Starting phenix.real_space_refine on Sat Dec 28 16:02:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8azs_15770/12_2024/8azs_15770.cif Found real_map, /net/cci-nas-00/data/ceres_data/8azs_15770/12_2024/8azs_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_15770/12_2024/8azs_15770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8azs_15770/12_2024/8azs_15770.map" model { file = "/net/cci-nas-00/data/ceres_data/8azs_15770/12_2024/8azs_15770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8azs_15770/12_2024/8azs_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 2.39, per 1000 atoms: 0.26 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: 17.16 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: 1.16 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: 17.24 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: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 35.660 Find NCS groups from input model: 0.360 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: 0.010 Load rotamer database and sin/cos tables:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.290 ------------------------------------------------------------------------------- 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 : 0.978 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: 1.5058 time to fit residues: 261.5206 Evaluate side-chains 153 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2169 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 : 1.009 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: 0.2413 (OUTLIER) cc_final: 0.1192 (p90) REVERT: L 28 LYS cc_start: 0.4318 (mttt) cc_final: 0.3849 (tmmt) REVERT: P 14 HIS cc_start: -0.1082 (OUTLIER) cc_final: -0.1295 (t-90) REVERT: Q 23 ASP cc_start: 0.1920 (OUTLIER) cc_final: 0.1463 (t70) REVERT: E 17 LEU cc_start: -0.0168 (OUTLIER) cc_final: -0.0398 (tp) REVERT: E 19 PHE cc_start: 0.0690 (OUTLIER) cc_final: 0.0221 (t80) REVERT: V 16 LYS cc_start: 0.4674 (OUTLIER) cc_final: 0.4410 (tttt) REVERT: W 32 ILE cc_start: 0.1570 (OUTLIER) cc_final: 0.1358 (mt) REVERT: X 23 ASP cc_start: 0.4424 (OUTLIER) cc_final: 0.3971 (t70) REVERT: X 31 ILE cc_start: -0.0485 (OUTLIER) cc_final: -0.0708 (mm) REVERT: 2 26 SER cc_start: 0.5811 (OUTLIER) cc_final: 0.5466 (t) REVERT: 2 27 ASN cc_start: 0.1648 (OUTLIER) cc_final: 0.0866 (m110) REVERT: 3 27 ASN cc_start: 0.4789 (OUTLIER) cc_final: 0.3084 (t0) REVERT: 5 10 TYR cc_start: 0.3796 (m-80) cc_final: 0.3416 (m-80) REVERT: 8 41 ILE cc_start: 0.1780 (OUTLIER) cc_final: 0.1517 (mp) outliers start: 411 outliers final: 233 residues processed: 488 average time/residue: 0.6344 time to fit residues: 353.0088 Evaluate side-chains 376 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 130 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 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 14 HIS 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 23 ASP 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 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 16 LYS 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 23 ASP 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 54 optimal weight: 40.0000 chunk 30 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 66 optimal weight: 30.0000 chunk 27 optimal weight: 30.0000 chunk 98 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 33 optimal weight: 40.0000 chunk 78 optimal weight: 40.0000 overall best weight: 10.1992 ------------------------------------------------------------------------------- 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 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 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** ** 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** ** R 27 ASN ** 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** ** S 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 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 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 14 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2407 moved from start: 7.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.091 1.836 9180 Z= 6.217 Angle : 8.827 67.564 12348 Z= 5.395 Chirality : 0.601 4.576 1404 Planarity : 0.061 0.200 1584 Dihedral : 38.029 112.475 1260 Min Nonbonded Distance : 1.074 Molprobity Statistics. All-atom Clashscore : 874.63 Ramachandran Plot: Outliers : 38.63 % Allowed : 37.67 % Favored : 23.70 % Rotamer: Outliers : 44.78 % Allowed : 20.44 % Favored : 34.78 % Cbeta Deviations : 52.68 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 43.18 % 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: -9.13 (0.10), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.95 (0.07), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.073 0.020 HIS H 14 PHE 0.217 0.028 PHE A 19 TYR 0.168 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 525 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 403 poor density : 122 time to evaluate : 0.959 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: I 26 SER cc_start: 0.5842 (OUTLIER) cc_final: 0.5559 (p) REVERT: J 17 LEU cc_start: 0.0205 (OUTLIER) cc_final: -0.0556 (pp) REVERT: N 20 PHE cc_start: 0.4382 (OUTLIER) cc_final: 0.4147 (m-80) REVERT: N 28 LYS cc_start: -0.0252 (OUTLIER) cc_final: -0.0790 (mttt) REVERT: R 20 PHE cc_start: 0.2391 (OUTLIER) cc_final: 0.1721 (p90) REVERT: A 12 VAL cc_start: -0.0763 (OUTLIER) cc_final: -0.0970 (m) REVERT: A 27 ASN cc_start: -0.0768 (OUTLIER) cc_final: -0.1368 (t0) REVERT: A 31 ILE cc_start: 0.2093 (OUTLIER) cc_final: 0.1811 (mt) REVERT: B 15 GLN cc_start: 0.1841 (OUTLIER) cc_final: 0.1635 (tt0) REVERT: T 27 ASN cc_start: 0.3255 (OUTLIER) cc_final: 0.2328 (m110) REVERT: W 15 GLN cc_start: 0.2641 (OUTLIER) cc_final: 0.1463 (mt0) REVERT: 1 13 HIS cc_start: 0.5083 (OUTLIER) cc_final: 0.4830 (p90) REVERT: 3 12 VAL cc_start: -0.0190 (OUTLIER) cc_final: -0.0541 (t) REVERT: 6 15 GLN cc_start: 0.5508 (OUTLIER) cc_final: 0.5297 (tt0) REVERT: 6 41 ILE cc_start: 0.3832 (OUTLIER) cc_final: 0.3594 (mm) REVERT: 9 27 ASN cc_start: 0.4640 (OUTLIER) cc_final: 0.3728 (t0) outliers start: 403 outliers final: 224 residues processed: 466 average time/residue: 0.6608 time to fit residues: 349.3659 Evaluate side-chains 351 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 111 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 TYR 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 14 HIS Chi-restraints excluded: chain G residue 20 PHE Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 26 SER 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 17 LEU Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 35 MET Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 41 ILE 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 18 VAL Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 41 ILE 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 22 GLU Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 