2 residue 14 HIS Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 2 residue 27 ASN Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 35 MET Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 19 PHE Chi-restraints excluded: chain 3 residue 27 ASN Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 4 residue 11 GLU Chi-restraints excluded: chain 4 residue 13 HIS Chi-restraints excluded: chain 4 residue 14 HIS Chi-restraints excluded: chain 4 residue 19 PHE Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 35 MET Chi-restraints excluded: chain 4 residue 41 ILE Chi-restraints excluded: chain 5 residue 13 HIS Chi-restraints excluded: chain 5 residue 15 GLN Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 19 PHE Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 5 residue 34 LEU Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 36 VAL Chi-restraints excluded: chain 5 residue 40 VAL Chi-restraints excluded: chain 5 residue 41 ILE Chi-restraints excluded: chain 6 residue 11 GLU Chi-restraints excluded: chain 6 residue 14 HIS Chi-restraints excluded: chain 6 residue 19 PHE Chi-restraints excluded: chain 6 residue 23 ASP Chi-restraints excluded: chain 6 residue 32 ILE Chi-restraints excluded: chain 6 residue 34 LEU Chi-restraints excluded: chain 7 residue 13 HIS Chi-restraints excluded: chain 7 residue 14 HIS Chi-restraints excluded: chain 7 residue 15 GLN Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 22 GLU Chi-restraints excluded: chain 7 residue 27 ASN Chi-restraints excluded: chain 7 residue 28 LYS Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 7 residue 34 LEU Chi-restraints excluded: chain 7 residue 41 ILE Chi-restraints excluded: chain 8 residue 27 ASN Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 8 residue 41 ILE Chi-restraints excluded: chain 9 residue 19 PHE Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 35 MET Chi-restraints excluded: chain 9 residue 40 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6741 r_free = 0.6741 target = 0.561053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.6774 r_free = 0.6774 target = 0.533323 restraints weight = 15572.713| |-----------------------------------------------------------------------------| r_work (start): 0.6688 rms_B_bonded: 2.39 r_work: 0.6731 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.6614 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.6614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1932 moved from start: 8.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.077 1.637 9832 Z= 4.871 Angle : 8.560 63.604 14304 Z= 5.134 Chirality : 0.412 4.510 1404 Planarity : 0.062 0.204 1584 Dihedral : 39.572 122.600 1260 Min Nonbonded Distance : 1.152 Molprobity Statistics. All-atom Clashscore : 665.48 Ramachandran Plot: Outliers : 36.11 % Allowed : 38.89 % Favored : 25.00 % Rotamer: Outliers : 30.89 % Allowed : 28.67 % Favored : 40.44 % Cbeta Deviations : 39.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 44.53 % 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 aren not related in a simple way. whole: -9.03 (0.10), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.88 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.146 0.013 TYR R 10 PHE 0.202 0.027 PHE J 20 HIS 0.068 0.015 HIS Z 14 Details of bonding type rmsd covalent geometry : bond 0.07387 ( 9180) covalent geometry : angle 7.58558 (12348) link_TRANS : bond 0.11419 ( 652) link_TRANS : angle 13.13860 ( 1956) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 278 poor density : 96 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 17 LEU cc_start: -0.1014 (OUTLIER) cc_final: -0.1360 (tt) REVERT: I 23 ASP cc_start: 0.2881 (OUTLIER) cc_final: 0.2659 (m-30) REVERT: P 41 ILE cc_start: -0.0214 (OUTLIER) cc_final: -0.0446 (mt) REVERT: H 39 VAL cc_start: 0.3779 (OUTLIER) cc_final: 0.3537 (m) REVERT: C 15 GLN cc_start: -0.1148 (OUTLIER) cc_final: -0.1809 (mm110) REVERT: E 14 HIS cc_start: 0.4214 (t70) cc_final: 0.3546 (t70) REVERT: 0 34 LEU cc_start: 0.2087 (OUTLIER) cc_final: 0.1874 (mt) REVERT: 2 14 HIS cc_start: 0.1385 (OUTLIER) cc_final: -0.1004 (t-90) REVERT: 7 22 GLU cc_start: 0.2298 (mp0) cc_final: 0.2068 (mp0) outliers start: 278 outliers final: 198 residues processed: 336 average time/residue: 0.2567 time to fit residues: 98.6986 Evaluate side-chains 300 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 95 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 20 PHE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 19 PHE Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 35 MET Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 13 