Starting phenix.real_space_refine on Thu Feb 13 06:47:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8azs_15770/02_2025/8azs_15770.cif Found real_map, /net/cci-nas-00/data/ceres_data/8azs_15770/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8azs_15770/02_2025/8azs_15770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8azs_15770/02_2025/8azs_15770.map" model { file = "/net/cci-nas-00/data/ceres_data/8azs_15770/02_2025/8azs_15770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8azs_15770/02_2025/8azs_15770.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9036 Number of models: 1 Model: "" Number of chains: 1 Chain: "1" 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: 0, 3, 2, 5, 4, 7, 6, 9, 8, A, C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, Y, X, Z Time building chain proxies: 2.47, per 1000 atoms: 0.27 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: 18.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.24 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: 18.17 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: 0.09 Found NCS groups: ncs_group { reference = chain '1' selection = chain '0' selection = chain '3' selection = chain '2' selection = chain '5' selection = chain '4' selection = chain '7' selection = chain '6' selection = chain '9' selection = chain '8' selection = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'Y' selection = chain 'X' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 36.680 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.690 ------------------------------------------------------------------------------- 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 : 0.011 0.072 9180 Z= 0.764 Angle : 1.502 7.059 12348 Z= 0.989 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.009 0.005 HIS P 13 PHE 0.031 0.009 PHE Z 19 TYR 0.017 0.004 TYR Z 10 *********************** 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 : 0.960 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: 1.5004 time to fit residues: 260.8802 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 : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 50.0000 chunk 81 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 40.0000 chunk 55 optimal weight: 0.0070 chunk 43 optimal weight: 50.0000 chunk 84 optimal weight: 40.0000 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 50.0000 chunk 63 optimal weight: 10.0000 chunk 98 optimal weight: 50.0000 overall best weight: 7.8010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 13 HIS ** 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 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 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 13 HIS ** 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** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 GLN ** 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 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 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 14 HIS ** 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 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 = 0.6593 r_free = 0.6593 target = 0.583804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.6732 r_free = 0.6732 target = 0.564504 restraints weight = 17837.184| |-----------------------------------------------------------------------------| r_work (start): 0.6580 rms_B_bonded: 0.61 r_work: 0.6754 rms_B_bonded: 0.18 restraints_weight: 0.5000 r_work: 0.6744 rms_B_bonded: 0.35 restraints_weight: 0.2500 r_work: 0.6616 rms_B_bonded: 2.09 restraints_weight: 0.1250 r_work (final): 0.6616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1618 moved from start: 6.7146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.107 1.962 9180 Z= 7.298 Angle : 10.166 74.513 12348 Z= 6.157 Chirality : 0.720 4.703 1404 Planarity : 0.061 0.202 1584 Dihedral : 35.824 101.630 1260 Min Nonbonded Distance : 1.071 Molprobity Statistics. All-atom Clashscore : 1022.93 Ramachandran Plot: Outliers : 41.41 % Allowed : 29.34 % Favored : 29.25 % Rotamer: Outliers : 45.67 % Allowed : 18.89 % Favored : 35.44 % Cbeta Deviations : 63.59 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 39.73 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -8.77 (0.11), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.68 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.100 0.026 HIS M 13 PHE 0.201 0.033 PHE M 20 TYR 0.155 0.021 TYR L 10 *********************** 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 555 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 411 poor density : 144 time to evaluate : 0.947 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: L 20 PHE cc_start: 0.2289 (OUTLIER) cc_final: 0.1222 (p90) REVERT: M 19 PHE cc_start: 0.4250 (OUTLIER) cc_final: 0.3910 (t80) REVERT: E 17 LEU cc_start: -0.0346 (OUTLIER) cc_final: -0.0658 (tp) REVERT: E 19 PHE cc_start: 0.0372 (OUTLIER) cc_final: -0.0181 (t80) REVERT: U 16 LYS cc_start: -0.3609 (OUTLIER) cc_final: -0.3870 (mttt) REVERT: W 32 ILE cc_start: 0.0704 (OUTLIER) cc_final: 0.0336 (mt) REVERT: X 31 ILE cc_start: -0.0236 (OUTLIER) cc_final: -0.0525 (mm) REVERT: 2 26 SER cc_start: 0.4798 (OUTLIER) cc_final: 0.4530 (t) REVERT: 2 27 ASN cc_start: 0.2661 (OUTLIER) cc_final: 0.1333 (m110) REVERT: 3 27 ASN cc_start: 0.3513 (OUTLIER) cc_final: 0.2341 (t0) REVERT: 8 41 ILE cc_start: 0.1910 (OUTLIER) cc_final: 0.1523 (mp) outliers start: 411 outliers final: 233 residues processed: 488 average time/residue: 0.6322 time to fit residues: 352.4702 Evaluate side-chains 374 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 130 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 14 HIS 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 G residue 34 LEU Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 12 VAL 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 17 LEU Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 40 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 20 PHE Chi-restraints excluded: chain L residue 22 GLU 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 39 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain M residue 13 HIS 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 N residue 13 HIS Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 35 MET Chi-restraints excluded: chain O residue 34 LEU 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 36 VAL Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 13 HIS Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain R residue 10 TYR 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 31 ILE Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain R residue 39 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 27 ASN 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 40 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 14 HIS Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 27 ASN 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 34 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 13 HIS 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 39 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain D residue 12 VAL 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 23 ASP Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LEU 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 17 LEU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 31 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 17 LEU Chi-restraints excluded: chain S residue 22 GLU Chi-restraints excluded: chain S residue 27 ASN 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 12 VAL Chi-restraints excluded: chain T residue 13 HIS Chi-restraints excluded: chain T residue 14 HIS 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 16 LYS 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 31 ILE 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 17 LEU Chi-restraints excluded: chain V residue 20 PHE Chi-restraints excluded: chain V residue 24 VAL Chi-restraints excluded: chain V residue 35 MET 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 23 ASP 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 14 HIS 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 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 17 LEU 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 24 VAL Chi-restraints excluded: chain Z residue 27 ASN Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain 0 residue 12 VAL Chi-restraints excluded: chain 0 residue 13 HIS Chi-restraints excluded: chain 0 residue 17 LEU Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 27 ASN 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 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 32 ILE Chi-restraints excluded: chain 1 residue 34 LEU 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 26 SER 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 40 VAL Chi-restraints excluded: chain 3 residue 27 ASN 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 24 VAL 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 32 ILE Chi-restraints excluded: chain 5 residue 34 LEU 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 15 GLN 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 31 ILE Chi-restraints