Starting phenix.real_space_refine on Fri Sep 11 22:00:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ofe_20043/09_2026/6ofe_20043.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ofe_20043/09_2026/6ofe_20043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ofe_20043/09_2026/6ofe_20043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ofe_20043/09_2026/6ofe_20043.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ofe_20043/09_2026/6ofe_20043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ofe_20043/09_2026/6ofe_20043.map" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 7740 2.51 5 N 2020 2.21 5 O 2460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12220 Number of models: 1 Model: "" Number of chains: 1 Chain: "P" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 611 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Restraints were copied for chains: Q, R, S, T, K, L, M, N, O, F, G, H, I, J, D, A, B, C, E Time building chain proxies: 1.37, per 1000 atoms: 0.11 Number of scatterers: 12220 At special positions: 0 Unit cell: (90.915, 90.915, 154.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2460 8.00 N 2020 7.00 C 7740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 523.0 milliseconds 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3040 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 89.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'P' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE P 16 " --> pdb=" O VAL P 12 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA P 36 " --> pdb=" O ASP P 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS P 37 " --> pdb=" O LYS P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA P 46 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA P 49 " --> pdb=" O ALA P 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL P 65 " --> pdb=" O GLN P 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS P 66 " --> pdb=" O SER P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 74 through 79 removed outlier: 4.529A pdb=" N GLN P 77 " --> pdb=" O ALA P 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE Q 16 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA Q 36 " --> pdb=" O ASP Q 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS Q 37 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL Q 65 " --> pdb=" O GLN Q 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS Q 66 " --> pdb=" O SER Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN Q 77 " --> pdb=" O ALA Q 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE R 16 " --> pdb=" O VAL R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR R 28 " --> pdb=" O GLN R 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA R 36 " --> pdb=" O ASP R 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL R 65 " --> pdb=" O GLN R 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS R 66 " --> pdb=" O SER R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN R 77 " --> pdb=" O ALA R 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE S 16 " --> pdb=" O VAL S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR S 28 " --> pdb=" O GLN S 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA S 36 " --> pdb=" O ASP S 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS S 37 " --> pdb=" O LYS S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA S 46 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL S 65 " --> pdb=" O GLN S 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS S 66 " --> pdb=" O SER S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN S 77 " --> pdb=" O ALA S 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE T 16 " --> pdb=" O VAL T 12 " (cutoff:3.500A) Processing helix chain 'T' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR T 28 " --> pdb=" O GLN T 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA T 36 " --> pdb=" O ASP T 32 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS T 37 " --> pdb=" O LYS T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA T 46 " --> pdb=" O ALA T 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL T 65 " --> pdb=" O GLN T 61 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS T 66 " --> pdb=" O SER T 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN T 77 " --> pdb=" O ALA T 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE K 16 " --> pdb=" O VAL K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR K 28 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA K 36 " --> pdb=" O ASP K 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS K 37 " --> pdb=" O LYS K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA K 46 " --> pdb=" O ALA K 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL K 65 " --> pdb=" O GLN K 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS K 66 " --> pdb=" O SER K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN K 77 " --> pdb=" O ALA K 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE L 16 " --> pdb=" O VAL L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR L 28 " --> pdb=" O GLN L 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA L 36 " --> pdb=" O ASP L 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS L 37 " --> pdb=" O LYS L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 73 removed outlier: 3.729A pdb=" N ALA L 46 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA L 49 " --> pdb=" O ALA L 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL L 65 " --> pdb=" O GLN L 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS L 66 " --> pdb=" O SER L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN L 77 " --> pdb=" O ALA L 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE M 16 " --> pdb=" O VAL M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR M 28 " --> pdb=" O GLN M 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA M 36 " --> pdb=" O ASP M 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS M 37 " --> pdb=" O LYS M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 73 removed outlier: 3.731A pdb=" N ALA M 46 " --> pdb=" O ALA M 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL M 65 " --> pdb=" O GLN M 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS M 66 " --> pdb=" O SER M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN M 77 " --> pdb=" O ALA M 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE N 16 " --> pdb=" O VAL N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR N 28 " --> pdb=" O GLN N 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS N 37 " --> pdb=" O LYS N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 73 removed outlier: 3.729A pdb=" N ALA N 46 " --> pdb=" O ALA N 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA N 49 " --> pdb=" O ALA N 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL N 65 " --> pdb=" O GLN N 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS N 66 " --> pdb=" O SER N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 