HIS Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 41 ILE Chi-restraints excluded: chain R residue 14 HIS Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 14 HIS Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 23 ASP Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 14 HIS Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 19 PHE Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 35 MET Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 20 PHE Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain W residue 10 TYR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 19 PHE Chi-restraints excluded: chain W residue 20 PHE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 27 ASN Chi-restraints excluded: chain Y residue 13 HIS Chi-restraints excluded: chain Y residue 14 HIS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 19 PHE Chi-restraints excluded: chain Y residue 35 MET Chi-restraints excluded: chain Y residue 41 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 13 HIS Chi-restraints excluded: chain Z residue 19 PHE Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 35 MET Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain 0 residue 12 VAL Chi-restraints excluded: chain 0 residue 15 GLN Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 23 ASP Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 0 residue 34 LEU Chi-restraints excluded: chain 0 residue 35 MET Chi-restraints excluded: chain 1 residue 11 GLU Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 32 ILE Chi-restraints excluded: chain 1 residue 39 VAL Chi-restraints excluded: chain 1 residue 41 ILE Chi-restraints excluded: chain 2 residue 14 HIS Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 27 ASN Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 35 MET Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 3 residue 13 HIS Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 4 residue 13 HIS Chi-restraints excluded: chain 4 residue 14 HIS Chi-restraints excluded: chain 4 residue 19 PHE Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 35 MET Chi-restraints excluded: chain 4 residue 36 VAL Chi-restraints excluded: chain 4 residue 41 ILE Chi-restraints excluded: chain 5 residue 11 GLU Chi-restraints excluded: chain 5 residue 13 HIS Chi-restraints excluded: chain 5 residue 15 GLN Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 19 PHE Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 5 residue 34 LEU Chi-restraints excluded: chain 5 residue 40 VAL Chi-restraints excluded: chain 5 residue 41 ILE Chi-restraints excluded: chain 6 residue 11 GLU Chi-restraints excluded: chain 6 residue 14 HIS Chi-restraints excluded: chain 6 residue 19 PHE Chi-restraints excluded: chain 6 residue 23 ASP Chi-restraints excluded: chain 6 residue 24 VAL Chi-restraints excluded: chain 6 residue 32 ILE Chi-restraints excluded: chain 6 residue 34 LEU Chi-restraints excluded: chain 7 residue 13 HIS Chi-restraints excluded: chain 7 residue 14 HIS Chi-restraints excluded: chain 7 residue 15 GLN Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 27 ASN Chi-restraints excluded: chain 7 residue 28 LYS Chi-restraints excluded: chain 7 residue 34 LEU Chi-restraints excluded: chain 7 residue 35 MET Chi-restraints excluded: chain 7 residue 41 ILE Chi-restraints excluded: chain 8 residue 17 LEU Chi-restraints excluded: chain 8 residue 27 ASN Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 8 residue 41 ILE Chi-restraints excluded: chain 9 residue 13 HIS Chi-restraints excluded: chain 9 residue 19 PHE Chi-restraints excluded: chain 9 residue 23 ASP Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 35 MET Chi-restraints excluded: chain 9 residue 40 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 36 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6750 r_free = 0.6750 target = 0.561441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.6775 r_free = 0.6775 target = 0.533940 restraints weight = 14180.942| |-----------------------------------------------------------------------------| r_work (start): 0.6682 rms_B_bonded: 2.27 r_work: 0.6737 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.6619 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.6619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1883 moved from start: 8.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.076 1.648 9832 Z= 4.822 Angle : 8.476 66.858 14304 Z= 5.086 Chirality : 0.407 4.392 1404 Planarity : 0.063 0.205 1584 Dihedral : 39.551 120.215 1260 Min Nonbonded Distance : 1.137 Molprobity Statistics. All-atom Clashscore : 642.54 Ramachandran Plot: Outliers : 36.28 % Allowed : 38.11 % Favored : 25.61 % Rotamer: Outliers : 28.67 % Allowed : 30.11 % Favored : 41.22 % Cbeta Deviations : 38.