excluded: chain 6 residue 32 ILE Chi-restraints excluded: chain 6 residue 34 LEU Chi-restraints excluded: chain 6 residue 35 MET Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 7 residue 13 HIS Chi-restraints excluded: chain 7 residue 15 GLN Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 24 VAL 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 13 HIS Chi-restraints excluded: chain 8 residue 14 HIS Chi-restraints excluded: chain 8 residue 27 ASN Chi-restraints excluded: chain 8 residue 34 LEU Chi-restraints excluded: chain 8 residue 41 ILE Chi-restraints excluded: chain 9 residue 32 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 30.0000 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 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** ** 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 13 HIS ** 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 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** ** 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 13 HIS ** 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 13 HIS ** 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** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** 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** ** 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** ** 1 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 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** ** 4 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 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** ** 9 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 15 GLN ** 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 = 0.6718 r_free = 0.6718 target = 0.594341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.6855 r_free = 0.6855 target = 0.573700 restraints weight = 19132.619| |-----------------------------------------------------------------------------| r_work (start): 0.6705 rms_B_bonded: 0.45 r_work: 0.6857 rms_B_bonded: 0.16 restraints_weight: 0.5000 r_work: 0.6851 rms_B_bonded: 0.32 restraints_weight: 0.2500 r_work: 0.6724 rms_B_bonded: 1.99 restraints_weight: 0.1250 r_work (final): 0.6724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1639 moved from start: 7.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.091 1.819 9180 Z= 6.168 Angle : 8.760 66.961 12348 Z= 5.354 Chirality : 0.586 4.512 1404 Planarity : 0.061 0.205 1584 Dihedral : 38.116 111.071 1260 Min Nonbonded Distance : 1.041 Molprobity Statistics. All-atom Clashscore : 867.41 Ramachandran Plot: Outliers : 38.54 % Allowed : 38.37 % Favored : 23.09 % Rotamer: Outliers : 44.00 % Allowed : 20.89 % Favored : 35.11 % Cbeta Deviations : 52.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 42.42 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.14 (0.10), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.96 (0.07), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.092 0.021 HIS V 14 PHE 0.202 0.028 PHE A 19 TYR 0.166 0.018 TYR R 10 *********************** 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 514 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 396 poor density : 118 time to evaluate : 0.883 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: J 17 LEU cc_start: 0.0590 (OUTLIER) cc_final: -0.0694 (pp) REVERT: N 23 ASP cc_start: 0.1085 (OUTLIER) cc_final: 0.0820 (m-30) REVERT: N 41 ILE cc_start: -0.0485 (OUTLIER) cc_final: -0.2540 (pp) REVERT: R 20 PHE cc_start: 0.2231 (OUTLIER) cc_final: 0.1619 (p90) REVERT: A 31 ILE cc_start: 0.1922 (OUTLIER) cc_final: 0.1549 (mt) REVERT: S 36 VAL cc_start: -0.0084 (OUTLIER) cc_final: -0.0349 (t) REVERT: T 27 ASN cc_start: 0.2559 (OUTLIER) cc_final: 0.2000 (m110) REVERT: U 40 VAL cc_start: -0.0188 (OUTLIER) cc_final: -0.0464 (t) REVERT: W 15 GLN cc_start: 0.2461 (OUTLIER) cc_final: 0.1538 (mt0) REVERT: Y 24 VAL cc_start: 0.3186 (OUTLIER) cc_final: 0.2928 (m) REVERT: 2 40 VAL cc_start: 0.1535 (OUTLIER) cc_final: 0.1314 (t) REVERT: 3 12 VAL cc_start: -0.0418 (OUTLIER) cc_final: -0.0770 (t) REVERT: 4 35 MET cc_start: 0.0515 (OUTLIER) cc_final: 0.0066 (mpp) REVERT: 6 41 ILE cc_start: 0.2752 (OUTLIER) cc_final: 0.2410 (mm) REVERT: 9 27 ASN cc_start: 0.4462 (OUTLIER) cc_final: 0.2940 (t0) outliers start: 396 outliers final: 230 residues processed: 460 average time/residue: 0.6550 time to fit residues: 341.4787 Evaluate side-chains 354 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 109 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 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 35 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 14 HIS 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 I residue 13 HIS Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 22 GLU Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 17 LEU 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 14 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 31 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain N residue 15 GLN 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 34 LEU Chi-restraints excluded: chain N residue 35 MET Chi-restraints excluded: chain N residue 41 ILE Chi-restraints excluded: chain O residue 13 HIS Chi-restraints excluded: chain O residue 22 GLU Chi-restraints excluded: chain O residue 32 ILE Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain P residue 20 PHE Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 41 ILE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 14 HIS Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 20 PHE Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 35 MET 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 24 VAL 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 14 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 32 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 35 MET 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 13 HIS 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 32 ILE 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 24 VAL Chi-restraints excluded: chain D residue 34 LEU 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 18 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain S residue 14 HIS Chi-restraints excluded: chain S residue 20 PHE Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 13 HIS Chi-restraints excluded: chain T residue 14 HIS Chi-restraints excluded: chain T residue 22 GLU Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 27 ASN Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 35 MET Chi-restraints excluded: chain U residue 14 HIS Chi-restraints excluded: chain U residue 15 GLN Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 20 PHE Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 40 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 14 HIS 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 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 34 LEU 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 17 LEU Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 34 LEU Chi-restraints excluded: chain X residue 35 MET 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 17 LEU Chi-restraints excluded: chain Y residue 24 VAL 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 18 VAL Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 32 ILE 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 15 GLN Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 24 VAL 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 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 34 LEU 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 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 40 VAL Chi-restraints excluded: chain 3 residue 10 TYR Chi-restraints excluded: chain 3 residue 12 VAL Chi-restraints excluded: chain 3 residue 31 ILE 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 32 ILE Chi-restraints excluded: chain 4 residue 35 MET 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 17 LEU Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 19 PHE Chi-restraints excluded: chain 5 residue 32 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 12 VAL Chi-restraints excluded: chain 6 residue 13 HIS Chi-restraints excluded: chain 6 residue 14 HIS Chi-restraints excluded: chain 6 residue 15 GLN 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 32 ILE Chi-restraints excluded: chain 6 residue 34 LEU Chi-restraints excluded: chain 6 residue 41 ILE Chi-restraints excluded: chain 7 residue 11 GLU 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 24 VAL Chi-restraints excluded: chain 7 residue 34 LEU 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 24 VAL Chi-restraints excluded: chain 8 residue 27 ASN Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 8 residue 32 ILE Chi-restraints excluded: chain 8 residue 34 LEU Chi-restraints excluded: chain 8 residue 40 VAL Chi-restraints excluded: chain 9 residue 27 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 74 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 35 optimal weight: 50.0000 chunk 2 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 27 ASN ** 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 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** 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 