79 removed outlier: 4.527A pdb=" N GLN N 77 " --> pdb=" O ALA N 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE O 16 " --> pdb=" O VAL O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA O 36 " --> pdb=" O ASP O 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS O 37 " --> pdb=" O LYS O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA O 46 " --> pdb=" O ALA O 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL O 65 " --> pdb=" O GLN O 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS O 66 " --> pdb=" O SER O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN O 77 " --> pdb=" O ALA O 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA F 49 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL F 65 " --> pdb=" O GLN F 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS F 66 " --> pdb=" O SER F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN F 77 " --> pdb=" O ALA F 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE G 16 " --> pdb=" O VAL G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA G 36 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA G 46 " --> pdb=" O ALA G 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL G 65 " --> pdb=" O GLN G 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN G 77 " --> pdb=" O ALA G 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE H 16 " --> pdb=" O VAL H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA H 36 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS H 37 " --> pdb=" O LYS H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 73 removed outlier: 3.729A pdb=" N ALA H 46 " --> pdb=" O ALA H 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA H 49 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL H 65 " --> pdb=" O GLN H 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN H 77 " --> pdb=" O ALA H 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE I 16 " --> pdb=" O VAL I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA I 36 " --> pdb=" O ASP I 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 73 removed outlier: 3.731A pdb=" N ALA I 46 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA I 49 " --> pdb=" O ALA I 45 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL I 65 " --> pdb=" O GLN I 61 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS I 66 " --> pdb=" O SER I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN I 77 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE J 16 " --> pdb=" O VAL J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA J 36 " --> pdb=" O ASP J 32 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS J 37 " --> pdb=" O LYS J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 73 removed outlier: 3.731A pdb=" N ALA J 46 " --> pdb=" O ALA J 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA J 49 " --> pdb=" O ALA J 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL J 65 " --> pdb=" O GLN J 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS J 66 " --> pdb=" O SER J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN J 77 " --> pdb=" O ALA J 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL D 65 " --> pdb=" O GLN D 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS D 66 " --> pdb=" O SER D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN D 77 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 37 removed outlier: 3.913A pdb=" N THR A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 65 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN A 77 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE B 16 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 36 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN B 77 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 20 removed outlier: 3.558A pdb=" N PHE C 16 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR C 28 " --> pdb=" O GLN C 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA C 46 " --> pdb=" O ALA C 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C 65 " --> pdb=" O GLN C 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN C 77 " --> pdb=" O ALA C 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 20 removed outlier: 3.559A pdb=" N PHE E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 37 removed outlier: 3.914A pdb=" N THR E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS E 37 " --> pdb=" O LYS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 73 removed outlier: 3.730A pdb=" N ALA E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL E 65 " --> pdb=" O GLN E 61 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS E 66 " --> pdb=" O SER E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 79 removed outlier: 4.528A pdb=" N GLN E 77 " --> pdb=" O ALA E 74 " (cutoff:3.500A) 920 hydrogen bonds defined for protein. 2640 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 2180 1.29 - 1.35: 1840 1.35 - 1.41: 1193 1.41 - 1.48: 1867 1.48 - 1.54: 5360 Bond restraints: 12440 Sorted by residual: bond pdb=" C LYS J 37 " pdb=" N PRO J 38 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.65e+00 bond pdb=" C LYS T 37 " pdb=" N PRO T 38 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.64e+00 bond pdb=" C LYS G 37 " pdb=" N PRO G 38 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.63e+00 bond pdb=" C LYS C 37 " pdb=" N PRO C 38 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.62e+00 bond pdb=" C LYS L 37 " pdb=" N PRO L 38 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.62e+00 ... (remaining 12435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.63: 13065 0.63 - 1.25: 2821 1.25 - 1.88: 732 1.88 - 2.51: 219 2.51 - 3.13: 103 Bond angle restraints: 16940 Sorted by residual: angle pdb=" NE ARG N 58 " pdb=" CZ ARG N 58 " pdb=" NH1 ARG N 58 " ideal model delta sigma weight residual 121.50 119.93 1.57 1.00e+00 1.00e+00 2.45e+00 angle pdb=" C ILE L 75 " pdb=" N ILE L 76 " pdb=" CA ILE L 76 " ideal model delta sigma weight residual 120.46 122.59 -2.13 1.37e+00 5.33e-01 2.42e+00 angle pdb=" NE ARG J 58 " pdb=" CZ ARG J 58 " pdb=" NH1 ARG J 58 " ideal model delta sigma weight residual 121.50 119.96 1.54 1.00e+00 1.00e+00 2.38e+00 angle pdb=" NE ARG P 58 " pdb=" CZ ARG P 58 " pdb=" NH1 ARG P 58 " ideal model delta sigma weight residual 121.50 119.96 1.54 1.00e+00 1.00e+00 2.38e+00 angle pdb=" NE ARG D 58 " pdb=" CZ ARG D 58 " pdb=" NH1 ARG D 58 " ideal model delta sigma weight residual 121.50 119.96 1.54 1.00e+00 1.00e+00 2.36e+00 ... (remaining 16935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.77: 6306 8.77 - 17.54: 974 17.54 - 26.32: 100 26.32 - 35.09: 80 35.09 - 43.86: 80 Dihedral angle restraints: 7540 sinusoidal: 2880 harmonic: 4660 Sorted by residual: dihedral pdb=" CB LYS R 50 " pdb=" CG LYS R 50 " pdb=" CD LYS R 50 " pdb=" CE LYS R 50 " ideal model delta sinusoidal sigma weight residual 60.00 103.86 -43.86 3 1.50e+01 4.44e-03 7.89e+00 dihedral pdb=" CB LYS G 50 " pdb=" CG LYS