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 45.03 % 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 aren not related in a simple way. whole: -9.02 (0.11), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.87 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.141 0.012 TYR L 10 PHE 0.209 0.026 PHE J 20 HIS 0.091 0.014 HIS H 14 Details of bonding type rmsd covalent geometry : bond 0.07296 ( 9180) covalent geometry : angle 7.53720 (12348) link_TRANS : bond 0.11388 ( 652) link_TRANS : angle 12.91090 ( 1956) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 258 poor density : 96 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 17 LEU cc_start: -0.1511 (OUTLIER) cc_final: -0.1810 (tt) REVERT: K 22 GLU cc_start: -0.0300 (OUTLIER) cc_final: -0.0879 (pt0) REVERT: O 31 ILE cc_start: 0.0388 (OUTLIER) cc_final: -0.0032 (mt) REVERT: P 41 ILE cc_start: -0.0313 (OUTLIER) cc_final: -0.0817 (mt) REVERT: Q 35 MET cc_start: 0.2558 (ptt) cc_final: 0.2177 (ptt) REVERT: H 35 MET cc_start: 0.0295 (mtt) cc_final: -0.0131 (mtm) REVERT: H 39 VAL cc_start: 0.3855 (OUTLIER) cc_final: 0.3619 (m) REVERT: C 15 GLN cc_start: -0.1187 (OUTLIER) cc_final: -0.2090 (mm110) REVERT: D 27 ASN cc_start: -0.1640 (OUTLIER) cc_final: -0.2260 (t0) REVERT: E 14 HIS cc_start: 0.3882 (t70) cc_final: 0.3542 (t70) REVERT: Y 15 GLN cc_start: 0.0161 (OUTLIER) cc_final: -0.1266 (mm-40) REVERT: 2 14 HIS cc_start: 0.0927 (OUTLIER) cc_final: -0.1350 (t-90) outliers start: 258 outliers final: 190 residues processed: 319 average time/residue: 0.2712 time to fit residues: 98.6391 Evaluate side-chains 291 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 92 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 13 HIS Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 20 PHE Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 19 PHE Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 13 HIS Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain S residue 14 HIS Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 14 HIS Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 19 PHE Chi-restraints excluded: chain T residue 22 GLU Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 35 MET Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 20 PHE Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 19 PHE Chi-restraints excluded: chain W residue 20 PHE Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 34 LEU Chi-restraints excluded: chain Y residue 14 HIS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 19 PHE Chi-restraints excluded: chain Y residue 35 MET Chi-restraints excluded: chain Y residue 41 ILE Chi-restraints excluded: chain Z residue 13 HIS Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 19 PHE Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 35 MET Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain 0 residue 12 VAL Chi-restraints excluded: chain 0 residue 14 HIS Chi-restraints excluded: chain 0 residue 15 GLN Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 23 ASP Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 0 residue 32 ILE Chi-restraints excluded: chain 0 residue 35 MET Chi-restraints excluded: chain 1 residue 11 GLU Chi-restraints excluded: chain 1 residue 13 HIS Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 32 ILE Chi-restraints excluded: chain 1 residue 39 VAL Chi-restraints excluded: chain 1 residue 41 ILE Chi-restraints excluded: chain 2 residue 10 TYR Chi-restraints excluded: chain 2 residue 14 HIS Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 27 ASN Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 35 MET Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 3 residue 13 HIS Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 4 residue 13 HIS Chi-restraints excluded: chain 4 residue 14 HIS Chi-restraints excluded: chain 4 residue 19 PHE Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 35 MET Chi-restraints excluded: chain 4 residue 36 VAL Chi-restraints excluded: chain 4 residue 41 ILE Chi-restraints excluded: chain 5 residue 11 GLU Chi-restraints excluded: chain 5 residue 13 HIS Chi-restraints excluded: chain 5 residue 15 GLN Chi-restraints excluded: chain 5 residue 19 PHE Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 5 residue 34 LEU Chi-restraints excluded: chain 5 residue 41 ILE Chi-restraints excluded: chain 6 residue 11 GLU Chi-restraints excluded: chain 6 residue 14 HIS Chi-restraints excluded: chain 6 residue 18 VAL Chi-restraints excluded: chain 6 residue 19 PHE Chi-restraints excluded: chain 6 residue 20 PHE