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 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** ** H 13 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** ** A 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** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 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** ** E 14 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** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 14 HIS ** 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 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 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 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 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** ** 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 = 0.6720 r_free = 0.6720 target = 0.588714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.6856 r_free = 0.6856 target = 0.560670 restraints weight = 21380.420| |-----------------------------------------------------------------------------| r_work (start): 0.6706 rms_B_bonded: 0.86 r_work: 0.6841 rms_B_bonded: 0.23 restraints_weight: 0.5000 r_work: 0.6831 rms_B_bonded: 0.46 restraints_weight: 0.2500 r_work: 0.6675 rms_B_bonded: 3.07 restraints_weight: 0.1250 r_work (final): 0.6675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1741 moved from start: 7.7408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 1.833 9180 Z= 5.618 Angle : 8.155 77.519 12348 Z= 5.031 Chirality : 0.502 4.348 1404 Planarity : 0.061 0.203 1584 Dihedral : 38.862 113.411 1260 Min Nonbonded Distance : 1.075 Molprobity Statistics. All-atom Clashscore : 772.02 Ramachandran Plot: Outliers : 37.59 % Allowed : 37.50 % Favored : 24.91 % Rotamer: Outliers : 43.78 % Allowed : 22.00 % Favored : 34.22 % Cbeta Deviations : 46.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 45.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.04 (0.11), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.89 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.078 0.017 HIS S 14 PHE 0.191 0.025 PHE P 20 TYR 0.169 0.015 TYR R 10 *********************** 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 513 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 394 poor density : 119 time to evaluate : 0.997 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: G 19 PHE cc_start: 0.4087 (OUTLIER) cc_final: 0.2767 (m-80) REVERT: G 23 ASP cc_start: -0.0398 (OUTLIER) cc_final: -0.2213 (t70) REVERT: G 24 VAL cc_start: 0.0599 (OUTLIER) cc_final: 0.0342 (p) REVERT: K 23 ASP cc_start: 0.2383 (OUTLIER) cc_final: 0.2179 (t70) REVERT: M 15 GLN cc_start: 0.0111 (OUTLIER) cc_final: -0.0261 (pt0) REVERT: N 28 LYS cc_start: 0.0933 (OUTLIER) cc_final: 0.0400 (mptt) REVERT: B 16 LYS cc_start: 0.0028 (OUTLIER) cc_final: -0.0856 (mppt) REVERT: B 26 SER cc_start: 0.4721 (m) cc_final: 0.4320 (p) REVERT: C 35 MET cc_start: -0.1137 (OUTLIER) cc_final: -0.1574 (ttp) REVERT: S 15 GLN cc_start: 0.5180 (mt0) cc_final: 0.4818 (mt0) REVERT: U 32 ILE cc_start: 0.1935 (OUTLIER) cc_final: 0.1447 (mt) REVERT: V 14 HIS cc_start: 0.3792 (t70) cc_final: 0.3589 (t70) REVERT: W 16 LYS cc_start: 0.3201 (tttt) cc_final: 0.2966 (mttt) REVERT: Z 23 ASP cc_start: 0.0774 (OUTLIER) cc_final: 0.0548 (m-30) REVERT: 4 31 ILE cc_start: 0.1378 (OUTLIER) cc_final: 0.1167 (mm) REVERT: 5 15 GLN cc_start: 0.3574 (OUTLIER) cc_final: 0.2908 (tp40) REVERT: 6 19 PHE cc_start: 0.0437 (OUTLIER) cc_final: -0.0240 (m-10) outliers start: 394 outliers final: 224 residues processed: 461 average time/residue: 0.6800 time to fit residues: 353.6322 Evaluate side-chains 342 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 105 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 VAL 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 40 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 20 PHE Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain I residue 31 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 20 PHE Chi-restraints excluded: chain J residue 22 GLU Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 23 ASP 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 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 14 HIS Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 PHE Chi-restraints excluded: chain L residue 20 PHE Chi-restraints excluded: chain L residue 22 GLU 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 15 GLN Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 40 VAL 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 27 ASN Chi-restraints excluded: chain N residue 28 LYS 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 13 HIS Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain Q residue 14 HIS Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 40 VAL 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 14 HIS Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 27 ASN Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 34 LEU 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 31 ILE Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 16 LYS 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 35 MET 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 12 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain S residue 11 GLU Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain S residue 23 ASP Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain S residue 32 ILE 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 17 LEU Chi-restraints excluded: chain T residue 19 PHE Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain U residue 14 HIS Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 20 PHE Chi-restraints excluded: chain U residue 27 ASN Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain V residue 12 VAL 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 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 40 VAL Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 19 PHE Chi-restraints excluded: chain X residue 20 PHE Chi-restraints excluded: chain X residue 35 MET 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 16 LYS Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 27 ASN 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 40 VAL Chi-restraints excluded: chain Y residue 41 ILE Chi-restraints excluded: chain Z residue 19 PHE Chi-restraints excluded: chain Z residue 23 ASP 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 14 HIS Chi-restraints excluded: chain 0 residue 15 GLN Chi-restraints excluded: chain 0 residue 17 LEU Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 19 PHE 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 19 PHE Chi-restraints excluded: chain 1 residue 34 LEU 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 27 ASN Chi-restraints excluded: chain 2 residue 36 VAL 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 22 GLU 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 16 LYS Chi-restraints excluded: chain 4 residue 19 PHE Chi-restraints excluded: chain 4 residue 22 GLU Chi-restraints excluded: chain 4 residue 31 ILE Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 34 LEU 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 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 40 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 14 HIS Chi-restraints excluded: chain 6 residue 17 LEU 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 32 ILE Chi-restraints excluded: chain 6 residue 34 LEU 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 18 VAL Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 24 VAL Chi-restraints excluded: chain 7 residue 31 ILE 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 15 GLN Chi-restraints excluded: chain 8 residue 20 PHE Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 27 ASN Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 8 residue 32 ILE Chi-restraints excluded: chain 8 residue 34 LEU Chi-restraints excluded: chain 9 residue 22 GLU Chi-restraints excluded: chain 9 residue 27 ASN Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 35 MET Chi-restraints excluded: chain 9 residue 40 VAL Chi-restraints excluded: chain 9 residue 41 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 27 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** 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 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 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 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 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** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** 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** ** V 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 13 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 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 27 ASN ** 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** ** 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 = 0.6771 r_free = 0.6771 target = 0.555578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.6822 r_free = 0.6822 target = 0.542117 restraints weight = 19613.382| |-----------------------------------------------------------------------------| r_work (start): 0.6726 rms_B_bonded: 1.25 r_work: 0.6813 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.6775 rms_B_bonded: 1.58 restraints_weight: 0.2500 r_work (final): 0.6775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1791 moved from start: 7.8509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 1.784 9180 Z= 5.406 Angle : 7.905 68.820 12348 Z= 4.884 Chirality : 0.431 3.534 1404 Planarity : 0.062 0.197 1584 Dihedral : 38.970 114.787 1260 Min Nonbonded Distance : 1.121 Molprobity Statistics. All-atom Clashscore : 737.30 Ramachandran Plot: Outliers : 36.46 % Allowed : 38.63 % Favored : 24.91 % Rotamer: Outliers : 40.56 % Allowed : 24.44 % Favored : 35.00 % Cbeta Deviations : 44.