G 50 " pdb=" CD LYS G 50 " pdb=" CE LYS G 50 " ideal model delta sinusoidal sigma weight residual 60.00 103.85 -43.85 3 1.50e+01 4.44e-03 7.88e+00 dihedral pdb=" CB LYS F 50 " pdb=" CG LYS F 50 " pdb=" CD LYS F 50 " pdb=" CE LYS F 50 " ideal model delta sinusoidal sigma weight residual 60.00 103.83 -43.83 3 1.50e+01 4.44e-03 7.88e+00 ... (remaining 7537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 588 0.022 - 0.044: 747 0.044 - 0.065: 446 0.065 - 0.087: 139 0.087 - 0.109: 20 Chirality restraints: 1940 Sorted by residual: chirality pdb=" CA PRO I 41 " pdb=" N PRO I 41 " pdb=" C PRO I 41 " pdb=" CB PRO I 41 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.97e-01 chirality pdb=" CA PRO N 41 " pdb=" N PRO N 41 " pdb=" C PRO N 41 " pdb=" CB PRO N 41 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.94e-01 chirality pdb=" CA PRO S 41 " pdb=" N PRO S 41 " pdb=" C PRO S 41 " pdb=" CB PRO S 41 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.94e-01 ... (remaining 1937 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 40 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 41 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP R 40 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO R 41 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO R 41 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 41 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP T 40 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO T 41 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO T 41 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO T 41 " -0.022 5.00e-02 4.00e+02 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4239 2.84 - 3.36: 11891 3.36 - 3.87: 19701 3.87 - 4.39: 24705 4.39 - 4.90: 40716 Nonbonded interactions: 101252 Sorted by model distance: nonbonded pdb=" OD1 ASP T 17 " pdb=" OH TYR T 57 " model vdw 2.325 3.040 nonbonded pdb=" OD1 ASP H 17 " pdb=" OH TYR H 57 " model vdw 2.325 3.040 nonbonded pdb=" OD1 ASP K 17 " pdb=" OH TYR K 57 " model vdw 2.325 3.040 nonbonded pdb=" OD1 ASP P 17 " pdb=" OH TYR P 57 " model vdw 2.325 3.040 nonbonded pdb=" OD1 ASP F 17 " pdb=" OH TYR F 57 " model vdw 2.325 3.040 ... (remaining 101247 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: 0.05 Found NCS groups: ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'D' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.720 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 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 : 0.006 0.031 12440 Z= 0.256 Angle : 0.633 3.134 16940 Z= 0.358 Chirality : 0.041 0.109 1940 Planarity : 0.005 0.040 2220 Dihedral : 10.068 43.861 4500 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.24 (0.12), residues: 1520 helix: -3.97 (0.07), residues: 1320 sheet: None (None), residues: 0 loop : -2.59 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG I 58 TYR 0.009 0.001 TYR D 57 PHE 0.012 0.002 PHE M 79 TRP 0.015 0.003 TRP G 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.26 (12440) covalent geometry : angle 0.63262 / 0.36 (16940) hydrogen bonds : bond 0.22534 / 14.61 ( 920) hydrogen bonds : angle 9.53785 / 6.60 ( 2640) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 47 TYR cc_start: 0.9273 (t80) cc_final: 0.8932 (t80) REVERT: T 15 LYS cc_start: 0.8101 (mttt) cc_final: 0.7744 (tttt) REVERT: T 47 TYR cc_start: 0.9346 (t80) cc_final: 0.9008 (t80) REVERT: K 25 THR cc_start: 0.9286 (m) cc_final: 0.8722 (p) REVERT: K 37 LYS cc_start: 0.8587 (ttmt) cc_final: 0.7938 (tptt) REVERT: K 47 TYR cc_start: 0.9330 (t80) cc_final: 0.9011 (t80) REVERT: K 55 ASN cc_start: 0.8335 (t0) cc_final: 0.8021 (t0) REVERT: L 25 THR cc_start: 0.9141 (m) cc_final: 0.8682 (p) REVERT: L 39 SER cc_start: 0.8965 (m) cc_final: 0.8038 (p) REVERT: L 70 ASP cc_start: 0.8142 (m-30) cc_final: 0.7871 (m-30) REVERT: M 25 THR cc_start: 0.9206 (m) cc_final: 0.8855 (p) REVERT: M 32 ASP cc_start: 0.7748 (m-30) cc_final: 0.7422 (m-30) REVERT: M 39 SER cc_start: 0.9152 (m) cc_final: 0.8522 (p) REVERT: N 39 SER cc_start: 0.9110 (m) cc_final: 0.8397 (p) REVERT: N 47 TYR cc_start: 0.9238 (t80) cc_final: 0.8941 (t80) REVERT: N 55 ASN cc_start: 0.8362 (t0) cc_final: 0.8071 (t0) REVERT: O 39 SER cc_start: 0.8989 (m) cc_final: 0.8054 (p) REVERT: O 52 SER cc_start: 0.8954 (m) cc_final: 0.8700 (p) REVERT: F 37 LYS cc_start: 0.8655 (ttmt) cc_final: 0.7951 (tptp) REVERT: F 39 SER cc_start: 0.8645 (m) cc_final: 0.7835 (m) REVERT: G 37 LYS cc_start: 0.8541 (ttmt) cc_final: 0.7815 (tptt) REVERT: G 39 SER cc_start: 0.8925 (m) cc_final: 0.7320 (m) REVERT: H 37 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7482 (tptt) REVERT: I 37 LYS cc_start: 0.8386 (ttmt) cc_final: 0.7638 (tptt) REVERT: I 57 TYR cc_start: 0.9073 (t80) cc_final: 0.8861 (t80) REVERT: J 37 LYS cc_start: 0.8202 (ttmt) cc_final: 0.7576 (tptt) REVERT: J 55 ASN cc_start: 0.8251 (t0) cc_final: 0.7880 (t0) REVERT: D 24 GLN cc_start: 0.7877 (mp10) cc_final: 0.7666 (mp10) REVERT: D 37 LYS cc_start: 0.8736 (ttmt) cc_final: 0.7633 (tptt) REVERT: A 37 LYS cc_start: 0.8767 (ttmt) cc_final: 0.7670 (tptp) REVERT: B 37 LYS cc_start: 0.8792 (ttmt) cc_final: 0.7830 (tptt) REVERT: C 37 LYS cc_start: 0.8887 (ttmt) cc_final: 0.8088 (tptt) REVERT: E 37 LYS cc_start: 0.9042 (ttmt) cc_final: 0.8153 (tptt) outliers start: 0 outliers final: 0 residues processed: 425 average time/residue: 0.1079 time to fit residues: 66.2509 Evaluate side-chains 332 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 63 ASN T 63 ASN K 63 ASN L 63 ASN M 63 ASN M 78 ASN N 63 ASN O 24 GLN O 78 ASN G 63 ASN J 63 ASN C 78 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.091696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.081427 restraints weight = 21715.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.083807 restraints weight = 10670.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.085405 restraints weight = 6542.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.086475 restraints weight = 4547.