Chi-restraints excluded: chain 6 residue 23 ASP Chi-restraints excluded: chain 6 residue 24 VAL Chi-restraints excluded: chain 6 residue 32 ILE Chi-restraints excluded: chain 6 residue 34 LEU Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 13 HIS Chi-restraints excluded: chain 7 residue 14 HIS Chi-restraints excluded: chain 7 residue 15 GLN Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 27 ASN Chi-restraints excluded: chain 7 residue 28 LYS Chi-restraints excluded: chain 7 residue 34 LEU Chi-restraints excluded: chain 7 residue 41 ILE Chi-restraints excluded: chain 8 residue 27 ASN Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 8 residue 41 ILE Chi-restraints excluded: chain 9 residue 13 HIS Chi-restraints excluded: chain 9 residue 19 PHE Chi-restraints excluded: chain 9 residue 23 ASP Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 35 MET Chi-restraints excluded: chain 9 residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 3 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6746 r_free = 0.6746 target = 0.560093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.6775 r_free = 0.6775 target = 0.531858 restraints weight = 14344.623| |-----------------------------------------------------------------------------| r_work (start): 0.6681 rms_B_bonded: 2.36 r_work: 0.6726 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.6609 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.6609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1945 moved from start: 8.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.076 1.652 9832 Z= 4.797 Angle : 8.462 66.749 14304 Z= 5.072 Chirality : 0.413 4.376 1404 Planarity : 0.063 0.204 1584 Dihedral : 39.613 122.188 1260 Min Nonbonded Distance : 1.118 Molprobity Statistics. All-atom Clashscore : 638.38 Ramachandran Plot: Outliers : 35.76 % Allowed : 38.19 % Favored : 26.04 % Rotamer: Outliers : 25.22 % Allowed : 33.00 % Favored : 41.78 % Cbeta Deviations : 37.70 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 45.29 % 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 aren not related in a simple way. whole: -9.02 (0.10), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.87 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.142 0.011 TYR L 10 PHE 0.205 0.026 PHE J 20 HIS 0.113 0.014 HIS H 14 Details of bonding type rmsd covalent geometry : bond 0.07285 ( 9180) covalent geometry : angle 7.53898 (12348) link_TRANS : bond 0.11322 ( 652) link_TRANS : angle 12.84120 ( 1956) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 92 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 17 LEU cc_start: -0.1410 (OUTLIER) cc_final: -0.1715 (tt) REVERT: I 14 HIS cc_start: 0.2952 (m90) cc_final: 0.2220 (m90) REVERT: K 22 GLU cc_start: -0.0121 (OUTLIER) cc_final: -0.1191 (pt0) REVERT: O 13 HIS cc_start: 0.0987 (OUTLIER) cc_final: 0.0663 (p90) REVERT: O 31 ILE cc_start: 0.0526 (OUTLIER) cc_final: 0.0245 (mt) REVERT: P 41 ILE cc_start: -0.0176 (OUTLIER) cc_final: -0.0528 (mt) REVERT: Q 35 MET cc_start: 0.2399 (ptt) cc_final: 0.2033 (ptt) REVERT: H 35 MET cc_start: 0.0361 (mtt) cc_final: 0.0146 (mtm) REVERT: H 39 VAL cc_start: 0.4040 (OUTLIER) cc_final: 0.3775 (m) REVERT: C 15 GLN cc_start: -0.1081 (OUTLIER) cc_final: -0.2144 (mm110) REVERT: E 14 HIS cc_start: 0.4006 (t70) cc_final: 0.3770 (t70) REVERT: S 17 LEU cc_start: -0.1521 (OUTLIER) cc_final: -0.2242 (mt) REVERT: X 34 LEU cc_start: 0.1770 (OUTLIER) cc_final: 0.1374 (tp) REVERT: Y 15 GLN cc_start: 0.0175 (OUTLIER) cc_final: -0.0552 (mm-40) REVERT: 2 14 HIS cc_start: 0.0534 (OUTLIER) cc_final: -0.1552 (t-90) outliers start: 227 outliers final: 188 residues processed: 283 average time/residue: 0.2697 time to fit residues: 87.6368 Evaluate side-chains 290 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 91 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 20 PHE Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 19 PHE Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 13 HIS Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain S residue 14 HIS Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 14 HIS Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 19 PHE Chi-restraints excluded: chain T residue 22 GLU Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 35 MET Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 20 PHE Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 19 PHE Chi-restraints excluded: chain W residue 20 PHE Chi-restraints excluded: chain W residue 24 VAL Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 34 LEU Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 19 PHE Chi-restraints excluded: chain Y