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 44.61 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -8.99 (0.11), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.85 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.068 0.017 HIS Y 14 PHE 0.161 0.025 PHE P 20 TYR 0.162 0.013 TYR L 10 *********************** 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 477 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 365 poor density : 112 time to evaluate : 1.032 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: I 41 ILE cc_start: 0.4835 (mm) cc_final: 0.4619 (mm) REVERT: P 35 MET cc_start: 0.5134 (mmt) cc_final: 0.4582 (mmt) REVERT: C 15 GLN cc_start: -0.1421 (OUTLIER) cc_final: -0.2692 (tp-100) REVERT: D 12 VAL cc_start: -0.1135 (OUTLIER) cc_final: -0.1516 (p) REVERT: E 14 HIS cc_start: 0.5172 (t70) cc_final: 0.4834 (t70) REVERT: S 26 SER cc_start: -0.1399 (OUTLIER) cc_final: -0.1653 (m) REVERT: U 27 ASN cc_start: 0.1796 (OUTLIER) cc_final: 0.1536 (p0) REVERT: Z 35 MET cc_start: 0.1826 (OUTLIER) cc_final: 0.1434 (mmm) REVERT: Z 41 ILE cc_start: -0.0092 (OUTLIER) cc_final: -0.0310 (mm) REVERT: 8 27 ASN cc_start: 0.3384 (OUTLIER) cc_final: 0.1359 (p0) outliers start: 365 outliers final: 224 residues processed: 421 average time/residue: 0.7067 time to fit residues: 340.6211 Evaluate side-chains 331 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 100 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 34 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 20 PHE Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 22 GLU 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 L residue 10 TYR Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 PHE Chi-restraints excluded: chain L residue 26 SER 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 M residue 22 GLU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 39 VAL 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 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 15 GLN Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 36 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 20 PHE Chi-restraints excluded: chain Q residue 13 HIS Chi-restraints excluded: chain Q residue 14 HIS Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 40 VAL 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 14 HIS Chi-restraints excluded: chain R residue 39 VAL 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 27 ASN Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 34 LEU 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 22 GLU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 12 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 B residue 40 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 31 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 32 ILE 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 24 VAL Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain S residue 11 GLU Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain S residue 23 ASP Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 35 MET Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain T residue 13 HIS 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 31 ILE Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 20 PHE 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 11 GLU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 24 VAL Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain W residue 10 TYR 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 W residue 24 VAL Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 20 PHE 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 17 LEU Chi-restraints excluded: chain Y residue 19 PHE Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 32 ILE 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 23 ASP Chi-restraints excluded: chain Z residue 31 ILE 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 Z residue 41 ILE 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 17 LEU Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 19 PHE 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 11 GLU 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 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 27 ASN Chi-restraints excluded: chain 2 residue 36 VAL 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 32 ILE Chi-restraints excluded: chain 4 residue 14 HIS 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 12 VAL 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 41 ILE Chi-restraints excluded: chain 6 residue 11 GLU Chi-restraints excluded: chain 6 residue 12 VAL Chi-restraints excluded: chain 6 residue 14 HIS Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 19 PHE Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 32 ILE Chi-restraints excluded: chain 6 residue 34 LEU 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 18 VAL Chi-restraints excluded: chain 7 residue 19 PHE 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 11 GLU 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 24 VAL Chi-restraints excluded: chain 8 residue 27 ASN Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 8 residue 32 ILE Chi-restraints excluded: chain 8 residue 34 LEU Chi-restraints excluded: chain 8 residue 40 VAL Chi-restraints excluded: chain 8 residue 41 ILE Chi-restraints excluded: chain 9 residue 22 GLU Chi-restraints excluded: chain 9 residue 27 ASN Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 35 MET Chi-restraints excluded: chain 9 residue 40 VAL Chi-restraints excluded: chain 9 residue 41 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 77 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** 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 27 ASN ** 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** ** 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** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 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 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 15 GLN ** 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** ** 6 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 15 GLN ** 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 = 0.6783 r_free = 0.6783 target = 0.557447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.6843 r_free = 0.6843 target = 0.545312 restraints weight = 15708.891| |-----------------------------------------------------------------------------| r_work (start): 0.6759 rms_B_bonded: 0.99 r_work: 0.6828 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.6784 rms_B_bonded: 1.61 restraints_weight: 0.2500 r_work (final): 0.6784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1797 moved from start: 7.8747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 1.781 9180 Z= 5.397 Angle : 7.897 66.037 12348 Z= 4.860 Chirality : 0.425 3.933 1404 Planarity : 0.062 0.196 1584 Dihedral : 39.122 114.332 1260 Min Nonbonded Distance : 1.107 Molprobity Statistics. All-atom Clashscore : 741.64 Ramachandran Plot: Outliers : 36.55 % Allowed : 38.63 % Favored : 24.83 % Rotamer: Outliers : 37.44 % Allowed : 27.67 % Favored : 34.89 % Cbeta Deviations : 43.65 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 45.