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.087245 restraints weight = 3456.170| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 12440 Z= 0.117 Angle : 0.465 6.174 16940 Z= 0.256 Chirality : 0.033 0.097 1940 Planarity : 0.005 0.025 2220 Dihedral : 3.835 13.310 1680 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.38 % Allowed : 15.92 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.17), residues: 1520 helix: -1.06 (0.11), residues: 1380 sheet: None (None), residues: 0 loop : -4.01 (0.41), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 80 TYR 0.008 0.001 TYR J 57 PHE 0.008 0.001 PHE N 16 TRP 0.007 0.001 TRP M 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (12440) covalent geometry : angle 0.46544 / 0.26 (16940) hydrogen bonds : bond 0.03714 / 2.41 ( 920) hydrogen bonds : angle 3.61896 / 2.49 ( 2640) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 344 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7725 (mt-10) REVERT: T 39 SER cc_start: 0.9246 (m) cc_final: 0.8962 (p) REVERT: T 69 LYS cc_start: 0.8588 (tmtp) cc_final: 0.7396 (tttt) REVERT: K 37 LYS cc_start: 0.8573 (ttmt) cc_final: 0.7902 (tptt) REVERT: K 53 GLU cc_start: 0.6667 (mt-10) cc_final: 0.6440 (mt-10) REVERT: K 55 ASN cc_start: 0.8337 (t0) cc_final: 0.7986 (t0) REVERT: L 25 THR cc_start: 0.9069 (m) cc_final: 0.8848 (p) REVERT: L 39 SER cc_start: 0.8667 (m) cc_final: 0.8329 (p) REVERT: L 47 TYR cc_start: 0.9168 (t80) cc_final: 0.8965 (t80) REVERT: L 70 ASP cc_start: 0.7978 (m-30) cc_final: 0.7731 (m-30) REVERT: N 39 SER cc_start: 0.8793 (m) cc_final: 0.8535 (p) REVERT: O 52 SER cc_start: 0.9004 (m) cc_final: 0.8739 (p) REVERT: F 37 LYS cc_start: 0.8632 (ttmt) cc_final: 0.7862 (tptp) REVERT: G 37 LYS cc_start: 0.8541 (ttmt) cc_final: 0.7789 (tptt) REVERT: H 37 LYS cc_start: 0.8273 (ttmt) cc_final: 0.7377 (tptt) REVERT: I 37 LYS cc_start: 0.8433 (ttmt) cc_final: 0.7670 (tptt) REVERT: J 37 LYS cc_start: 0.8358 (ttmt) cc_final: 0.7613 (tptt) REVERT: J 39 SER cc_start: 0.8905 (m) cc_final: 0.8556 (p) REVERT: J 55 ASN cc_start: 0.8263 (t0) cc_final: 0.7958 (t0) REVERT: D 37 LYS cc_start: 0.8658 (ttmt) cc_final: 0.7507 (tptt) REVERT: A 24 GLN cc_start: 0.8322 (mp10) cc_final: 0.7849 (mp10) REVERT: A 33 LYS cc_start: 0.8840 (mtpt) cc_final: 0.8630 (mtpt) REVERT: A 37 LYS cc_start: 0.8679 (ttmt) cc_final: 0.7542 (tptp) REVERT: B 37 LYS cc_start: 0.8652 (ttmt) cc_final: 0.7707 (tptt) REVERT: B 57 TYR cc_start: 0.9333 (OUTLIER) cc_final: 0.8808 (t80) REVERT: C 37 LYS cc_start: 0.8831 (ttmt) cc_final: 0.7858 (tptt) REVERT: C 40 ASP cc_start: 0.8012 (t0) cc_final: 0.7804 (t0) REVERT: E 37 LYS cc_start: 0.9019 (ttmt) cc_final: 0.8191 (tptp) outliers start: 18 outliers final: 9 residues processed: 349 average time/residue: 0.1096 time to fit residues: 54.9782 Evaluate side-chains 313 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 303 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain E residue 57 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 63 ASN L 24 GLN N 55 ASN C 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.091475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.080899 restraints weight = 21790.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.083332 restraints weight = 10936.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.084896 restraints weight = 6767.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.086016 restraints weight = 4781.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.086772 restraints weight = 3634.748| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12440 Z= 0.102 Angle : 0.423 6.359 16940 Z= 0.224 Chirality : 0.033 0.103 1940 Planarity : 0.003 0.029 2220 Dihedral : 3.581 14.041 1680 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.23 % Allowed : 21.08 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.20), residues: 1520 helix: 0.71 (0.13), residues: 1360 sheet: None (None), residues: 0 loop : -2.25 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 80 TYR 0.009 0.001 TYR O 54 PHE 0.006 0.001 PHE O 16 TRP 0.005 0.001 TRP G 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (12440) covalent geometry : angle 0.42331 / 0.22 (16940) hydrogen bonds : bond 0.03028 / 1.97 ( 920) hydrogen bonds : angle 3.06084 / 2.09 ( 2640) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 308 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: R 25 THR cc_start: 0.9069 (m) cc_final: 0.8749 (t) REVERT: K 37 LYS cc_start: 0.8462 (ttmt) cc_final: 0.7846 (tptt) REVERT: K 53 GLU cc_start: 0.6552 (mt-10) cc_final: 0.6347 (mt-10) REVERT: K 55 ASN cc_start: 0.8297 (t0) cc_final: 0.8013 (t0) REVERT: N 39 SER cc_start: 0.8736 (m) cc_final: 0.8250 (p) REVERT: O 47 TYR cc_start: 0.9063 (t80) cc_final: 0.8858 (t80) REVERT: O 52 SER cc_start: 0.9100 (m) cc_final: 0.8701 (p) REVERT: F 37 LYS cc_start: 0.8632 (ttmt) cc_final: 0.7785 (tptp) REVERT: G 37 LYS cc_start: 0.8518 (ttmt) cc_final: 0.7948 (tptp) REVERT: H 37 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7428 (tptt) REVERT: H 53 GLU cc_start: 0.8215 (tp30) cc_final: 0.8012 (tp30) REVERT: I 37 LYS cc_start: 0.8475 (ttmt) cc_final: 0.7587 (tptt) REVERT: I 55 ASN cc_start: 0.8333 (t0) cc_final: 0.8031 (t0) REVERT: J 37 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7453 (tptt) REVERT: J 55 ASN cc_start: 0.8252 (t0) cc_final: 0.7755 (t0) REVERT: D 37 LYS cc_start: 0.8671 (ttmt) cc_final: 0.7533 (tptt) REVERT: A 22 ASN cc_start: 0.7958 (p0) cc_final: 0.7727 (p0) REVERT: A 24 GLN cc_start: 0.8307 (mp10) cc_final: 0.7955 (mp10) REVERT: A 37 LYS cc_start: 0.8621 (ttmt) cc_final: 0.7557 (tptp) REVERT: B 37 LYS cc_start: 0.8701 (ttmt) cc_final: 0.7774 (tptt) REVERT: B 55 ASN cc_start: 0.8694 (t0) cc_final: 0.8386 (t0) REVERT: C 37 LYS cc_start: 0.8720 (ttmt) cc_final: 0.7827 (tptt) REVERT: C 53 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7689 (mm-30) REVERT: E 37 LYS cc_start: 0.9052 (ttmt) cc_final: 0.8224 (tptp) REVERT: E 53 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7790 (mm-30) outliers start: 16 outliers final: 10 residues processed: 317 average time/residue: 0.1025 time to fit residues: 47.2615 Evaluate side-chains 295 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 285 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain E residue 57 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 136 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 87 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.091127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.080640 restraints weight = 21697.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.083025 restraints weight = 10877.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.084630 restraints weight = 6718.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.085723 restraints weight = 4706.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.086484 restraints weight = 3584.183| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12440 Z= 0.100 Angle : 0.411 5.755 16940 Z= 0.217 Chirality : 0.033 0.101 1940 Planarity : 0.003 0.029 2220 Dihedral : 3.472 13.947 1680 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.62 % Allowed : 22.15 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.21), residues: 1520 helix: 1.53 (0.13), residues: 1360 sheet: None (None), residues: 0 loop : -1.99 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 80 TYR 0.009 0.001 TYR O 54 PHE 0.005 0.001 PHE N 16 TRP 0.004 0.001 TRP F 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (12440) covalent geometry : angle 0.41084 / 0.22 (16940) hydrogen bonds : bond 0.02757 / 1.80 ( 920) hydrogen bonds : angle 2.88588 / 1.97 ( 2640) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 306 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7553 (mt-10) REVERT: Q 37 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8515 (ttmm) REVERT: T 62 SER cc_start: 0.9405 (t) cc_final: 0.8985 (t) REVERT: K 18 THR cc_start: 0.8769 (p) cc_final: 