35 MET Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain N residue 20 PHE 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 22 GLU Chi-restraints excluded: chain O residue 32 ILE Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain P residue 20 PHE Chi-restraints excluded: chain P residue 31 ILE 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 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 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 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 40 VAL 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 19 PHE 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 36 VAL 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 14 HIS 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 34 LEU 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 31 ILE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 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 17 LEU 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 17 LEU Chi-restraints excluded: chain S residue 20 PHE Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain T residue 14 HIS Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 27 ASN Chi-restraints excluded: chain T residue 31 ILE 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 V residue 12 VAL Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 39 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 19 PHE Chi-restraints excluded: chain W residue 20 PHE Chi-restraints excluded: chain W residue 24 VAL Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 14 HIS 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 16 LYS 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 36 VAL Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 24 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 17 LEU 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 23 ASP 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 39 VAL Chi-restraints excluded: chain 3 residue 12 VAL Chi-restraints excluded: chain 3 residue 15 GLN Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 39 VAL 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 32 ILE 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 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 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 34 LEU Chi-restraints excluded: chain 6 residue 40 VAL 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 18 VAL 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 13 HIS Chi-restraints excluded: chain 8 residue 14 HIS Chi-restraints excluded: chain 8 residue 15 GLN Chi-restraints excluded: chain 8 residue 24 VAL 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 23 ASP 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 97 optimal weight: 40.0000 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 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 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 HIS ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 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** ** 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 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 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 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** ** 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** ** D 14 HIS ** 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 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 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** ** 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 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2136 moved from start: 7.6818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 1.777 9180 Z= 5.614 Angle : 8.202 76.773 12348 Z= 5.053 Chirality : 0.508 4.505 1404 Planarity : 0.062 0.198 1584 Dihedral : 38.954 110.358 1260 Min Nonbonded Distance : 1.075 Molprobity Statistics. All-atom Clashscore : 789.74 Ramachandran Plot: Outliers : 37.50 % Allowed : 38.11 % Favored : 24.39 % Rotamer: Outliers : 42.89 % Allowed : 23.78 % Favored : 33.33 % Cbeta Deviations : 46.43 % 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: -9.01 (0.11), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.86 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.075 0.017 HIS S 14 PHE 0.190 0.025 PHE S 20 TYR 0.170 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 501 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 386 poor density : 115 time to evaluate : 0.931 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: F 23 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7125 (t0) REVERT: G 14 HIS cc_start: 0.2149 (OUTLIER) cc_final: 0.1688 (m90) REVERT: G 19 PHE cc_start: 0.4426 (OUTLIER) cc_final: 0.3064 (m-80) REVERT: G 20 PHE cc_start: 0.4915 (OUTLIER) cc_final: 0.4649 (m-80) REVERT: I 22 GLU cc_start: 0.4029 (OUTLIER) cc_final: 0.3656 (tt0) REVERT: I 23 ASP cc_start: 0.3441 (m-30) cc_final: 0.3218 (m-30) REVERT: J 27 ASN cc_start: -0.0720 (OUTLIER) cc_final: -0.1107 (m110) REVERT: N 27 ASN cc_start: 0.2720 (OUTLIER) cc_final: 0.0704 (p0) REVERT: N 41 ILE cc_start: -0.1710 (OUTLIER) cc_final: -0.2318 (mt) REVERT: B 24 VAL cc_start: 0.0677 (OUTLIER) cc_final: 0.0135 (t) REVERT: S 27 ASN cc_start: 0.0419 (OUTLIER) cc_final: 0.0022 (t0) REVERT: T 27 ASN cc_start: 0.4023 (OUTLIER) cc_final: 0.3284 (m110) REVERT: U 22 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5853 (mt-10) REVERT: U 32 ILE cc_start: 0.2383 (OUTLIER) cc_final: 0.2150 (mt) REVERT: V 17 LEU cc_start: 0.1198 (OUTLIER) cc_final: 0.0835 (mp) REVERT: V 22 GLU cc_start: 0.1811 (OUTLIER) cc_final: 0.1394 (mm-30) REVERT: W 16 LYS cc_start: 0.3366 (tttt) cc_final: 0.3072 (mttp) REVERT: X 23 ASP cc_start: 0.2689 (OUTLIER) cc_final: 0.2261 (t0) REVERT: 4 24 VAL cc_start: -0.5120 (OUTLIER) cc_final: -0.5364 (t) REVERT: 8 27 ASN cc_start: 0.5217 (OUTLIER) cc_final: 0.1100 (p0) REVERT: 9 32 ILE cc_start: 0.4266 (mt) cc_final: 0.3925 (mt) outliers start: 386 outliers final: 218 residues processed: 445 average time/residue: 0.6335 time to fit residues: 320.6271 Evaluate side-chains 344 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 108 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 20 PHE Chi-restraints excluded: chain F residue 23 ASP 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 13 HIS Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 20 PHE Chi-restraints excluded: chain G residue 27 ASN 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 22 GLU 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 17 LEU 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 17 LEU Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 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 22 GLU Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 20 PHE 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 