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.00 (0.11), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.85 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.069 0.016 HIS S 14 PHE 0.163 0.026 PHE P 20 TYR 0.160 0.013 TYR L 10 *********************** 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 443 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 337 poor density : 106 time to evaluate : 1.012 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: M 15 GLN cc_start: 0.0013 (OUTLIER) cc_final: -0.0337 (pt0) REVERT: M 17 LEU cc_start: -0.2325 (OUTLIER) cc_final: -0.2762 (mt) REVERT: C 15 GLN cc_start: -0.1070 (OUTLIER) cc_final: -0.2533 (tp-100) REVERT: E 14 HIS cc_start: 0.4878 (t70) cc_final: 0.4611 (t70) REVERT: S 15 GLN cc_start: 0.4834 (mp10) cc_final: 0.4155 (mt0) REVERT: S 26 SER cc_start: -0.1899 (OUTLIER) cc_final: -0.2130 (m) REVERT: T 17 LEU cc_start: -0.2621 (OUTLIER) cc_final: -0.2877 (mt) REVERT: U 27 ASN cc_start: 0.2064 (OUTLIER) cc_final: 0.1733 (p0) REVERT: U 31 ILE cc_start: 0.3112 (mm) cc_final: 0.2599 (mm) REVERT: 0 41 ILE cc_start: 0.0615 (OUTLIER) cc_final: 0.0409 (mm) REVERT: 3 35 MET cc_start: 0.3370 (OUTLIER) cc_final: 0.2440 (mmt) REVERT: 7 12 VAL cc_start: -0.0408 (p) cc_final: -0.1087 (m) REVERT: 8 27 ASN cc_start: 0.3178 (OUTLIER) cc_final: 0.1609 (p0) REVERT: 8 28 LYS cc_start: 0.4693 (OUTLIER) cc_final: 0.4308 (tmtt) outliers start: 337 outliers final: 238 residues processed: 394 average time/residue: 0.6156 time to fit residues: 277.2720 Evaluate side-chains 348 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 100 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 20 PHE Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 22 GLU 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 L residue 10 TYR Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 PHE Chi-restraints excluded: chain L residue 26 SER 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 15 GLN Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 39 VAL 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 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 15 GLN Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 36 VAL 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 20 PHE Chi-restraints excluded: chain Q residue 10 TYR Chi-restraints excluded: chain Q residue 13 HIS Chi-restraints excluded: chain Q residue 14 HIS Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 40 VAL 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 39 VAL 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 27 ASN Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 35 MET 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 20 PHE Chi-restraints excluded: chain A residue 22 GLU 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 A residue 41 ILE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 14 HIS 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 36 VAL Chi-restraints excluded: chain B residue 40 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 31 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 41 ILE 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 32 ILE 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 23 ASP Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain S residue 11 GLU Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain S residue 23 ASP Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 35 MET Chi-restraints excluded: chain S residue 41 ILE 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 17 LEU Chi-restraints excluded: chain T residue 19 PHE 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 19 PHE Chi-restraints excluded: chain U residue 20 PHE Chi-restraints excluded: chain U residue 27 ASN 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 17 LEU Chi-restraints excluded: chain V residue 24 VAL 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 15 GLN 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 W residue 24 VAL Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 13 HIS Chi-restraints excluded: chain X residue 20 PHE 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 16 LYS Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 19 PHE Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 32 ILE 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 23 ASP 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 13 HIS Chi-restraints excluded: chain 0 residue 14 HIS Chi-restraints excluded: chain 0 residue 15 GLN Chi-restraints excluded: chain 0 residue 17 LEU Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 19 PHE 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 0 residue 41 ILE 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 18 VAL Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 27 ASN Chi-restraints excluded: chain 1 residue 28 LYS 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 27 ASN Chi-restraints excluded: chain 2 residue 36 VAL 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 24 VAL Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 35 MET Chi-restraints excluded: chain 4 residue 12 VAL 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 36 VAL Chi-restraints excluded: chain 4 residue 41 ILE Chi-restraints excluded: chain 5 residue 11 GLU Chi-restraints excluded: chain 5 residue 12 VAL 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 31 ILE Chi-restraints excluded: chain 5 residue 32 ILE Chi-restraints excluded: chain 5 residue 34 LEU Chi-restraints excluded: chain 5 residue 35 MET 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 12 VAL Chi-restraints excluded: chain 6 residue 14 HIS Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 19 PHE Chi-restraints excluded: chain 6 residue 24 VAL Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 32 ILE Chi-restraints excluded: chain 6 residue 34 LEU 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 18 VAL Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 7 residue 41 ILE Chi-restraints excluded: chain 8 residue 10 TYR Chi-restraints excluded: chain 8 residue 11 GLU Chi-restraints excluded: chain 8 residue 13 HIS Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 27 ASN Chi-restraints excluded: chain 8 residue 28 LYS Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 8 residue 34 LEU Chi-restraints excluded: chain 8 residue 41 ILE Chi-restraints excluded: chain 9 residue 22 GLU Chi-restraints excluded: chain 9 residue 27 ASN Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 35 MET Chi-restraints excluded: chain 9 residue 40 VAL Chi-restraints excluded: chain 9 residue 41 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 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 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** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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** ** 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** ** O 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** 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 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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** ** A 27 ASN ** 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 13 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** ** 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** ** T 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** 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** ** W 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 13 HIS ** 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 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 14 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** ** 9 13 HIS ** 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 = 0.6838 r_free = 0.6838 target = 0.601254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.6999 r_free = 0.6999 target = 0.583158 restraints weight = 19538.876| |-----------------------------------------------------------------------------| r_work (start): 0.6831 rms_B_bonded: 0.54 r_work: 0.6966 rms_B_bonded: 0.18 restraints_weight: 0.5000 r_work: 0.6961 rms_B_bonded: 0.34 restraints_weight: 0.2500 r_work: 0.6892 rms_B_bonded: 1.57 restraints_weight: 0.1250 r_work (final): 0.6892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1625 moved from start: 8.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.077 1.789 9180 Z= 5.209 Angle : 7.762 63.618 12348 Z= 4.784 Chirality : 0.440 3.975 1404 Planarity : 0.062 0.200 1584 Dihedral : 39.654 118.505 1260 Min Nonbonded Distance : 1.149 Molprobity Statistics. All-atom Clashscore : 694.89 Ramachandran Plot: Outliers : 36.72 % Allowed : 37.41 % Favored : 25.87 % Rotamer: Outliers : 34.89 % Allowed : 27.00 % Favored : 38.11 % Cbeta Deviations : 40.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 45.96 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.06 (0.10), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.90 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.085 0.017 HIS G 14 PHE 0.214 0.025 PHE E 20 TYR 0.163 0.012 TYR L 10 *********************** 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 423 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 314 poor density : 109 time to evaluate : 0.945 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: G 23 ASP cc_start: -0.0702 (OUTLIER) cc_final: -0.1133 (m-30) REVERT: J 27 ASN cc_start: -0.0024 (OUTLIER) cc_final: -0.0593 (t0) REVERT: L 19 PHE cc_start: -0.1476 (OUTLIER) cc_final: -0.2991 (m-80) REVERT: N 41 ILE cc_start: -0.1661 (OUTLIER) cc_final: -0.1945 (tt) REVERT: O 23 ASP cc_start: 0.1006 (OUTLIER) cc_final: 0.0452 (t0) REVERT: Q 14 HIS cc_start: 0.3296 (OUTLIER) cc_final: 0.2956 (p90) REVERT: C 32 ILE cc_start: 0.5820 (OUTLIER) cc_final: 0.5145 (mp) REVERT: D 20 PHE cc_start: 0.1306 (OUTLIER) cc_final: 0.1083 (p90) REVERT: S 19 PHE cc_start: 0.1047 (OUTLIER) cc_final: 0.0757 (p90) REVERT: T 41 ILE cc_start: -0.2212 (OUTLIER) cc_final: -0.3100 (OUTLIER) REVERT: X 26 SER cc_start: -0.2636 (OUTLIER) cc_final: -0.2914 (p) REVERT: Y 16 LYS cc_start: -0.3317 (OUTLIER) cc_final: -0.3698 (mttt) REVERT: 0 41 ILE cc_start: 0.1358 (OUTLIER) cc_final: 0.1105 (mm) REVERT: 9 27 ASN cc_start: -0.0123 (OUTLIER) cc_final: -0.1932 (t0) outliers start: 314 outliers final: 206 residues processed: 376 average time/residue: 0.6422 time to fit residues: 274.3582 Evaluate side-chains 324 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 105 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain J residue 15 GLN Chi-restraints excluded: chain J residue 19 PHE