0.8535 (t) REVERT: K 37 LYS cc_start: 0.8411 (ttmt) cc_final: 0.7744 (tptt) REVERT: K 53 GLU cc_start: 0.6548 (mt-10) cc_final: 0.6342 (mt-10) REVERT: K 55 ASN cc_start: 0.8325 (t0) cc_final: 0.8038 (t0) REVERT: L 22 ASN cc_start: 0.7540 (p0) cc_final: 0.7230 (p0) REVERT: M 47 TYR cc_start: 0.9094 (t80) cc_final: 0.8688 (t80) REVERT: N 39 SER cc_start: 0.8722 (m) cc_final: 0.8518 (p) REVERT: O 47 TYR cc_start: 0.9111 (t80) cc_final: 0.8878 (t80) REVERT: O 52 SER cc_start: 0.9107 (m) cc_final: 0.8729 (p) REVERT: F 37 LYS cc_start: 0.8623 (ttmt) cc_final: 0.7823 (tptp) REVERT: G 37 LYS cc_start: 0.8472 (ttmt) cc_final: 0.7879 (tptp) REVERT: H 37 LYS cc_start: 0.8298 (ttmt) cc_final: 0.7364 (tptt) REVERT: I 37 LYS cc_start: 0.8408 (ttmt) cc_final: 0.7494 (tptt) REVERT: I 55 ASN cc_start: 0.8346 (t0) cc_final: 0.8071 (t0) REVERT: J 37 LYS cc_start: 0.8153 (ttmt) cc_final: 0.7374 (tptt) REVERT: J 53 GLU cc_start: 0.8354 (tp30) cc_final: 0.8153 (mm-30) REVERT: J 55 ASN cc_start: 0.8347 (t0) cc_final: 0.8027 (t0) REVERT: D 37 LYS cc_start: 0.8720 (ttmt) cc_final: 0.7590 (tptt) REVERT: A 24 GLN cc_start: 0.8281 (mp10) cc_final: 0.7969 (mp10) REVERT: A 37 LYS cc_start: 0.8633 (ttmt) cc_final: 0.7564 (tptp) REVERT: B 37 LYS cc_start: 0.8701 (ttmt) cc_final: 0.7743 (tptt) REVERT: B 53 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7769 (mm-30) REVERT: B 55 ASN cc_start: 0.8723 (t0) cc_final: 0.8412 (t0) REVERT: C 37 LYS cc_start: 0.8731 (ttmt) cc_final: 0.7826 (tptt) REVERT: E 37 LYS cc_start: 0.9054 (ttmt) cc_final: 0.8222 (tptp) REVERT: E 53 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7634 (mm-30) REVERT: E 55 ASN cc_start: 0.8498 (t0) cc_final: 0.8247 (t0) outliers start: 21 outliers final: 18 residues processed: 321 average time/residue: 0.1067 time to fit residues: 50.1058 Evaluate side-chains 310 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 292 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain M residue 53 GLU Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain J residue 21 ASP Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 62 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 85 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 55 ASN Q 63 ASN ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN M 78 ASN N 24 GLN N 55 ASN ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN C 24 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.087099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.076518 restraints weight = 22005.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.078853 restraints weight = 11135.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.080391 restraints weight = 6938.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.081506 restraints weight = 4931.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.082298 restraints weight = 3771.215| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12440 Z= 0.179 Angle : 0.481 6.234 16940 Z= 0.254 Chirality : 0.036 0.112 1940 Planarity : 0.003 0.028 2220 Dihedral : 3.776 18.985 1680 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.08 % Allowed : 21.08 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.21), residues: 1520 helix: 1.93 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.74 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 80 TYR 0.015 0.002 TYR P 54 PHE 0.008 0.001 PHE D 68 TRP 0.008 0.001 TRP E 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (12440) covalent geometry : angle 0.48054 / 0.25 (16940) hydrogen bonds : bond 0.03049 / 1.98 ( 920) hydrogen bonds : angle 3.10016 / 2.12 ( 2640) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 318 time to evaluate : 0.360 Fit side-chains REVERT: Q 29 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7547 (mt-10) REVERT: Q 37 LYS cc_start: 0.8737 (ttmm) cc_final: 0.8486 (ttmm) REVERT: S 62 SER cc_start: 0.9168 (t) cc_final: 0.8926 (t) REVERT: K 37 LYS cc_start: 0.8415 (ttmt) cc_final: 0.7760 (tptt) REVERT: K 55 ASN cc_start: 0.8466 (t0) cc_final: 0.8170 (t0) REVERT: K 57 TYR cc_start: 0.9277 (OUTLIER) cc_final: 0.8440 (t80) REVERT: L 22 ASN cc_start: 0.7733 (p0) cc_final: 0.7479 (p0) REVERT: O 47 TYR cc_start: 0.9203 (t80) cc_final: 0.8964 (t80) REVERT: O 52 SER cc_start: 0.9141 (m) cc_final: 0.8766 (p) REVERT: F 22 ASN cc_start: 0.8123 (p0) cc_final: 0.7815 (p0) REVERT: F 37 LYS cc_start: 0.8666 (ttmt) cc_final: 0.7829 (tptp) REVERT: G 24 GLN cc_start: 0.8217 (mp10) cc_final: 0.7866 (mp10) REVERT: G 37 LYS cc_start: 0.8481 (ttmt) cc_final: 0.7933 (tptp) REVERT: H 37 LYS cc_start: 0.8310 (ttmt) cc_final: 0.7465 (tptp) REVERT: I 22 ASN cc_start: 0.8183 (p0) cc_final: 0.7881 (p0) REVERT: I 37 LYS cc_start: 0.8479 (ttmt) cc_final: 0.7634 (tptt) REVERT: I 55 ASN cc_start: 0.8464 (t0) cc_final: 0.8236 (t0) REVERT: J 17 ASP cc_start: 0.8218 (m-30) cc_final: 0.7997 (m-30) REVERT: J 37 LYS cc_start: 0.8125 (ttmt) cc_final: 0.7438 (tptt) REVERT: J 53 GLU cc_start: 0.8330 (tp30) cc_final: 0.8020 (mm-30) REVERT: J 55 ASN cc_start: 0.8400 (t0) cc_final: 0.8143 (t0) REVERT: D 33 LYS cc_start: 0.8959 (mtpt) cc_final: 0.8668 (mtmt) REVERT: D 37 LYS cc_start: 0.8793 (ttmt) cc_final: 0.7652 (tptt) REVERT: A 10 ASP cc_start: 0.8332 (m-30) cc_final: 0.8043 (m-30) REVERT: A 22 ASN cc_start: 0.8055 (p0) cc_final: 0.7844 (p0) REVERT: A 24 GLN cc_start: 0.8362 (mp10) cc_final: 0.8066 (mp10) REVERT: A 37 LYS cc_start: 0.8691 (ttmt) cc_final: 0.7538 (tptp) REVERT: B 37 LYS cc_start: 0.8698 (ttmt) cc_final: 0.7597 (tptt) REVERT: B 53 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7693 (mm-30) REVERT: B 57 TYR cc_start: 0.9356 (OUTLIER) cc_final: 0.9036 (t80) REVERT: C 22 ASN cc_start: 0.8218 (p0) cc_final: 0.7875 (p0) REVERT: C 37 LYS cc_start: 0.8951 (ttmt) cc_final: 0.7993 (tptt) REVERT: E 37 LYS cc_start: 0.9105 (ttmt) cc_final: 0.8209 (tptp) REVERT: E 53 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7394 (mm-30) outliers start: 40 outliers final: 27 residues processed: 343 average time/residue: 0.1004 time to fit residues: 50.4678 Evaluate side-chains 330 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 301 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain S residue 57 TYR Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 77 GLN Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 62 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 107 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 36 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.5476 > 50:) chunk 109 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 26 GLN ** H 55 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 = 0.3087 r_free = 0.3087 target = 0.087707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.077261 restraints weight = 21916.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.079613 restraints weight = 11009.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.081206 restraints weight = 6808.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.082274 restraints weight = 4768.