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 34 LEU Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain Q residue 14 HIS 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 35 MET 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 27 ASN Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 36 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 35 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 22 GLU 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 15 GLN Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 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 19 PHE Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain S residue 11 GLU Chi-restraints excluded: chain S residue 17 LEU 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 27 ASN Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 35 MET Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 27 ASN Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain U residue 15 GLN Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 20 PHE Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 27 ASN Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 35 MET Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 22 GLU Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 39 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 17 LEU 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 14 HIS Chi-restraints excluded: chain X residue 19 PHE Chi-restraints excluded: chain X residue 20 PHE Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 11 GLU 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 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 39 VAL Chi-restraints excluded: chain Y residue 41 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 32 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 19 PHE Chi-restraints excluded: chain 0 residue 23 ASP Chi-restraints excluded: chain 0 residue 40 VAL 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 39 VAL Chi-restraints excluded: chain 1 residue 41 ILE Chi-restraints excluded: chain 2 residue 14 HIS Chi-restraints excluded: chain 2 residue 15 GLN Chi-restraints excluded: chain 2 residue 17 LEU 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 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 18 VAL Chi-restraints excluded: chain 5 residue 19 PHE 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 17 LEU Chi-restraints excluded: chain 6 residue 18 VAL Chi-restraints excluded: chain 6 residue 32 ILE Chi-restraints excluded: chain 6 residue 40 VAL Chi-restraints excluded: chain 7 residue 13 HIS Chi-restraints excluded: chain 7 residue 14 HIS Chi-restraints excluded: chain 7 residue 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 13 HIS Chi-restraints excluded: chain 8 residue 14 HIS Chi-restraints excluded: chain 8 residue 17 LEU Chi-restraints excluded: chain 8 residue 22 GLU 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 41 ILE Chi-restraints excluded: chain 9 residue 18 VAL 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 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 86 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 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 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 27 ASN ** 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 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 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 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** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 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** 3 27 ASN ** 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** ** 7 14 HIS ** 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 13 HIS ** 9 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1947 moved from start: 7.9605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 1.774 9180 Z= 5.361 Angle : 7.994 84.641 12348 Z= 4.901 Chirality : 0.442 4.415 1404 Planarity : 0.062 0.200 1584 Dihedral : 39.432 110.431 1260 Min Nonbonded Distance : 1.160 Molprobity Statistics. All-atom Clashscore : 724.66 Ramachandran Plot: Outliers : 37.33 % Allowed : 37.07 % Favored : 25.61 % Rotamer: Outliers : 38.44 % Allowed : 25.44 % Favored : 36.11 % Cbeta Deviations : 42.86 % 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: -8.95 (0.11), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.82 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.071 0.016 HIS H 14 PHE 0.167 0.025 PHE 6 19 TYR 0.154 0.013 TYR R 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 451 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 346 poor density : 105 time to evaluate : 1.256 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: I 22 GLU cc_start: 0.2406 (OUTLIER) cc_final: 0.2178 (tt0) REVERT: J 14 HIS cc_start: 0.4683 (OUTLIER) cc_final: 0.4089 (t-90) REVERT: J 23 ASP cc_start: 0.2860 (OUTLIER) cc_final: 0.2055 (t0) REVERT: J 27 ASN cc_start: -0.1645 (OUTLIER) cc_final: -0.2629 (t0) REVERT: N 27 ASN cc_start: 0.1402 (OUTLIER) cc_final: -0.0169 (p0) REVERT: Q 10 TYR cc_start: -0.1850 (OUTLIER) cc_final: -0.2151 (m-80) REVERT: Q 41 ILE cc_start: -0.0376 (OUTLIER) cc_final: -0.0883 (mm) REVERT: B 16 LYS cc_start: -0.4438 (OUTLIER) cc_final: -0.4650 (pttt) REVERT: B 20 PHE cc_start: 0.0058 (OUTLIER) cc_final: -0.0405 (m-80) REVERT: C 15 GLN cc_start: -0.1247 (OUTLIER) cc_final: -0.2057 (tp40) REVERT: D 23 ASP cc_start: 0.4371 (OUTLIER) cc_final: 0.3857 (t70) REVERT: E 14 HIS cc_start: 0.4971 (t70) cc_final: 0.4736 (t70) REVERT: S 27 ASN cc_start: -0.0710 (OUTLIER) cc_final: -0.0925 (t0) REVERT: T 27 ASN cc_start: 0.3885 (OUTLIER) cc_final: 0.2633 (m-40) REVERT: U 31 ILE cc_start: 0.3238 (mm) cc_final: 0.2998 (mm) REVERT: V 34 LEU cc_start: 0.3499 (OUTLIER) cc_final: 0.3206 (mt) REVERT: W 10 TYR cc_start: 0.1088 (OUTLIER) cc_final: 0.0768 (m-80) outliers start: 346 outliers final: 202 residues processed: 409 average time/residue: 0.6464 time to fit residues: 300.3233 Evaluate side-chains 311 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 94 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 23 ASP 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 20 PHE Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain K residue 14 HIS 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 26 SER Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 20 PHE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 19 PHE Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain O residue 13 HIS Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain Q residue 10 TYR Chi-restraints excluded: chain Q residue 13 HIS Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 35 MET Chi-restraints excluded: chain Q residue 41 ILE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 14 HIS Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain H residue 12 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 