Chi-restraints excluded: chain J residue 20 PHE 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 18 VAL 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 L residue 10 TYR Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 PHE Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 35 MET Chi-restraints excluded: chain M residue 39 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 41 ILE Chi-restraints excluded: chain O residue 13 HIS Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 36 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 41 ILE Chi-restraints excluded: chain Q residue 10 TYR Chi-restraints excluded: chain Q residue 13 HIS Chi-restraints excluded: chain Q residue 14 HIS Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 22 GLU 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 39 VAL 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 35 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 22 GLU 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 14 HIS 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 36 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 12 VAL 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 34 LEU 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 32 ILE 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 24 VAL Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain S residue 10 TYR Chi-restraints excluded: chain S residue 12 VAL 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 34 LEU Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain T residue 13 HIS 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 31 ILE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 20 PHE Chi-restraints excluded: chain U residue 24 VAL 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 17 LEU Chi-restraints excluded: chain V residue 24 VAL Chi-restraints excluded: chain V residue 36 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 15 GLN Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain W residue 20 PHE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 20 PHE Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 34 LEU Chi-restraints excluded: chain X residue 40 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 27 ASN Chi-restraints excluded: chain Y residue 32 ILE 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 23 ASP 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 Z residue 41 ILE 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 19 PHE Chi-restraints excluded: chain 0 residue 23 ASP Chi-restraints excluded: chain 0 residue 34 LEU Chi-restraints excluded: chain 0 residue 35 MET Chi-restraints excluded: chain 0 residue 40 VAL Chi-restraints excluded: chain 0 residue 41 ILE 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 18 VAL Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 28 LYS Chi-restraints excluded: chain 1 residue 34 LEU 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 27 ASN Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 2 residue 40 VAL Chi-restraints excluded: chain 2 residue 41 ILE Chi-restraints excluded: chain 3 residue 10 TYR Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 22 GLU Chi-restraints excluded: chain 3 residue 32 ILE 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 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 41 ILE Chi-restraints excluded: chain 6 residue 12 VAL Chi-restraints excluded: chain 6 residue 14 HIS Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 19 PHE Chi-restraints excluded: chain 6 residue 24 VAL Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 34 LEU 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 19 PHE 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 14 HIS Chi-restraints excluded: chain 8 residue 24 VAL 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 27 ASN Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 35 MET Chi-restraints excluded: chain 9 residue 40 VAL Chi-restraints excluded: chain 9 residue 41 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 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 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 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** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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 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 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 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 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 GLN ** 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 ** W 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 13 HIS ** 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** ** 4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 14 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** 9 14 HIS ** 9 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6755 r_free = 0.6755 target = 0.547207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.6754 r_free = 0.6754 target = 0.525186 restraints weight = 15967.147| |-----------------------------------------------------------------------------| r_work (start): 0.6711 rms_B_bonded: 1.44 r_work: 0.6734 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.6674 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.6674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1691 moved from start: 8.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.074 1.786 9180 Z= 5.049 Angle : 7.619 63.837 12348 Z= 4.700 Chirality : 0.423 4.009 1404 Planarity : 0.062 0.206 1584 Dihedral : 40.140 119.068 1260 Min Nonbonded Distance : 1.160 Molprobity Statistics. All-atom Clashscore : 652.36 Ramachandran Plot: Outliers : 36.11 % Allowed : 38.63 % Favored : 25.26 % Rotamer: Outliers : 31.11 % Allowed : 29.56 % Favored : 39.33 % Cbeta Deviations : 39.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 45.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.04 (0.11), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.89 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.074 0.016 HIS G 14 PHE 0.180 0.027 PHE P 20 TYR 0.154 0.012 TYR R 10 *********************** 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 390 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 280 poor density : 110 time to evaluate : 0.964 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: J 27 ASN cc_start: -0.0595 (OUTLIER) cc_final: -0.2166 (t0) REVERT: K 10 TYR cc_start: 0.0001 (m-10) cc_final: -0.1294 (m-10) REVERT: N 41 ILE cc_start: -0.1920 (OUTLIER) cc_final: -0.3012 (mt) REVERT: P 41 ILE cc_start: 0.1126 (OUTLIER) cc_final: 0.0868 (mm) REVERT: Q 35 MET cc_start: 0.3046 (ptt) cc_final: 0.2815 (ptt) REVERT: B 20 PHE cc_start: -0.0654 (OUTLIER) cc_final: -0.0939 (m-80) REVERT: C 32 ILE cc_start: 0.5941 (OUTLIER) cc_final: 0.5737 (mp) REVERT: S 34 LEU cc_start: 0.3547 (OUTLIER) cc_final: 0.2924 (mm) REVERT: W 15 GLN cc_start: 0.0616 (OUTLIER) cc_final: -0.0895 (mp10) REVERT: 0 34 LEU cc_start: 0.0740 (OUTLIER) cc_final: 0.0501 (tt) REVERT: 0 41 ILE cc_start: 0.1638 (OUTLIER) cc_final: 0.1128 (mm) REVERT: 1 11 GLU cc_start: 0.5366 (OUTLIER) cc_final: 0.4953 (mt-10) REVERT: 4 11 GLU cc_start: 0.0683 (OUTLIER) cc_final: -0.0519 (pt0) REVERT: 4 35 MET cc_start: 0.1949 (OUTLIER) cc_final: 0.1509 (mpp) REVERT: 8 10 TYR cc_start: -0.0312 (OUTLIER) cc_final: -0.0626 (m-10) outliers start: 280 outliers final: 180 residues processed: 353 average time/residue: 0.6082 time to fit residues: 245.4715 Evaluate side-chains 293 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 100 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain J residue 15 GLN Chi-restraints excluded: chain J residue 19 PHE Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain K residue 18 VAL 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 18 VAL Chi-restraints excluded: chain L residue 19 PHE Chi-restraints excluded: chain L residue 27 ASN 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 M residue 10 TYR Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 20 PHE Chi-restraints excluded: chain M residue 35 MET Chi-restraints excluded: chain M residue 39 VAL 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 19 PHE Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 41 ILE Chi-restraints excluded: chain O residue 13 HIS 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 19 PHE Chi-restraints excluded: chain P residue 20 PHE Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 35 MET Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 13 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 14 HIS Chi-restraints excluded: chain R residue 34 LEU 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 27 ASN Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain A residue 13 HIS 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 12 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 18 VAL 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 34 LEU Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 20 PHE 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 24 VAL Chi-restraints excluded: chain S residue 13 HIS Chi-restraints excluded: chain S residue 14 HIS Chi-restraints excluded: chain S residue 31 ILE 