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.083059 restraints weight = 3647.288| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12440 Z= 0.125 Angle : 0.443 5.816 16940 Z= 0.232 Chirality : 0.035 0.105 1940 Planarity : 0.003 0.030 2220 Dihedral : 3.679 18.631 1680 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.46 % Allowed : 22.69 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.21), residues: 1520 helix: 2.10 (0.14), residues: 1340 sheet: None (None), residues: 0 loop : -1.48 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 80 TYR 0.010 0.001 TYR N 54 PHE 0.005 0.001 PHE R 68 TRP 0.005 0.001 TRP E 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (12440) covalent geometry : angle 0.44268 / 0.23 (16940) hydrogen bonds : bond 0.02804 / 1.83 ( 920) hydrogen bonds : angle 2.96001 / 2.02 ( 2640) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 318 time to evaluate : 0.442 Fit side-chains REVERT: Q 29 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7534 (mt-10) REVERT: Q 37 LYS cc_start: 0.8657 (ttmm) cc_final: 0.8343 (ttmm) REVERT: S 62 SER cc_start: 0.9151 (t) cc_final: 0.8935 (t) REVERT: T 5 TRP cc_start: 0.8869 (t60) cc_final: 0.8614 (t60) REVERT: T 62 SER cc_start: 0.9373 (t) cc_final: 0.8953 (t) REVERT: K 37 LYS cc_start: 0.8401 (ttmt) cc_final: 0.7738 (tptt) REVERT: K 55 ASN cc_start: 0.8411 (t0) cc_final: 0.8129 (t0) REVERT: K 57 TYR cc_start: 0.9213 (OUTLIER) cc_final: 0.8328 (t80) REVERT: L 22 ASN cc_start: 0.7790 (p0) cc_final: 0.7502 (p0) REVERT: M 53 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8047 (tp30) REVERT: N 32 ASP cc_start: 0.7879 (m-30) cc_final: 0.7667 (m-30) REVERT: O 47 TYR cc_start: 0.9172 (t80) cc_final: 0.8929 (t80) REVERT: O 52 SER cc_start: 0.9130 (m) cc_final: 0.8754 (p) REVERT: F 22 ASN cc_start: 0.8151 (p0) cc_final: 0.7834 (p0) REVERT: F 37 LYS cc_start: 0.8643 (ttmt) cc_final: 0.7800 (tptp) REVERT: G 24 GLN cc_start: 0.8258 (mp10) cc_final: 0.7877 (mp10) REVERT: G 37 LYS cc_start: 0.8478 (ttmt) cc_final: 0.7896 (tptp) REVERT: H 37 LYS cc_start: 0.8308 (ttmt) cc_final: 0.7442 (tptp) REVERT: I 22 ASN cc_start: 0.8242 (p0) cc_final: 0.7900 (p0) REVERT: I 55 ASN cc_start: 0.8334 (t0) cc_final: 0.8029 (t0) REVERT: J 17 ASP cc_start: 0.8196 (m-30) cc_final: 0.7963 (m-30) REVERT: J 37 LYS cc_start: 0.8136 (ttmt) cc_final: 0.7436 (tptt) REVERT: J 53 GLU cc_start: 0.8383 (tp30) cc_final: 0.8053 (mm-30) REVERT: J 55 ASN cc_start: 0.8316 (t0) cc_final: 0.8099 (t0) REVERT: D 37 LYS cc_start: 0.8768 (ttmt) cc_final: 0.7640 (tptt) REVERT: A 22 ASN cc_start: 0.8102 (p0) cc_final: 0.7856 (p0) REVERT: A 24 GLN cc_start: 0.8379 (mp10) cc_final: 0.8020 (mp10) REVERT: A 37 LYS cc_start: 0.8664 (ttmt) cc_final: 0.7517 (tptp) REVERT: B 37 LYS cc_start: 0.8658 (ttmt) cc_final: 0.7567 (tptt) REVERT: B 53 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7749 (mm-30) REVERT: B 57 TYR cc_start: 0.9309 (OUTLIER) cc_final: 0.8942 (t80) REVERT: E 37 LYS cc_start: 0.9095 (ttmt) cc_final: 0.8202 (tptp) outliers start: 32 outliers final: 27 residues processed: 344 average time/residue: 0.1016 time to fit residues: 51.3742 Evaluate side-chains 331 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 302 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain S residue 57 TYR Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 77 GLN Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 26 GLN Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 77 GLN Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 62 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 103 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN H 26 GLN ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.087347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.077103 restraints weight = 21972.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.079392 restraints weight = 11345.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.080915 restraints weight = 7069.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.081943 restraints weight = 5036.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.082706 restraints weight = 3897.088| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12440 Z= 0.133 Angle : 0.447 5.719 16940 Z= 0.234 Chirality : 0.035 0.106 1940 Planarity : 0.003 0.025 2220 Dihedral : 3.669 19.143 1680 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.69 % Allowed : 23.15 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.21), residues: 1520 helix: 2.25 (0.14), residues: 1340 sheet: None (None), residues: 0 loop : -1.48 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 80 TYR 0.011 0.001 TYR M 54 PHE 0.006 0.001 PHE N 16 TRP 0.005 0.001 TRP E 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (12440) covalent geometry : angle 0.44732 / 0.23 (16940) hydrogen bonds : bond 0.02777 / 1.81 ( 920) hydrogen bonds : angle 2.94128 / 2.01 ( 2640) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 313 time to evaluate : 0.454 Fit side-chains REVERT: P 15 LYS cc_start: 0.7496 (mmtt) cc_final: 0.5869 (tttt) REVERT: Q 29 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7515 (mt-10) REVERT: Q 37 LYS cc_start: 0.8725 (ttmm) cc_final: 0.8423 (ttmm) REVERT: S 62 SER cc_start: 0.9165 (t) cc_final: 0.8887 (t) REVERT: T 5 TRP cc_start: 0.8863 (t60) cc_final: 0.8593 (t60) REVERT: T 62 SER cc_start: 0.9392 (t) cc_final: 0.8996 (t) REVERT: K 37 LYS cc_start: 0.8417 (ttmt) cc_final: 0.7787 (tptt) REVERT: K 55 ASN cc_start: 0.8416 (t0) cc_final: 0.8137 (t0) REVERT: K 57 TYR cc_start: 0.9250 (OUTLIER) cc_final: 0.8370 (t80) REVERT: L 22 ASN cc_start: 0.7937 (p0) cc_final: 0.7676 (p0) REVERT: O 47 TYR cc_start: 0.9181 (t80) cc_final: 0.8935 (t80) REVERT: O 52 SER cc_start: 0.9153 (m) cc_final: 0.8787 (p) REVERT: F 22 ASN cc_start: 0.8147 (p0) cc_final: 0.7855 (p0) REVERT: F 37 LYS cc_start: 0.8602 (ttmt) cc_final: 0.7767 (tptp) REVERT: G 37 LYS cc_start: 0.8499 (ttmt) cc_final: 0.8021 (tptp) REVERT: H 37 LYS cc_start: 0.8302 (ttmt) cc_final: 0.7519 (tptp) REVERT: I 22 ASN cc_start: 0.8273 (p0) cc_final: 0.7869 (p0) REVERT: I 55 ASN cc_start: 0.8403 (t0) cc_final: 0.8135 (t0) REVERT: J 17 ASP cc_start: 0.8162 (m-30) cc_final: 0.7955 (m-30) REVERT: J 37 LYS cc_start: 0.8153 (ttmt) cc_final: 0.7453 (tptt) REVERT: J 53 GLU cc_start: 0.8366 (tp30) cc_final: 0.8041 (mm-30) REVERT: J 55 ASN cc_start: 0.8338 (t0) cc_final: 0.8125 (t0) REVERT: D 37 LYS cc_start: 0.8793 (ttmt) cc_final: 0.7689 (tptt) REVERT: A 22 ASN cc_start: 0.8085 (p0) cc_final: 0.7852 (p0) REVERT: A 24 GLN cc_start: 0.8324 (mp10) cc_final: 0.7978 (mp10) REVERT: A 37 LYS cc_start: 0.8673 (ttmt) cc_final: 0.7535 (tptp) REVERT: B 37 LYS cc_start: 0.8717 (ttmt) cc_final: 0.7646 (tptt) REVERT: B 53 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7739 (mm-30) REVERT: B 57 TYR cc_start: 0.9333 (OUTLIER) cc_final: 0.8953 (t80) REVERT: E 37 LYS cc_start: 0.9118 (ttmt) cc_final: 0.8261 (tptp) outliers start: 35 outliers final: 30 residues processed: 340 average time/residue: 0.0988 time to fit residues: 49.7199 Evaluate side-chains 334 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 302 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain S residue 57 TYR Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 77 GLN Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 77 GLN Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 62 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 0 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN E 26 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.086608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.076356 restraints weight = 22052.