35 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 16 LYS 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 13 HIS Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 34 LEU 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 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 14 HIS 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 12 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain S residue 11 GLU Chi-restraints excluded: chain S residue 14 HIS Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain S residue 23 ASP Chi-restraints excluded: chain S residue 27 ASN Chi-restraints excluded: chain S residue 35 MET Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 27 ASN Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain U residue 15 GLN 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 V residue 12 VAL Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 39 VAL 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 35 MET Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 35 MET Chi-restraints excluded: chain X residue 39 VAL 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 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 0 residue 12 VAL Chi-restraints excluded: chain 0 residue 15 GLN Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 19 PHE Chi-restraints excluded: chain 0 residue 20 PHE Chi-restraints excluded: chain 0 residue 23 ASP 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 41 ILE Chi-restraints excluded: chain 2 residue 10 TYR Chi-restraints excluded: chain 2 residue 14 HIS Chi-restraints excluded: chain 2 residue 22 GLU 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 3 residue 10 TYR Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 35 MET Chi-restraints excluded: chain 4 residue 13 HIS Chi-restraints excluded: chain 4 residue 14 HIS Chi-restraints excluded: chain 4 residue 17 LEU Chi-restraints excluded: chain 4 residue 32 ILE 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 18 VAL Chi-restraints excluded: chain 5 residue 19 PHE Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 5 residue 41 ILE Chi-restraints excluded: chain 6 residue 11 GLU Chi-restraints excluded: chain 6 residue 12 VAL Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 32 ILE Chi-restraints excluded: chain 7 residue 13 HIS Chi-restraints excluded: chain 7 residue 14 HIS Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 35 MET Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 7 residue 41 ILE Chi-restraints excluded: chain 8 residue 13 HIS Chi-restraints excluded: chain 8 residue 15 GLN Chi-restraints excluded: chain 8 residue 16 LYS 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 35 MET Chi-restraints excluded: chain 8 residue 40 VAL Chi-restraints excluded: chain 8 residue 41 ILE Chi-restraints excluded: chain 9 residue 17 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 36 VAL 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 35 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** 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** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 13 HIS ** 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** ** 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 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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** ** 7 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1847 moved from start: 8.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.076 1.739 9180 Z= 5.126 Angle : 7.736 53.366 12348 Z= 4.754 Chirality : 0.393 2.479 1404 Planarity : 0.062 0.198 1584 Dihedral : 39.893 111.301 1260 Min Nonbonded Distance : 1.141 Molprobity Statistics. All-atom Clashscore : 667.09 Ramachandran Plot: Outliers : 37.41 % Allowed : 36.28 % Favored : 26.30 % Rotamer: Outliers : 35.33 % Allowed : 26.44 % Favored : 38.22 % Cbeta Deviations : 39.98 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 45.88 % 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: -9.02 (0.10), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.87 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.069 0.015 HIS Z 14 PHE 0.189 0.026 PHE E 20 TYR 0.151 0.012 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 416 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 318 poor density : 98 time to evaluate : 0.892 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: J 23 ASP cc_start: 0.3096 (OUTLIER) cc_final: 0.2251 (t70) REVERT: J 27 ASN cc_start: -0.1584 (OUTLIER) cc_final: -0.3097 (m-40) REVERT: K 22 GLU cc_start: -0.0019 (OUTLIER) cc_final: -0.1378 (mt-10) REVERT: L 20 PHE cc_start: 0.0236 (OUTLIER) cc_final: 0.0006 (m-10) REVERT: P 12 VAL cc_start: -0.1171 (OUTLIER) cc_final: -0.1609 (m) REVERT: Q 41 ILE cc_start: -0.1944 (OUTLIER) cc_final: -0.2483 (mm) REVERT: B 20 PHE cc_start: -0.0836 (OUTLIER) cc_final: -0.1070 (m-80) REVERT: D 14 HIS cc_start: 0.4499 (OUTLIER) cc_final: 0.3952 (p-80) REVERT: E 16 LYS cc_start: -0.0658 (OUTLIER) cc_final: -0.0872 (ttmt) REVERT: T 27 ASN cc_start: 0.3872 (OUTLIER) cc_final: 0.3170 (m-40) REVERT: U 32 ILE cc_start: 0.0439 (OUTLIER) cc_final: -0.0212 (mt) REVERT: V 34 LEU cc_start: 0.3455 (OUTLIER) cc_final: 0.3238 (mt) REVERT: W 15 GLN cc_start: 0.0215 (OUTLIER) cc_final: -0.0729 (mp10) REVERT: 2 15 GLN cc_start: 0.1722 (OUTLIER) cc_final: 0.1461 (mp10) REVERT: 4 11 GLU cc_start: -0.0777 (OUTLIER) cc_final: -0.0978 (pt0) REVERT: 4 34 LEU cc_start: 0.5126 (OUTLIER) cc_final: 0.4881 (pt) outliers start: 318 outliers final: 176 residues processed: 381 average time/residue: 0.6042 time to fit residues: 263.6899 Evaluate side-chains 282 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 90 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 TYR 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 31 ILE Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 19 PHE Chi-restraints excluded: chain L residue 20 PHE Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 16 LYS 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 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 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 Q residue 31 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 41 ILE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 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 D residue 12 VAL Chi-restraints excluded: chain D residue 14 HIS 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 35 MET Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain S residue 14 HIS Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 35 MET Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 13 HIS Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 19 PHE Chi-restraints excluded: chain T residue 27 ASN Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 35 MET Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 20 PHE Chi-restraints excluded: chain U residue 27 ASN Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 35 MET Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain W residue 15 GLN Chi-restraints excluded: chain W residue 20 PHE Chi-restraints excluded: chain W residue 24 VAL Chi-restraints excluded: chain W residue 35 MET Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain X residue 10 TYR 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 19 PHE Chi-restraints excluded: chain Y residue 20 PHE Chi-restraints excluded: chain Y residue 27 ASN 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 15 GLN 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 0 residue 12 VAL Chi-restraints excluded: chain 0 residue 14 HIS Chi-restraints excluded: chain 0 residue 15 GLN Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 19 PHE Chi-restraints excluded: chain 0 residue 20 PHE Chi-restraints excluded: chain 0 residue 23 ASP 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 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 15 GLN Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 23 ASP Chi-restraints excluded: chain 2 residue 34 LEU Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 3 residue 13 HIS Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 35 MET Chi-restraints excluded: chain 4 residue 11 GLU Chi-restraints excluded: chain 4 residue 13 HIS Chi-restraints excluded: chain 4 residue 19 PHE Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 41 ILE Chi-restraints excluded: chain 5 residue 11 GLU Chi-restraints excluded: chain 5 residue 13 HIS Chi-restraints excluded: chain 5 residue 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 11 GLU Chi-restraints excluded: chain 6 residue 12 VAL Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 20 PHE Chi-restraints excluded: chain 6 residue 32 ILE Chi-restraints excluded: chain 7 residue 14 HIS Chi-restraints excluded: chain 7 residue 16 LYS Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 7 residue 35 MET Chi-restraints excluded: chain 7 residue 41 ILE Chi-restraints excluded: chain 8 residue 15 GLN 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 13 HIS Chi-restraints excluded: chain 9 residue 17 LEU Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 35 MET Chi-restraints excluded: chain 9 residue 36 VAL 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 100 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 HIS ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 HIS ** Q 13 HIS ** 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 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 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 ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 15 GLN ** Y 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1821 moved from start: 8.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.073 1.736 9180 Z= 4.936 Angle : 7.496 60.232 12348 Z= 4.637 Chirality : 0.377 2.733 1404 Planarity : 0.063 0.204 1584 Dihedral : 40.285 111.374 1260 Min Nonbonded Distance : 1.140 Molprobity Statistics. All-atom Clashscore : 620.04 Ramachandran Plot: Outliers : 36.46 % Allowed : 38.02 % Favored : 25.52 % Rotamer: Outliers : 31.67 % Allowed : 26.33 % Favored : 42.00 % Cbeta Deviations : 38.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 45.88 % 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 (0.09), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.97 (0.07), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.074 0.015 HIS 5 14 PHE 0.205 0.026 PHE 6 19 TYR 0.151 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 385 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 285 poor density : 100 time to evaluate : 0.933 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: F 16 LYS cc_start: 0.2424 (tttt) cc_final: 0.2093 (mmtm) REVERT: J 27 ASN cc_start: -0.1672 (OUTLIER) cc_final: -0.2929 (m-40) REVERT: K 20 PHE cc_start: 0.6462 (t80) cc_final: 0.6154 (t80) REVERT: K 22 GLU cc_start: 0.1060 (OUTLIER) cc_final: 0.0718 (mm-30) REVERT: Q 41 ILE cc_start: -0.2129 (OUTLIER) cc_final: -0.2692 (mm) REVERT: H 11 GLU cc_start: 0.1312 (OUTLIER) cc_final: 0.0830 (tp30) REVERT: C 18 VAL cc_start: 0.1774 (OUTLIER) cc_final: 0.1548 (p) REVERT: D 14 HIS cc_start: 0.4148 (OUTLIER) cc_final: 0.3408 (p90) REVERT: T 35 MET cc_start: 0.4600 (OUTLIER) cc_final: 0.4296 (mtt) REVERT: U 28 LYS cc_start: 0.2495 (OUTLIER) cc_final: 0.2264 (mttt) REVERT: V 40 VAL cc_start: 0.3630 (OUTLIER) cc_final: 0.3378 (t) REVERT: W 15 GLN cc_start: -0.0700 (OUTLIER) cc_final: -0.1599 (mp10) REVERT: X 23 ASP cc_start: 0.2221 (OUTLIER) cc_final: 0.1692 (t70) REVERT: Y 15 GLN cc_start: 0.0189 (OUTLIER) cc_final: -0.1089 (mp10) REVERT: Y 17 LEU cc_start: -0.0258 (OUTLIER) cc_final: -0.0628 (mt) REVERT: 1 13 HIS cc_start: 0.1752 (OUTLIER) cc_final: 0.1484 (p90) REVERT: 2 14 HIS cc_start: 0.2979 (OUTLIER) cc_final: 0.1343 (m90) REVERT: 4 35 MET cc_start: 0.0690 (OUTLIER) cc_final: 0.0230 (mpp) REVERT: 5 19 PHE cc_start: 0.5204 (OUTLIER) cc_final: 0.4871 (m-80) REVERT: 6 31 ILE cc_start: 0.4580 (OUTLIER) cc_final: 0.4336 (mm) outliers start: 285 outliers final: 180 residues processed: 355 average time/residue: 0.6610 time to fit residues: 265.5960 Evaluate side-chains 287 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 89 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 19 PHE Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 34 LEU 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 12 VAL Chi-restraints excluded: chain L residue 19 PHE Chi-restraints excluded: chain L residue 20 PHE Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 20 PHE Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 16 LYS 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 36 VAL Chi-restraints excluded: chain N residue 41 ILE Chi-restraints excluded: chain O residue 13 HIS Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 31 ILE 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 31 ILE Chi-restraints excluded: chain Q residue 41 ILE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 27 ASN Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 23 ASP 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 11 GLU Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 34 LEU 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 27 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 17 LEU 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 D residue 14 HIS Chi-restraints excluded: chain D residue 15 GLN 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 35 MET Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 18 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 39 VAL Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain T residue 13 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 34 LEU Chi-restraints excluded: chain T residue 35 MET Chi-restraints excluded: chain T residue 39 VAL 