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 13 HIS Chi-restraints excluded: chain T residue 14 HIS 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 U residue 19 PHE Chi-restraints excluded: chain U residue 20 PHE Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain W residue 10 TYR Chi-restraints excluded: chain W residue 15 GLN Chi-restraints excluded: chain W residue 20 PHE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 20 PHE Chi-restraints excluded: chain X residue 40 VAL 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 27 ASN Chi-restraints excluded: chain Y residue 32 ILE 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 23 ASP Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 41 ILE Chi-restraints excluded: chain 0 residue 15 GLN Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 19 PHE 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 0 residue 41 ILE 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 18 VAL Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 28 LYS 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 14 HIS Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 2 residue 40 VAL Chi-restraints excluded: chain 2 residue 41 ILE Chi-restraints excluded: chain 3 residue 10 TYR Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 22 GLU Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 4 residue 11 GLU Chi-restraints excluded: chain 4 residue 19 PHE 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 6 residue 12 VAL 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 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 40 VAL Chi-restraints excluded: chain 6 residue 41 ILE Chi-restraints excluded: chain 7 residue 15 GLN Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 32 ILE 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 14 HIS Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 35 MET Chi-restraints excluded: chain 9 residue 40 VAL Chi-restraints excluded: chain 9 residue 41 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 32 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 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 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 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** 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 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 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** 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** ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 GLN ** 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 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** 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 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 13 HIS ** 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 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 14 HIS ** 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 = 0.6745 r_free = 0.6745 target = 0.590394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.6850 r_free = 0.6850 target = 0.565827 restraints weight = 18619.277| |-----------------------------------------------------------------------------| r_work (start): 0.6736 rms_B_bonded: 0.92 r_work: 0.6763 rms_B_bonded: 0.77 restraints_weight: 0.5000 r_work: 0.6732 rms_B_bonded: 1.45 restraints_weight: 0.2500 r_work (final): 0.6732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1758 moved from start: 8.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.074 1.774 9180 Z= 5.010 Angle : 7.583 63.686 12348 Z= 4.657 Chirality : 0.415 4.027 1404 Planarity : 0.063 0.208 1584 Dihedral : 40.372 117.573 1260 Min Nonbonded Distance : 1.160 Molprobity Statistics. All-atom Clashscore : 645.30 Ramachandran Plot: Outliers : 35.50 % Allowed : 38.89 % Favored : 25.61 % Rotamer: Outliers : 27.00 % Allowed : 32.78 % Favored : 40.22 % Cbeta Deviations : 38.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 46.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.03 (0.11), 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 HIS 0.105 0.016 HIS 0 14 PHE 0.182 0.027 PHE P 20 TYR 0.155 0.013 TYR L 10 *********************** 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 346 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 243 poor density : 103 time to evaluate : 0.916 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: K 10 TYR cc_start: -0.0174 (m-10) cc_final: -0.1660 (m-10) REVERT: N 41 ILE cc_start: -0.1731 (OUTLIER) cc_final: -0.2391 (mt) REVERT: P 17 LEU cc_start: 0.0886 (OUTLIER) cc_final: -0.0400 (tm) REVERT: P 41 ILE cc_start: 0.0452 (OUTLIER) cc_final: 0.0072 (mm) REVERT: Q 19 PHE cc_start: 0.6357 (m-80) cc_final: 0.5355 (m-80) REVERT: Q 35 MET cc_start: 0.2931 (ptt) cc_final: 0.2592 (ptt) REVERT: C 32 ILE cc_start: 0.6109 (OUTLIER) cc_final: 0.5554 (mp) REVERT: W 15 GLN cc_start: -0.1286 (OUTLIER) cc_final: -0.1966 (mp10) REVERT: 0 20 PHE cc_start: 0.1284 (OUTLIER) cc_final: 0.1066 (m-10) REVERT: 0 41 ILE cc_start: 0.1474 (OUTLIER) cc_final: 0.1016 (mm) REVERT: 2 14 HIS cc_start: 0.2873 (OUTLIER) cc_final: 0.2521 (m-70) REVERT: 3 13 HIS cc_start: 0.3635 (OUTLIER) cc_final: 0.3390 (p90) REVERT: 4 35 MET cc_start: 0.2163 (OUTLIER) cc_final: 0.1407 (mpp) outliers start: 243 outliers final: 173 residues processed: 314 average time/residue: 0.6554 time to fit residues: 236.2236 Evaluate side-chains 284 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 101 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 32 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain J residue 15 GLN Chi-restraints excluded: chain J residue 19 PHE Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 15 GLN Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 20 PHE Chi-restraints excluded: chain M residue 39 VAL 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 19 PHE Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 41 ILE Chi-restraints excluded: chain O residue 10 TYR Chi-restraints excluded: chain O residue 13 HIS Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 36 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 20 PHE Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 35 MET Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 13 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 14 HIS Chi-restraints excluded: chain R residue 34 LEU 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 27 ASN Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 ILE 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 31 ILE Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 18 VAL 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 34 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain S residue 13 HIS Chi-restraints excluded: chain S residue 14 HIS 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 13 HIS Chi-restraints excluded: chain T residue 14 HIS Chi-restraints excluded: chain T residue 19 PHE Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 20 PHE Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain W residue 10 TYR Chi-restraints excluded: chain W residue 15 GLN Chi-restraints excluded: chain W residue 20 PHE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 20 PHE Chi-restraints excluded: chain X residue 40 VAL 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 27 ASN Chi-restraints excluded: chain Y residue 32 ILE 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 23 ASP Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 41 ILE Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 19 PHE Chi-restraints excluded: chain 0 residue 20 PHE Chi-restraints excluded: chain 0 residue 35 MET Chi-restraints excluded: chain 0 residue 41 ILE Chi-restraints excluded: chain 1 residue 11 GLU 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 34 LEU Chi-restraints excluded: chain 1 residue 39 VAL Chi-restraints excluded: chain 1 residue 41 ILE Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 13 HIS Chi-restraints excluded: chain 2 residue 14 HIS Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 2 residue 40 VAL Chi-restraints excluded: chain 2 residue 41 ILE Chi-restraints excluded: chain 3 residue 10 TYR Chi-restraints excluded: chain 3 residue 13 HIS Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 22 GLU Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 4 residue 13 HIS Chi-restraints excluded: chain 4 residue 19 PHE Chi-restraints excluded: chain 4 residue 31 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 19 PHE 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 12 VAL 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 19 PHE Chi-restraints excluded: chain 6 residue 20 PHE 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 40 VAL Chi-restraints excluded: chain 6 residue 41 ILE Chi-restraints excluded: chain 7 residue 15 GLN Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 7 residue 35 MET Chi-restraints excluded: chain 7 residue 41 ILE Chi-restraints excluded: chain 8 residue 14 HIS Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 27 ASN Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 35 MET Chi-restraints excluded: chain 9 residue 40 VAL Chi-restraints excluded: chain 9 residue 41 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** 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 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 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** 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 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** ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 GLN ** 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 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** 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 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 14 HIS ** 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 = 0.6755 r_free = 0.6755 target = 0.547353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.6749 r_free = 0.6749 target = 0.525003 restraints weight = 11825.373| |-----------------------------------------------------------------------------| r_work (start): 0.6712 rms_B_bonded: 1.55 r_work: 0.6731 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.6656 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.6656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1843 moved from start: 8.