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.078578 restraints weight = 11410.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.080127 restraints weight = 7230.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.081185 restraints weight = 5126.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.081902 restraints weight = 3932.936| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12440 Z= 0.148 Angle : 0.470 6.657 16940 Z= 0.244 Chirality : 0.035 0.106 1940 Planarity : 0.003 0.025 2220 Dihedral : 3.715 20.045 1680 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.77 % Allowed : 23.69 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.21), residues: 1520 helix: 2.30 (0.13), residues: 1340 sheet: None (None), residues: 0 loop : -1.51 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 80 TYR 0.014 0.001 TYR S 47 PHE 0.006 0.001 PHE G 68 TRP 0.006 0.001 TRP E 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (12440) covalent geometry : angle 0.46958 / 0.24 (16940) hydrogen bonds : bond 0.02811 / 1.83 ( 920) hydrogen bonds : angle 2.96628 / 2.03 ( 2640) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 312 time to evaluate : 0.364 Fit side-chains REVERT: P 15 LYS cc_start: 0.7537 (mmtt) cc_final: 0.5852 (tttt) REVERT: Q 29 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7539 (mt-10) REVERT: R 62 SER cc_start: 0.9191 (t) cc_final: 0.8795 (t) REVERT: S 5 TRP cc_start: 0.8653 (t60) cc_final: 0.8368 (t60) REVERT: S 62 SER cc_start: 0.9166 (t) cc_final: 0.8906 (t) REVERT: T 5 TRP cc_start: 0.8877 (t60) cc_final: 0.8532 (t60) REVERT: T 62 SER cc_start: 0.9382 (t) cc_final: 0.8990 (t) REVERT: K 37 LYS cc_start: 0.8452 (ttmt) cc_final: 0.7823 (tptt) REVERT: K 55 ASN cc_start: 0.8435 (t0) cc_final: 0.8147 (t0) REVERT: K 57 TYR cc_start: 0.9259 (OUTLIER) cc_final: 0.8380 (t80) REVERT: L 22 ASN cc_start: 0.7989 (p0) cc_final: 0.7712 (p0) REVERT: O 47 TYR cc_start: 0.9182 (t80) cc_final: 0.8940 (t80) REVERT: O 52 SER cc_start: 0.9157 (m) cc_final: 0.8801 (p) REVERT: F 22 ASN cc_start: 0.8041 (p0) cc_final: 0.7766 (p0) REVERT: F 37 LYS cc_start: 0.8618 (ttmt) cc_final: 0.7811 (tptp) REVERT: G 24 GLN cc_start: 0.8199 (mp10) cc_final: 0.7835 (mp10) REVERT: G 29 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7907 (mt-10) REVERT: G 37 LYS cc_start: 0.8516 (ttmt) cc_final: 0.7947 (tptp) REVERT: H 37 LYS cc_start: 0.8351 (ttmt) cc_final: 0.7562 (tptp) REVERT: I 22 ASN cc_start: 0.8330 (p0) cc_final: 0.7918 (p0) REVERT: I 55 ASN cc_start: 0.8434 (t0) cc_final: 0.8149 (t0) REVERT: J 17 ASP cc_start: 0.8216 (m-30) cc_final: 0.7988 (m-30) REVERT: J 37 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7558 (tptt) REVERT: J 53 GLU cc_start: 0.8360 (tp30) cc_final: 0.8061 (mm-30) REVERT: J 55 ASN cc_start: 0.8361 (t0) cc_final: 0.8144 (t0) REVERT: D 37 LYS cc_start: 0.8803 (ttmt) cc_final: 0.7674 (tptt) REVERT: A 22 ASN cc_start: 0.8073 (p0) cc_final: 0.7843 (p0) REVERT: A 24 GLN cc_start: 0.8335 (mp10) cc_final: 0.7984 (mp10) REVERT: A 37 LYS cc_start: 0.8660 (ttmt) cc_final: 0.7481 (tptp) REVERT: B 37 LYS cc_start: 0.8728 (ttmt) cc_final: 0.7641 (tptt) REVERT: B 53 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7754 (mm-30) REVERT: B 57 TYR cc_start: 0.9362 (OUTLIER) cc_final: 0.8996 (t80) REVERT: E 37 LYS cc_start: 0.9125 (ttmt) cc_final: 0.8246 (tptp) outliers start: 36 outliers final: 28 residues processed: 340 average time/residue: 0.0984 time to fit residues: 49.7462 Evaluate side-chains 340 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 310 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain S residue 57 TYR Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 77 GLN Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 77 GLN Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 62 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 64 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 GLN ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.087995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.077746 restraints weight = 21835.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.080079 restraints weight = 11274.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.081623 restraints weight = 7004.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.082660 restraints weight = 4963.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.083402 restraints weight = 3821.029| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12440 Z= 0.109 Angle : 0.437 6.083 16940 Z= 0.227 Chirality : 0.034 0.100 1940 Planarity : 0.003 0.027 2220 Dihedral : 3.587 17.781 1680 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.00 % Allowed : 24.69 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.30 (0.21), residues: 1520 helix: 2.63 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -1.12 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 80 TYR 0.009 0.001 TYR S 47 PHE 0.004 0.001 PHE O 16 TRP 0.004 0.001 TRP E 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (12440) covalent geometry : angle 0.43734 / 0.23 (16940) hydrogen bonds : bond 0.02643 / 1.72 ( 920) hydrogen bonds : angle 2.85765 / 1.95 ( 2640) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 324 time to evaluate : 0.502 Fit side-chains REVERT: P 15 LYS cc_start: 0.7491 (mmtt) cc_final: 0.5785 (tttt) REVERT: Q 29 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7535 (mt-10) REVERT: Q 37 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8395 (ttmm) REVERT: R 62 SER cc_start: 0.9311 (t) cc_final: 0.8989 (t) REVERT: S 62 SER cc_start: 0.9328 (t) cc_final: 0.9099 (t) REVERT: T 62 SER cc_start: 0.9447 (t) cc_final: 0.9073 (t) REVERT: K 37 LYS cc_start: 0.8426 (ttmt) cc_final: 0.7872 (tptp) REVERT: K 55 ASN cc_start: 0.8384 (t0) cc_final: 0.8107 (t0) REVERT: K 57 TYR cc_start: 0.9211 (OUTLIER) cc_final: 0.8317 (t80) REVERT: L 22 ASN cc_start: 0.7944 (p0) cc_final: 0.7672 (p0) REVERT: L 61 GLN cc_start: 0.8792 (tt0) cc_final: 0.8495 (tt0) REVERT: M 47 TYR cc_start: 0.9119 (t80) cc_final: 0.8708 (t80) REVERT: O 47 TYR cc_start: 0.9156 (t80) cc_final: 0.8920 (t80) REVERT: O 52 SER cc_start: 0.9199 (m) cc_final: 0.8827 (p) REVERT: F 22 ASN cc_start: 0.8009 (p0) cc_final: 0.7742 (p0) REVERT: F 37 LYS cc_start: 0.8661 (ttmt) cc_final: 