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 28 LYS Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 35 MET Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain W residue 13 HIS Chi-restraints excluded: chain W residue 15 GLN 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 40 VAL Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 40 VAL 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 20 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 Z residue 11 GLU Chi-restraints excluded: chain Z residue 13 HIS Chi-restraints excluded: chain Z residue 15 GLN 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 0 residue 12 VAL Chi-restraints excluded: chain 0 residue 15 GLN Chi-restraints excluded: chain 0 residue 19 PHE Chi-restraints excluded: chain 0 residue 23 ASP 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 34 LEU 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 17 LEU Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 23 ASP Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 3 residue 13 HIS Chi-restraints excluded: chain 3 residue 19 PHE Chi-restraints excluded: chain 3 residue 35 MET Chi-restraints excluded: chain 3 residue 36 VAL Chi-restraints excluded: chain 4 residue 19 PHE 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 13 HIS Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 19 PHE Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 5 residue 34 LEU Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 41 ILE Chi-restraints excluded: chain 6 residue 12 VAL Chi-restraints excluded: chain 6 residue 17 LEU Chi-restraints excluded: chain 6 residue 19 PHE Chi-restraints excluded: chain 6 residue 20 PHE Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 6 residue 32 ILE Chi-restraints excluded: chain 7 residue 14 HIS Chi-restraints excluded: chain 7 residue 16 LYS Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 7 residue 35 MET Chi-restraints excluded: chain 7 residue 41 ILE Chi-restraints excluded: chain 8 residue 15 GLN 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 41 ILE Chi-restraints excluded: chain 9 residue 17 LEU Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 35 MET 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 41 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** 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 13 HIS ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** 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** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** 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 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 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 15 GLN ** V 27 ASN ** 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** ** Z 15 GLN ** 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** ** 1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 13 HIS ** 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1599 moved from start: 8.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.070 1.723 9180 Z= 4.746 Angle : 7.336 77.495 12348 Z= 4.537 Chirality : 0.363 2.313 1404 Planarity : 0.064 0.204 1584 Dihedral : 40.693 114.409 1260 Min Nonbonded Distance : 1.191 Molprobity Statistics. All-atom Clashscore : 587.99 Ramachandran Plot: Outliers : 36.46 % Allowed : 37.50 % Favored : 26.04 % Rotamer: Outliers : 28.56 % Allowed : 29.00 % Favored : 42.44 % Cbeta Deviations : 35.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 47.31 % 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: -9.09 (0.10), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.92 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.054 0.012 HIS O 13 PHE 0.161 0.027 PHE B 20 TYR 0.152 0.013 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 358 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 257 poor density : 101 time to evaluate : 1.443 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: K 22 GLU cc_start: 0.1621 (OUTLIER) cc_final: 0.0890 (mm-30) REVERT: O 14 HIS cc_start: 0.3572 (m90) cc_final: 0.2617 (m90) REVERT: Q 41 ILE cc_start: -0.1128 (OUTLIER) cc_final: -0.1642 (mm) REVERT: C 16 LYS cc_start: 0.0880 (OUTLIER) cc_final: 0.0160 (tmmt) REVERT: E 23 ASP cc_start: -0.0240 (OUTLIER) cc_final: -0.0604 (t70) REVERT: T 13 HIS cc_start: 0.1633 (OUTLIER) cc_final: 0.1022 (m90) REVERT: X 23 ASP cc_start: 0.2257 (OUTLIER) cc_final: 0.1605 (t70) REVERT: Y 15 GLN cc_start: 0.0254 (OUTLIER) cc_final: -0.0500 (tp40) REVERT: 1 28 LYS cc_start: 0.4435 (OUTLIER) cc_final: 0.4103 (mptt) REVERT: 2 14 HIS cc_start: 0.2507 (OUTLIER) cc_final: 0.2210 (m90) REVERT: 4 35 MET cc_start: 0.0360 (OUTLIER) cc_final: -0.0081 (mpp) outliers start: 257 outliers final: 154 residues processed: 329 average time/residue: 0.6705 time to fit residues: 249.4049 Evaluate side-chains 259 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 95 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 19 PHE Chi-restraints excluded: chain J residue 27 ASN Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 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 39 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 20 PHE Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 16 LYS 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 36 VAL Chi-restraints excluded: chain N residue 41 ILE Chi-restraints excluded: chain O residue 13 HIS Chi-restraints excluded: chain O residue 18 VAL 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 Q residue 31 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 35 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 17 LEU 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 D residue 14 HIS Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain T residue 13 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 39 VAL Chi-restraints excluded: chain U residue 19 PHE Chi-restraints excluded: chain U residue 20 PHE Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain W residue 15 GLN Chi-restraints excluded: chain W residue 20 PHE Chi-restraints excluded: chain W residue 35 MET Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 19 PHE Chi-restraints excluded: chain Y residue 35 MET Chi-restraints excluded: chain Y residue 36 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 32 ILE Chi-restraints excluded: chain 0 residue 11 GLU Chi-restraints excluded: chain 0 residue 19 PHE Chi-restraints excluded: chain 0 residue 20 PHE Chi-restraints excluded: chain 0 residue 23 ASP Chi-restraints excluded: chain 0 residue 40 VAL Chi-restraints excluded: chain 1 residue 11 GLU Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 22 GLU Chi-restraints excluded: chain 1 residue 28 LYS 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 12 VAL Chi-restraints excluded: chain 2 residue 13 HIS Chi-restraints excluded: chain 2 residue 14 HIS Chi-restraints excluded: chain 2 residue 17 LEU Chi-restraints excluded: chain 2 residue 22 GLU Chi-restraints excluded: chain 2 residue 23 ASP Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 3 residue 10 TYR Chi-restraints excluded: chain 3 residue 19 PHE Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 34 LEU Chi-restraints excluded: chain 3 residue 35 MET Chi-restraints excluded: chain 4 residue 19 PHE Chi-restraints excluded: chain 4 residue 20 PHE Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 35 MET Chi-restraints excluded: chain 4 residue 36 VAL Chi-restraints excluded: chain 4 residue 41 ILE Chi-restraints excluded: chain 5 residue 11 GLU Chi-restraints excluded: chain 5 residue 13 HIS Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 5 residue 34 LEU Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 41 ILE Chi-restraints excluded: chain 6 residue 18 VAL Chi-restraints excluded: chain 6 residue 20 PHE Chi-restraints excluded: chain 6 residue 32 ILE Chi-restraints excluded: chain 7 residue 14 HIS Chi-restraints excluded: chain 7 residue 16 LYS Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 7 residue 41 ILE Chi-restraints excluded: chain 8 residue 15 GLN Chi-restraints excluded: chain 8 residue 16 LYS 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 9 residue 17 LEU Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 35 MET 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 90 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** 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 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** U 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 13 HIS ** 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 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1574 moved from start: 8.6956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.069 1.698 9180 Z= 4.666 Angle : 7.265 70.974 12348 Z= 4.479 Chirality : 0.361 2.532 1404 Planarity : 0.065 0.205 1584 Dihedral : 40.904 113.498 1260 Min Nonbonded Distance : 1.184 Molprobity Statistics. All-atom Clashscore : 562.72 Ramachandran Plot: Outliers : 36.11 % Allowed : 37.41 % Favored : 26.48 % Rotamer: Outliers : 24.00 % Allowed : 31.00 % Favored : 45.00 % Cbeta Deviations : 34.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 48.15 % 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 (0.10), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.88 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.062 0.012 HIS 6 14 PHE 0.251 0.026 PHE 6 19 TYR 0.154 0.013 TYR R 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 314 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 98 time to evaluate : 0.901 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: F 14 HIS cc_start: 0.5639 (t-90) cc_final: 0.5355 (t70) REVERT: B 15 GLN cc_start: 0.0286 (tp40) cc_final: -0.0525 (pt0) REVERT: C 16 LYS cc_start: 0.0758 (OUTLIER) cc_final: 0.0428 (mmtp) REVERT: E 23 ASP cc_start: 0.0701 (OUTLIER) cc_final: 0.0152 (t70) REVERT: T 13 HIS cc_start: 0.1444 (OUTLIER) cc_final: 0.1089 (m90) REVERT: V 35 MET cc_start: 0.3290 (OUTLIER) cc_final: 0.2413 (pp-130) REVERT: X 23 ASP cc_start: 0.2427 (OUTLIER) cc_final: 0.1864 (t70) REVERT: Z 31 ILE cc_start: -0.0301 (OUTLIER) cc_final: -0.0742 (mt) REVERT: Z 32 ILE cc_start: -0.1432 (OUTLIER) cc_final: -0.1916 (mm) REVERT: 2 14 HIS cc_start: 0.2406 (OUTLIER) cc_final: 0.1946 (m90) REVERT: 4 20 PHE cc_start: -0.1231 (OUTLIER) cc_final: -0.1542 (m-80) REVERT: 4 35 MET cc_start: 0.0785 (OUTLIER) cc_final: 0.0106 (mpp) REVERT: 6 28 LYS cc_start: 0.1196 (mttt) cc_final: 0.0900 (mtmm) outliers start: 216 outliers final: 142 residues processed: 290 average time/residue: 0.6749 time to fit residues: 221.0547 Evaluate side-chains 246 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 94 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 34 LEU Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 19 PHE Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 14 HIS 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 34 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain N residue 13 HIS 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 O residue 18 VAL Chi-restraints excluded: chain O residue 36 VAL 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 31 ILE Chi-restraints excluded: chain Q residue 35 MET 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 35 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 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 19 PHE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain 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 27 ASN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain S residue 10 TYR Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain T residue 13 HIS Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 19 PHE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 20 PHE Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 35 MET Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain W residue 20 PHE Chi-restraints excluded: chain W residue 31 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 23 ASP Chi-restraints excluded: chain X residue 27 ASN Chi-restraints excluded: chain X residue 40 VAL 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 35 MET Chi-restraints excluded: chain Z residue 13 HIS Chi-restraints excluded: chain Z residue 15 GLN Chi-restraints excluded: chain Z residue 18 VAL 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 0 residue 15 GLN Chi-restraints excluded: chain 0 residue 19 PHE Chi-restraints excluded: chain 0 residue 20 PHE Chi-restraints excluded: chain 0 residue 23 ASP Chi-restraints excluded: chain 0 residue 34 LEU Chi-restraints excluded: chain 0 residue 40 VAL Chi-restraints excluded: chain 1 residue 11 GLU Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 19 PHE Chi-restraints excluded: chain 1 residue 22 GLU Chi-restraints excluded: chain 1 residue 28 LYS Chi-restraints excluded: chain 1 residue 32 ILE 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 17 LEU Chi-restraints excluded: chain 2 residue 23 ASP Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 3 residue 23 ASP Chi-restraints excluded: chain 3 residue 35 MET Chi-restraints excluded: chain 4 residue 19 PHE Chi-restraints excluded: chain 4 residue 20 PHE 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 13 HIS Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 41 ILE Chi-restraints excluded: chain 6 residue 14 HIS Chi-restraints excluded: chain 6 residue 18 VAL Chi-restraints excluded: chain 6 residue 20 PHE Chi-restraints excluded: chain 6 residue 32 ILE Chi-restraints excluded: chain 7 residue 14 HIS Chi-restraints excluded: chain 7 residue 19 PHE Chi-restraints excluded: chain 7 residue 32 ILE 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 9 residue 12 VAL Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 35 MET 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 