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.077 1.863 9180 Z= 5.180 Angle : 7.614 63.696 12348 Z= 4.675 Chirality : 0.413 4.023 1404 Planarity : 0.063 0.207 1584 Dihedral : 40.380 118.318 1260 Min Nonbonded Distance : 1.165 Molprobity Statistics. All-atom Clashscore : 655.10 Ramachandran Plot: Outliers : 36.20 % Allowed : 38.54 % Favored : 25.26 % Rotamer: Outliers : 23.33 % Allowed : 35.56 % Favored : 41.11 % Cbeta Deviations : 39.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 46.55 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.03 (0.11), 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 HIS 0.072 0.016 HIS 0 14 PHE 0.182 0.028 PHE P 20 TYR 0.154 0.012 TYR L 10 ********************** 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 310 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 100 time to evaluate : 0.877 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: K 10 TYR cc_start: -0.0136 (m-10) cc_final: -0.1643 (m-10) REVERT: N 41 ILE cc_start: -0.1664 (OUTLIER) cc_final: -0.2262 (mt) REVERT: P 41 ILE cc_start: 0.0470 (OUTLIER) cc_final: 0.0011 (mm) REVERT: Q 19 PHE cc_start: 0.6341 (m-80) cc_final: 0.5262 (m-80) REVERT: Q 35 MET cc_start: 0.3233 (ptt) cc_final: 0.2907 (ptt) REVERT: C 32 ILE cc_start: 0.5934 (OUTLIER) cc_final: 0.5709 (mp) REVERT: C 35 MET cc_start: -0.0333 (ttp) cc_final: -0.0613 (ttp) REVERT: W 15 GLN cc_start: -0.1168 (OUTLIER) cc_final: -0.1970 (mp10) REVERT: 0 41 ILE cc_start: 0.1470 (OUTLIER) cc_final: 0.1011 (mm) REVERT: 2 14 HIS cc_start: 0.2411 (OUTLIER) cc_final: 0.2192 (m-70) REVERT: 3 13 HIS cc_start: 0.3844 (OUTLIER) cc_final: 0.3596 (p90) REVERT: 4 35 MET cc_start: 0.2371 (OUTLIER) cc_final: 0.1533 (mpp) outliers start: 210 outliers final: 183 residues processed: 281 average time/residue: 0.6154 time to fit residues: 197.4995 Evaluate side-chains 290 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 99 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 27 ASN Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain J residue 15 GLN Chi-restraints excluded: chain J residue 19 PHE Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 15 GLN Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 20 PHE Chi-restraints excluded: chain M residue 39 VAL 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 19 PHE Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 41 ILE Chi-restraints excluded: chain O residue 10 TYR Chi-restraints excluded: chain O residue 13 HIS Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 20 PHE Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 13 HIS Chi-restraints excluded: chain Q residue 22 GLU 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 34 LEU 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 27 ASN Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 ILE 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 31 ILE Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 18 VAL 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 34 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain S residue 13 HIS Chi-restraints excluded: chain S residue 14 HIS 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 13 HIS Chi-restraints excluded: chain T residue 14 HIS Chi-restraints excluded: chain T residue 16 LYS 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 31 ILE Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 20 PHE Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 20 PHE Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain W residue 10 TYR Chi-restraints excluded: chain W residue 15 GLN Chi-restraints excluded: chain W residue 20 PHE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 20 PHE Chi-restraints excluded: chain X residue 27 ASN Chi-restraints excluded: chain X residue 40 VAL 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 27 ASN Chi-restraints excluded: chain Y residue 32 ILE 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 23 ASP Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 41 ILE Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 19 PHE Chi-restraints excluded: chain 0 residue 35 MET Chi-restraints excluded: chain 0 residue 41 ILE Chi-restraints excluded: chain 1 residue 11 GLU Chi-restraints excluded: chain 1 residue 12 VAL 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 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 12 VAL Chi-restraints excluded: chain 2 residue 13 HIS Chi-restraints excluded: chain 2 residue 14 HIS Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 2 residue 40 VAL Chi-restraints excluded: chain 2 residue 41 ILE Chi-restraints excluded: chain 3 residue 10 TYR Chi-restraints excluded: chain 3 residue 13 HIS Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 22 GLU Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 4 residue 13 HIS Chi-restraints excluded: chain 4 residue 19 PHE 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 19 PHE 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 12 VAL 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 19 PHE Chi-restraints excluded: chain 6 residue 20 PHE 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 41 ILE Chi-restraints excluded: chain 7 residue 15 GLN Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 35 MET Chi-restraints excluded: chain 7 residue 41 ILE Chi-restraints excluded: chain 8 residue 14 HIS Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 27 ASN Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 35 MET Chi-restraints excluded: chain 9 residue 40 VAL Chi-restraints excluded: chain 9 residue 41 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 2 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- 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 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 HIS ** K 15 GLN ** 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 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** 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 13 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 27 ASN ** 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 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 GLN ** 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 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 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 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 13 HIS ** 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 13 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** ** 5 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 13 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 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6775 r_free = 0.6775 target = 0.594675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.6909 r_free = 0.6909 target = 0.573426 restraints weight = 17403.370| |-----------------------------------------------------------------------------| r_work (start): 0.6753 rms_B_bonded: 0.63 r_work: 0.6892 rms_B_bonded: 0.30 restraints_weight: 0.5000 r_work: 0.6881 rms_B_bonded: 0.56 restraints_weight: 0.2500 r_work: 0.6742 rms_B_bonded: 2.87 restraints_weight: 0.1250 r_work (final): 0.6742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1671 moved from start: 8.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.074 1.691 9180 Z= 4.993 Angle : 7.511 60.721 12348 Z= 4.610 Chirality : 0.404 3.953 1404 Planarity : 0.063 0.204 1584 Dihedral : 40.461 116.959 1260 Min Nonbonded Distance : 1.152 Molprobity Statistics. All-atom Clashscore : 629.53 Ramachandran Plot: Outliers : 36.37 % Allowed : 39.15 % Favored : 24.48 % Rotamer: Outliers : 23.00 % Allowed : 35.33 % Favored : 41.67 % Cbeta Deviations : 38.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 46.80 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -9.07 (0.10), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.91 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.077 0.016 HIS 0 14 PHE 0.203 0.028 PHE B 20 TYR 0.158 0.012 TYR L 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9770.65 seconds wall clock time: 178 minutes 26.57 seconds (10706.57 seconds total)