Starting phenix.real_space_refine on Sat Aug 23 11:52:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ofe_20043/08_2025/6ofe_20043.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ofe_20043/08_2025/6ofe_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_20043/08_2025/6ofe_20043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ofe_20043/08_2025/6ofe_20043.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ofe_20043/08_2025/6ofe_20043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ofe_20043/08_2025/6ofe_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-2.0-5787/lib/python3.9/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: 1.20, per 1000 atoms: 0.10 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: 1.11 Conformation dependent library (CDL) restraints added in 593.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.35 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: 1.94 Time building geometry restraints manager: 1.47 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: 0.03 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.650 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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 aren 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 covalent geometry : bond 0.00600 (12440) covalent geometry : angle 0.63262 (16940) hydrogen bonds : bond 0.22534 ( 920) hydrogen bonds : angle 9.53785 ( 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 : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 47 TYR cc_start: 0.9272 (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: 0.8964 (m) cc_final: 0.8038 (p) REVERT: L 70 ASP cc_start: 0.8141 (m-30) cc_final: 0.7870 (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: 0.7423 (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: 0.8363 (t0) cc_final: 0.8072 (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: 0.8257 (ttmt) cc_final: 0.7481 (tptt) REVERT: I 37 LYS cc_start: 0.8387 (ttmt) cc_final: 0.7639 (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: 0.8252 (t0) cc_final: 0.7881 (t0) REVERT: D 24 GLN cc_start: 0.7878 (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: 0.8793 (ttmt) cc_final: 0.7831 (tptt) REVERT: C 37 LYS cc_start: 0.8887 (ttmt) cc_final: 0.8087 (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: 0.1049 time to fit residues: 63.5095 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 : 0.356 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.8312 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 aren 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 covalent geometry : bond 0.00236 (12440) covalent geometry : angle 0.46544 (16940) hydrogen bonds : bond 0.03714 ( 920) hydrogen bonds : angle 3.61896 ( 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 : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7948 (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: 0.7901 (tptt) REVERT: K 53 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6439 (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: 0.7977 (m-30) cc_final: 0.7731 (m-30) REVERT: N 39 SER cc_start: 0.8794 (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: 0.7378 (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: 0.7957 (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: 0.7848 (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: 0.8830 (ttmt) cc_final: 0.7858 (tptt) REVERT: C 40 ASP cc_start: 0.8012 (t0) cc_final: 0.7805 (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: 0.1129 time to fit residues: 56.3301 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 : 0.464 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.8322 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 aren 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 covalent geometry : bond 0.00212 (12440) covalent geometry : angle 0.42331 (16940) hydrogen bonds : bond 0.03028 ( 920) hydrogen bonds : angle 3.06084 ( 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 : 0.486 Fit side-chains revert: symmetry clash REVERT: R 25 THR cc_start: 0.9069 (m) cc_final: 0.8748 (t) REVERT: K 37 LYS cc_start: 0.8463 (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: 0.8012 (t0) REVERT: N 39 SER cc_start: 0.8736 (m) cc_final: 0.8250 (p) REVERT: O 47 TYR cc_start: 0.9064 (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: 0.7786 (tptp) REVERT: G 37 LYS cc_start: 0.8518 (ttmt) cc_final: 0.7947 (tptp) REVERT: H 37 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7428 (tptt) REVERT: H 53 GLU cc_start: 0.8216 (tp30) cc_final: 0.8012 (tp30) REVERT: I 37 LYS cc_start: 0.8476 (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: 0.7754 (t0) REVERT: D 