102 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 107 optimal weight: 0.3980 chunk 99 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 HIS ** G 14 HIS ** 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 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** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 15 GLN ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 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** ** 4 27 ASN ** 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1262 moved from start: 8.7929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.068 1.697 9180 Z= 4.603 Angle : 7.210 66.391 12348 Z= 4.442 Chirality : 0.362 2.943 1404 Planarity : 0.065 0.207 1584 Dihedral : 41.019 112.010 1260 Min Nonbonded Distance : 1.185 Molprobity Statistics. All-atom Clashscore : 541.40 Ramachandran Plot: Outliers : 35.24 % Allowed : 38.54 % Favored : 26.22 % Rotamer: Outliers : 19.00 % Allowed : 34.22 % Favored : 46.78 % Cbeta Deviations : 33.93 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 48.15 % 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: -9.01 (0.11), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.86 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.092 0.012 HIS H 14 PHE 0.240 0.025 PHE 6 19 TYR 0.159 0.010 TYR R 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 266 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 95 time to evaluate : 0.928 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: F 14 HIS cc_start: 0.5518 (t-90) cc_final: 0.5238 (t-90) REVERT: N 10 TYR cc_start: 0.0256 (m-80) cc_final: -0.0379 (p90) REVERT: B 15 GLN cc_start: 0.0783 (tp40) cc_final: -0.0054 (pt0) REVERT: C 31 ILE cc_start: 0.3462 (OUTLIER) cc_final: 0.3246 (mm) REVERT: E 23 ASP cc_start: 0.1335 (OUTLIER) cc_final: 0.0712 (t70) REVERT: T 13 HIS cc_start: 0.0170 (OUTLIER) cc_final: -0.0073 (m90) REVERT: X 23 ASP cc_start: 0.2454 (OUTLIER) cc_final: 0.1890 (t70) REVERT: 1 12 VAL cc_start: 0.1174 (OUTLIER) cc_final: 0.0745 (m) REVERT: 2 14 HIS cc_start: 0.2330 (OUTLIER) cc_final: 0.1619 (m90) REVERT: 6 28 LYS cc_start: 0.1278 (mttt) cc_final: 0.0986 (mtmm) outliers start: 171 outliers final: 130 residues processed: 245 average time/residue: 0.6501 time to fit residues: 182.6854 Evaluate side-chains 228 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 92 time to evaluate : 1.529 ------------------------------------------------------------------------------- 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 34 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 28 LYS Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 14 HIS 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 34 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 19 PHE 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 O residue 18 VAL Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain P residue 20 PHE Chi-restraints excluded: chain P residue 34 LEU 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 35 MET Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain S residue 10 TYR Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain T residue 13 HIS Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 19 PHE Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 20 PHE Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain W residue 20 PHE Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 23 ASP Chi-restraints excluded: chain X residue 40 VAL 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 35 MET Chi-restraints excluded: chain Z residue 13 HIS Chi-restraints excluded: chain Z residue 15 GLN Chi-restraints excluded: chain Z residue 18 VAL 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 0 residue 15 GLN Chi-restraints excluded: chain 0 residue 19 PHE Chi-restraints excluded: chain 0 residue 20 PHE Chi-restraints excluded: chain 0 residue 23 ASP Chi-restraints excluded: chain 0 residue 40 VAL 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 19 PHE Chi-restraints excluded: chain 1 residue 22 GLU Chi-restraints excluded: chain 1 residue 28 LYS Chi-restraints excluded: chain 1 residue 34 LEU 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 36 VAL Chi-restraints excluded: chain 2 residue 39 VAL Chi-restraints excluded: chain 3 residue 23 ASP Chi-restraints excluded: chain 3 residue 35 MET Chi-restraints excluded: chain 4 residue 19 PHE 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 13 HIS Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 5 residue 34 LEU Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 41 ILE Chi-restraints excluded: chain 6 residue 18 VAL Chi-restraints excluded: chain 6 residue 20 PHE Chi-restraints excluded: chain 6 residue 32 ILE Chi-restraints excluded: chain 7 residue 14 HIS 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 8 residue 27 ASN Chi-restraints excluded: chain 8 residue 32 ILE Chi-restraints excluded: chain 8 residue 35 MET Chi-restraints excluded: chain 9 residue 12 VAL Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain 9 residue 35 MET 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 91 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 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 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 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** ** U 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 15 GLN ** X 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6824 r_free = 0.6824 target = 0.596727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.6959 r_free = 0.6959 target = 0.578738 restraints weight = 21005.205| |-----------------------------------------------------------------------------| r_work (start): 0.6816 rms_B_bonded: 0.58 r_work: 0.6899 rms_B_bonded: 0.31 restraints_weight: 0.5000 r_work: 0.6917 rms_B_bonded: 0.47 restraints_weight: 0.2500 r_work: 0.6797 rms_B_bonded: 2.76 restraints_weight: 0.1250 r_work (final): 0.6797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1348 moved from start: 8.8500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.067 1.715 9180 Z= 4.579 Angle : 7.150 58.223 12348 Z= 4.414 Chirality : 0.357 2.903 1404 Planarity : 0.065 0.208 1584 Dihedral : 41.214 111.440 1260 Min Nonbonded Distance : 1.184 Molprobity Statistics. All-atom Clashscore : 531.50 Ramachandran Plot: Outliers : 35.07 % Allowed : 38.63 % Favored : 26.30 % Rotamer: Outliers : 17.78 % Allowed : 35.78 % Favored : 46.44 % Cbeta Deviations : 33.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 49.33 % 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: -8.96 (0.11), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.83 (0.08), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.057 0.011 HIS S 14 PHE 0.243 0.025 PHE 6 19 TYR 0.155 0.011 TYR R 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6961.35 seconds wall clock time: 129 minutes 24.74 seconds (7764.74 seconds total)