residue 35 MET Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 41 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 13 HIS Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 19 PHE Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 35 MET Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain 0 residue 12 VAL Chi-restraints excluded: chain 0 residue 14 HIS Chi-restraints excluded: chain 0 residue 15 GLN Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 23 ASP Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 0 residue 32 ILE Chi-restraints excluded: chain 0 residue 35 MET Chi-restraints excluded: chain 1 residue 11 GLU Chi-restraints excluded: chain 1 residue 13 HIS Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 32 ILE Chi-restraints excluded: chain 1 residue 35 MET Chi-restraints excluded: chain 1 residue 39 VAL Chi-restraints excluded: chain 1 residue 41 ILE Chi-restraints excluded: chain 2 residue 10 TYR Chi-restraints excluded: chain 2 residue 14 HIS Chi-restraints excluded: chain 2 residue 16 LYS Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 27 ASN Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 35 MET Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 3 residue 13 HIS Chi-restraints excluded: chain 3 residue 17 LEU Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 4 residue 13 HIS Chi-restraints excluded: chain 4 residue 14 HIS Chi-restraints excluded: chain 4 residue 19 PHE Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 35 MET Chi-restraints excluded: chain 4 residue 36 VAL Chi-restraints excluded: chain 4 residue 41 ILE Chi-restraints excluded: chain 5 residue 11 GLU Chi-restraints excluded: chain 5 residue 13 HIS Chi-restraints excluded: chain 5 residue 15 GLN Chi-restraints excluded: chain 5 residue 19 PHE Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 5 residue 41 ILE Chi-restraints excluded: chain 6 residue 14 HIS Chi-restraints excluded: chain 6 residue 19 PHE Chi-restraints excluded: chain 6 residue 20 PHE Chi-restraints excluded: chain 6 residue 23 ASP Chi-restraints excluded: chain 6 residue 24 VAL Chi-restraints excluded: chain 6 residue 32 ILE Chi-restraints excluded: chain 6 residue 34 LEU Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 7 residue 12 VAL Chi-restraints excluded: chain 7 residue 13 HIS Chi-restraints excluded: chain 7 residue 14 HIS Chi-restraints excluded: chain 7 residue 15 GLN Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 27 ASN Chi-restraints excluded: chain 7 residue 28 LYS Chi-restraints excluded: chain 7 residue 34 LEU Chi-restraints excluded: chain 7 residue 41 ILE Chi-restraints excluded: chain 8 residue 27 ASN Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 8 residue 41 ILE Chi-restraints excluded: chain 9 residue 13 HIS Chi-restraints excluded: chain 9 residue 19 PHE Chi-restraints excluded: chain 9 residue 23 ASP Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 35 MET Chi-restraints excluded: chain 9 residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 75 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6755 r_free = 0.6755 target = 0.560866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.6767 r_free = 0.6767 target = 0.530931 restraints weight = 19479.625| |-----------------------------------------------------------------------------| r_work (start): 0.6680 rms_B_bonded: 2.74 r_work: 0.6707 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work (final): 0.6707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1857 moved from start: 8.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.077 1.662 9832 Z= 4.802 Angle : 8.475 67.029 14304 Z= 5.074 Chirality : 0.412 4.365 1404 Planarity : 0.063 0.203 1584 Dihedral : 39.633 121.788 1260 Min Nonbonded Distance : 1.118 Molprobity Statistics. All-atom Clashscore : 637.44 Ramachandran Plot: Outliers : 35.85 % Allowed : 37.93 % Favored : 26.22 % Rotamer: Outliers : 25.44 % Allowed : 33.11 % Favored : 41.44 % Cbeta Deviations : 38.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 45.71 % 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 aren not related in a simple way. whole: -9.02 (0.10), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.87 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.142 0.011 TYR L 10 PHE 0.200 0.026 PHE J 20 HIS 0.105 0.015 HIS H 14 Details of bonding type rmsd covalent geometry : bond 0.07323 ( 9180) covalent geometry : angle 7.56312 (12348) link_TRANS : bond 0.11342 ( 652) link_TRANS : angle 12.81410 ( 1956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3888.41 seconds wall clock time: 71 minutes 3.42 seconds (4263.42 seconds total)