37 LYS cc_start: 0.8672 (ttmt) cc_final: 0.7534 (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: 0.8702 (ttmt) cc_final: 0.7775 (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: 0.7789 (mm-30) outliers start: 16 outliers final: 10 residues processed: 317 average time/residue: 0.1115 time to fit residues: 51.1607 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 : 0.488 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8327 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 aren 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 covalent geometry : bond 0.00213 (12440) covalent geometry : angle 0.41084 (16940) hydrogen bonds : bond 0.02757 ( 920) hydrogen bonds : angle 2.88588 ( 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 : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7553 (mt-10) REVERT: Q 37 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8516 (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: 0.8536 (t) REVERT: K 37 LYS cc_start: 0.8411 (ttmt) cc_final: 0.7744 (tptt) REVERT: K 53 GLU cc_start: 0.6549 (mt-10) cc_final: 0.6342 (mt-10) REVERT: K 55 ASN cc_start: 0.8324 (t0) cc_final: 0.8037 (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: 0.8409 (ttmt) cc_final: 0.7495 (tptt) REVERT: I 55 ASN cc_start: 0.8347 (t0) cc_final: 0.8073 (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: 0.8634 (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: 0.8034 (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: 0.1106 time to fit residues: 51.4351 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 : 0.504 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.8403 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 aren 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 covalent geometry : bond 0.00411 (12440) covalent geometry : angle 0.48054 (16940) hydrogen bonds : bond 0.03049 ( 920) hydrogen bonds : angle 3.10016 ( 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 : 0.501 Fit side-chains REVERT: Q 29 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7547 (mt-10) REVERT: Q 37 LYS cc_start: 0.8736 (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: 0.8963 (t80) REVERT: O 52 SER cc_start: 0.9140 (m) cc_final: 0.8765 (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: 0.8237 (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: 0.8331 (tp30) cc_final: 0.8021 (mm-30) REVERT: J 55 ASN cc_start: 0.8399 (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: 0.8056 (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: 0.7852 (mm-30) cc_final: 0.7393 (mm-30) outliers start: 40 outliers final: 27 residues processed: 343 average time/residue: 0.1104 time to fit residues: 54.9676 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 : 0.487 ------------------------------------------------------------------------------- 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.5476 > 50: distance: 33 - 55: 20.621 distance: 44 - 62: 27.662 distance: 48 - 68: 31.388 distance: 51 - 55: 24.282 distance: 52 - 73: 31.120 distance: 55 - 56: 26.395 distance: 56 - 57: 33.572 distance: 56 - 59: 19.962 distance: 57 - 58: 41.276 distance: 57 - 62: 17.857 distance: 59 - 60: 20.331 distance: 62 - 63: 28.572 distance: 63 - 64: 17.732 distance: 63 - 66: 46.108 distance: 64 - 65: 5.453 distance: 64 - 68: 11.947 distance: 65 - 93: 37.903 distance: 66 - 67: 56.465 distance: 68 - 69: 45.082 distance: 69 - 70: 10.689 distance: 70 - 71: 29.493 distance: 70 - 73: 16.054 distance: 71 - 101: 46.509 distance: 73 - 74: 45.425 distance: 74 - 75: 54.091 distance: 74 - 77: 39.881 distance: 75 - 76: 51.829 distance: 75 - 82: 52.469 distance: 76 - 108: 45.918 distance: 77 - 78: 5.163 distance: 78 - 79: 39.854 distance: 79 - 80: 48.592 distance: 80 - 81: 36.556 distance: 82 - 83: 39.990 distance: 83 - 84: 38.821 distance: 83 - 86: 40.563 distance: 85 - 112: 57.814 distance: 86 - 87: 24.374 distance: 87 - 88: 42.690 distance: 87 - 89: 43.054 distance: 89 - 91: 31.189 distance: 91 - 92: 57.087 distance: 93 - 94: 34.952 distance: 94 - 95: 49.351 distance: 94 - 97: 41.539 distance: 95 - 101: 27.500 distance: 97 - 98: 39.785 distance: 101 - 102: 7.999 distance: 102 - 103: 20.603 distance: 102 - 105: 46.542 distance: 103 - 104: 39.759 distance: 103 - 108: 43.684 distance: 105 - 106: 26.610 distance: 105 - 107: 14.397 distance: 108 - 109: 46.238 distance: 110 - 112: 40.499 distance: 112 - 113: 19.275 distance: 113 - 114: 21.003 distance: 113 - 116: 18.990 distance: 114 - 115: 39.227 distance: 114 - 119: 11.018 distance: 116 - 117: 24.264 distance: 116 - 118: 26.819 distance: 119 - 120: 12.511 distance: 120 - 121: 18.951 distance: 121 - 122: 45.699 distance: 121 - 127: 27.321