0.7803 (tptp) REVERT: G 24 GLN cc_start: 0.8191 (mp10) cc_final: 0.7822 (mp10) REVERT: G 29 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7889 (mt-10) REVERT: G 37 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8024 (tptp) REVERT: H 37 LYS cc_start: 0.8328 (ttmt) cc_final: 0.7540 (tptp) REVERT: I 22 ASN cc_start: 0.8309 (p0) cc_final: 0.7981 (t0) REVERT: I 55 ASN cc_start: 0.8381 (t0) cc_final: 0.8096 (t0) REVERT: J 17 ASP cc_start: 0.8181 (m-30) cc_final: 0.7972 (m-30) REVERT: J 37 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7472 (tptt) REVERT: J 53 GLU cc_start: 0.8375 (tp30) cc_final: 0.8049 (mm-30) REVERT: J 55 ASN cc_start: 0.8318 (t0) cc_final: 0.8114 (t0) REVERT: D 37 LYS cc_start: 0.8821 (ttmt) cc_final: 0.7598 (tptt) REVERT: A 22 ASN cc_start: 0.8040 (p0) cc_final: 0.7811 (p0) REVERT: A 24 GLN cc_start: 0.8316 (mp10) cc_final: 0.7960 (mp10) REVERT: A 31 LEU cc_start: 0.9203 (tt) cc_final: 0.8987 (tt) REVERT: A 37 LYS cc_start: 0.8613 (ttmt) cc_final: 0.7444 (tptp) REVERT: B 37 LYS cc_start: 0.8687 (ttmt) cc_final: 0.7541 (tptt) REVERT: B 53 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7672 (mm-30) REVERT: E 37 LYS cc_start: 0.9062 (ttmt) cc_final: 0.8174 (tptp) REVERT: E 53 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7585 (mm-30) outliers start: 26 outliers final: 24 residues processed: 344 average time/residue: 0.1017 time to fit residues: 51.9146 Evaluate side-chains 342 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 317 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain S residue 57 TYR Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain K residue 53 GLU Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 77 GLN Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 123 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 91 optimal weight: 0.9980 chunk 101 optimal weight: 0.0030 chunk 88 optimal weight: 1.9990 chunk 112 optimal weight: 0.0980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.089920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.079808 restraints weight = 21868.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.082095 restraints weight = 11155.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.083617 restraints weight = 6953.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.084704 restraints weight = 4905.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.085319 restraints weight = 3724.877| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12440 Z= 0.089 Angle : 0.431 6.424 16940 Z= 0.222 Chirality : 0.033 0.099 1940 Planarity : 0.003 0.027 2220 Dihedral : 3.432 15.408 1680 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.46 % Allowed : 25.46 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.66 (0.21), residues: 1520 helix: 2.87 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.97 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 80 TYR 0.010 0.001 TYR M 54 PHE 0.005 0.001 PHE N 16 TRP 0.005 0.000 TRP S 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 (12440) covalent geometry : angle 0.43093 / 0.22 (16940) hydrogen bonds : bond 0.02511 / 1.63 ( 920) hydrogen bonds : angle 2.78542 / 1.90 ( 2640) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 327 time to evaluate : 0.490 Fit side-chains REVERT: P 15 LYS cc_start: 0.7456 (mmtt) cc_final: 0.5873 (tttt) REVERT: Q 29 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7572 (mt-10) REVERT: R 62 SER cc_start: 0.9393 (t) cc_final: 0.9105 (t) REVERT: S 62 SER cc_start: 0.9341 (t) cc_final: 0.9106 (t) REVERT: T 62 SER cc_start: 0.9485 (t) cc_final: 0.9082 (t) REVERT: K 37 LYS cc_start: 0.8308 (ttmt) cc_final: 0.7724 (tptp) REVERT: K 55 ASN cc_start: 0.8341 (t0) cc_final: 0.8068 (t0) REVERT: M 47 TYR cc_start: 0.9048 (t80) cc_final: 0.8710 (t80) REVERT: O 47 TYR cc_start: 0.9159 (t80) cc_final: 0.8931 (t80) REVERT: O 52 SER cc_start: 0.9212 (m) cc_final: 0.8787 (p) REVERT: F 22 ASN cc_start: 0.8101 (p0) cc_final: 0.7849 (p0) REVERT: F 37 LYS cc_start: 0.8691 (ttmt) cc_final: 0.7969 (tptp) REVERT: G 24 GLN cc_start: 0.8174 (mp10) cc_final: 0.7924 (mp10) REVERT: G 37 LYS cc_start: 0.8462 (ttmt) cc_final: 0.7955 (tptp) REVERT: H 37 LYS cc_start: 0.8371 (ttmt) cc_final: 0.7573 (tptp) REVERT: I 22 ASN cc_start: 0.8221 (p0) cc_final: 0.7961 (t0) REVERT: I 55 ASN cc_start: 0.8309 (t0) cc_final: 0.8028 (t0) REVERT: J 37 LYS cc_start: 0.8202 (ttmt) cc_final: 0.7428 (tptt) REVERT: J 53 GLU cc_start: 0.8393 (tp30) cc_final: 0.8064 (mm-30) REVERT: J 55 ASN cc_start: 0.8285 (t0) cc_final: 0.8047 (t0) REVERT: D 37 LYS cc_start: 0.8754 (ttmt) cc_final: 0.7572 (tptt) REVERT: A 22 ASN cc_start: 0.8067 (p0) cc_final: 0.7805 (p0) REVERT: A 24 GLN cc_start: 0.8290 (mp10) cc_final: 0.7941 (mp10) REVERT: A 31 LEU cc_start: 0.9148 (tt) cc_final: 0.8942 (tt) REVERT: A 37 LYS cc_start: 0.8577 (ttmt) cc_final: 0.7410 (tptp) REVERT: B 37 LYS cc_start: 0.8697 (ttmt) cc_final: 0.7552 (tptt) REVERT: E 37 LYS cc_start: 0.9040 (ttmt) cc_final: 0.8223 (tptp) REVERT: E 55 ASN cc_start: 0.8654 (t0) cc_final: 0.8251 (t0) outliers start: 19 outliers final: 17 residues processed: 342 average time/residue: 0.0996 time to fit residues: 50.5711 Evaluate side-chains 323 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 306 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain S residue 57 TYR Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain K residue 53 GLU Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 45 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 GLN L 61 GLN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 78 ASN ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.087979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.077563 restraints weight = 21878.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.079942 restraints weight = 11051.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.081507 restraints weight = 6799.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.082593 restraints weight = 4799.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.083323 restraints weight = 3665.213| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12440 Z= 0.124 Angle : 0.463 5.836 16940 Z= 0.238 Chirality : 0.034 0.104 1940 Planarity : 0.003 0.027 2220 Dihedral : 3.471 15.309 1680 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.38 % Allowed : 25.38 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.70 (0.21), residues: 1520 helix: 2.89 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.94 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 80 TYR 0.017 0.001 TYR N 47 PHE 0.006 0.001 PHE O 16 TRP 0.024 0.001 TRP S 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (12440) covalent geometry : angle 0.46306 / 0.24 (16940) hydrogen bonds : bond 0.02669 / 1.73 ( 920) hydrogen bonds : angle 2.86258 / 1.96 ( 2640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1852.97 seconds wall clock time: 33 minutes 6.74 seconds (1986.74 seconds total)