Starting phenix.real_space_refine on Thu Mar 13 08:40:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8azs_15770/03_2025/8azs_15770.cif Found real_map, /net/cci-nas-00/data/ceres_data/8azs_15770/03_2025/8azs_15770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8azs_15770/03_2025/8azs_15770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8azs_15770/03_2025/8azs_15770.map" model { file = "/net/cci-nas-00/data/ceres_data/8azs_15770/03_2025/8azs_15770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8azs_15770/03_2025/8azs_15770.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5868 2.51 5 N 1512 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 2.55, per 1000 atoms: 0.28 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: 17.38 Conformation dependent library (CDL) restraints added in 1.2 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: 1.22 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: 17.87 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: 0.10 Found NCS groups: ncs_group { reference = chain '1' selection = chain '0' selection = chain '3' selection = chain '2' selection = chain '5' selection = chain '4' selection = chain '7' selection = chain '6' selection = chain '9' selection = chain '8' selection = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'Y' selection = chain 'X' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 36.090 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.910 ------------------------------------------------------------------------------- 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 : 2.043 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: 1.6788 time to fit residues: 291.1166 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 : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.491 > 50: distance: 342 - 343: 24.389 distance: 343 - 344: 19.351 distance: 344 - 345: 5.688 distance: 344 - 346: 5.094 distance: 346 - 347: 7.992 distance: 347 - 348: 9.287 distance: 347 - 350: 11.160 distance: 348 - 349: 8.062 distance: 348 - 358: 3.452 distance: 350 - 351: 14.174 distance: 351 - 352: 12.943 distance: 351 - 353: 10.499 distance: 352 - 354: 11.870 distance: 353 - 355: 5.004 distance: 354 - 356: 8.693 distance: 355 - 356: 14.962 distance: 356 - 357: 5.144 distance: 358 - 359: 5.432 distance: 359 - 360: 4.665 distance: 359 - 362: 8.665 distance: 360 - 367: 5.695 distance: 362 - 363: 5.104 distance: 363 - 364: 10.130 distance: 364 - 365: 10.677 distance: 364 - 366: 6.267 distance: 367 - 368: 4.869 distance: 367 - 733: 5.600 distance: 368 - 369: 7.366 distance: 368 - 371: 17.821 distance: 369 - 370: 5.999 distance: 369 - 374: 12.257 distance: 371 - 372: 26.247 distance: 371 - 373: 27.847 distance: 374 - 375: 12.868 distance: 374 - 742: 11.708 distance: 375 - 378: 11.045 distance: 376 - 384: 3.605 distance: 378 - 379: 6.561 distance: 379 - 380: 19.616 distance: 379 - 381: 33.022 distance: 380 - 382: 3.496 distance: 381 - 383: 14.259 distance: 382 - 383: 35.928 distance: 384 - 385: 12.077 distance: 385 - 386: 16.372 distance: 385 - 388: 5.720 distance: 386 - 387: 9.617 distance: 386 - 394: 3.681 distance: 386 - 767: 21.514 distance: 388 - 389: 6.730 distance: 389 - 390: 15.082 distance: 389 - 391: 19.090 distance: 390 - 392: 19.713 distance: 392 - 393: 18.208 distance: 394 - 395: 5.352 distance: 395 - 396: 18.700 distance: 395 - 398: 4.327 distance: 396 - 397: 11.792 distance: 396 - 403: 19.354 distance: 398 - 399: 25.165 distance: 399 - 400: 28.094 distance: 400 - 401: 12.543 distance: 400 - 402: 8.508 distance: 403 - 404: 5.405 distance: 404 - 405: 10.770 distance: 404 - 407: 6.512 distance: 405 - 406: 14.828 distance: 405 - 412: 21.035 distance: 407 - 408: 12.378 distance: 408 - 409: 15.850 distance: 409 - 410: 20.473 distance: 410 - 411: 22.863 distance: 412 - 413: 6.331 distance: 412 - 778: 7.066 distance: 413 - 414: 4.486 distance: 413 - 416: 4.385 distance: 414 - 415: 3.038 distance: 416 - 417: 6.444 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