Starting phenix.real_space_refine on Wed Jul 30 02:21:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ofe_20043/07_2025/6ofe_20043.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ofe_20043/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ofe_20043/07_2025/6ofe_20043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ofe_20043/07_2025/6ofe_20043.map" model { file = "/net/cci-nas-00/data/ceres_data/6ofe_20043/07_2025/6ofe_20043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ofe_20043/07_2025/6ofe_20043.cif" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12220 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, T Time building chain proxies: 3.73, per 1000 atoms: 0.31 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: 2.98 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.04 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: 3.39 Time building geometry restraints manager: 3.56 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'T' } 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: 2.230 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 25.840 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.260 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.015 0.003 TRP G 5 PHE 0.012 0.002 PHE M 79 TYR 0.009 0.001 TYR D 57 ARG 0.002 0.001 ARG I 58 Details of bonding type rmsd hydrogen bonds : bond 0.22534 ( 920) hydrogen bonds : angle 9.53785 ( 2640) covalent geometry : bond 0.00600 (12440) covalent geometry : angle 0.63262 (16940) *********************** 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 : 1.305 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: 0.7937 (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: 0.8022 (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: 0.8521 (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: 0.8053 (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: 0.7952 (tptp) REVERT: F 39 SER cc_start: 0.8645 (m) cc_final: 0.7821 (m) REVERT: G 37 LYS cc_start: 0.8541 (ttmt) cc_final: 0.7814 (tptt) REVERT: G 39 SER cc_start: 0.8925 (m) cc_final: 0.7319 (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: 0.8088 (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: 0.2388 time to fit residues: 143.4003 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 : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 0.0470 chunk 109 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 overall best weight: 0.7484 ------------------------------------------------------------------------------- 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 = 0.3155 r_free = 0.3155 target = 0.091405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.081276 restraints weight = 21573.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.083577 restraints weight = 10946.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.085077 restraints weight = 6839.336| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2359 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= 0.118 Angle : 0.467 6.123 16940 Z= 0.257 Chirality : 0.033 0.099 1940 Planarity : 0.004 0.025 2220 Dihedral : 3.835 13.325 1680 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.38 % Allowed : 15.85 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.18), residues: 1520 helix: -1.02 (0.11), residues: 1380 sheet: None (None), residues: 0 loop : -4.02 (0.41), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 5 PHE 0.008 0.001 PHE N 16 TYR 0.009 0.001 TYR J 57 ARG 0.005 0.000 ARG J 80 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 920) hydrogen bonds : angle 3.60257 ( 2640) covalent geometry : bond 0.00241 (12440) covalent geometry : angle 0.46742 (16940) *********************** 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 363 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 345 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7701 (mt-10) REVERT: Q 37 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8542 (ttmm) REVERT: T 39 SER cc_start: 0.9222 (m) cc_final: 0.8957 (p) REVERT: T 69 LYS cc_start: 0.8628 (tmtp) cc_final: 0.7447 (tttt) REVERT: K 37 LYS cc_start: 0.8588 (ttmt) cc_final: 0.7936 (tptt) REVERT: K 53 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6340 (mt-10) REVERT: K 55 ASN cc_start: 0.8323 (t0) cc_final: 0.7972 (t0) REVERT: L 25 THR cc_start: 0.9066 (m) cc_final: 0.8849 (p) REVERT: L 39 SER cc_start: 0.8700 (m) cc_final: 0.8396 (p) REVERT: L 70 ASP cc_start: 0.7915 (m-30) cc_final: 0.7687 (m-30) REVERT: N 39 SER cc_start: 0.8740 (m) cc_final: 0.8497 (p) REVERT: O 52 SER cc_start: 0.8986 (m) cc_final: 0.8757 (p) REVERT: F 37 LYS cc_start: 0.8640 (ttmt) cc_final: 0.7888 (tptp) REVERT: F 39 SER cc_start: 0.8637 (m) cc_final: 0.7547 (m) REVERT: G 37 LYS cc_start: 0.8550 (ttmt) cc_final: 0.7852 (tptt) REVERT: G 39 SER cc_start: 0.8806 (m) cc_final: 0.8216 (p) REVERT: H 37 LYS cc_start: 0.8290 (ttmt) cc_final: 0.7409 (tptt) REVERT: I 37 LYS cc_start: 0.8453 (ttmt) cc_final: 0.7716 (tptt) REVERT: J 37 LYS cc_start: 0.8369 (ttmt) cc_final: 0.7599 (tptt) REVERT: J 55 ASN cc_start: 0.8246 (t0) cc_final: 0.7968 (t0) REVERT: D 37 LYS cc_start: 0.8678 (ttmt) cc_final: 0.7546 (tptt) REVERT: A 24 GLN cc_start: 0.8295 (mp10) cc_final: 0.7840 (mp10) REVERT: A 33 LYS cc_start: 0.8858 (mtpt) cc_final: 0.8642 (mtpt) REVERT: A 37 LYS cc_start: 0.8697 (ttmt) cc_final: 0.7562 (tptp) REVERT: A 53 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7953 (mm-30) REVERT: B 37 LYS cc_start: 0.8663 (ttmt) cc_final: 0.7727 (tptt) REVERT: B 57 TYR cc_start: 0.9368 (OUTLIER) cc_final: 0.8822 (t80) REVERT: C 37 LYS cc_start: 0.8837 (ttmt) cc_final: 0.7994 (tptt) REVERT: E 37 LYS cc_start: 0.9033 (ttmt) cc_final: 0.8221 (tptp) REVERT: E 53 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7390 (mm-30) outliers start: 18 outliers final: 9 residues processed: 350 average time/residue: 0.2417 time to fit residues: 120.0824 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 : 1.383 ------------------------------------------------------------------------------- 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 12 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.088322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.077614 restraints weight = 22124.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.080036 restraints weight = 11212.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.081633 restraints weight = 6947.367| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12440 Z= 0.166 Angle : 0.477 6.273 16940 Z= 0.255 Chirality : 0.035 0.111 1940 Planarity : 0.003 0.028 2220 Dihedral : 3.818 15.634 1680 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.31 % Allowed : 19.92 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1520 helix: 0.71 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -1.01 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 5 PHE 0.007 0.001 PHE N 16 TYR 0.015 0.002 TYR P 54 ARG 0.004 0.000 ARG J 80 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 920) hydrogen bonds : angle 3.24748 ( 2640) covalent geometry : bond 0.00373 (12440) covalent geometry : angle 0.47662 (16940) *********************** 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 348 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 318 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 25 THR cc_start: 0.9168 (m) cc_final: 0.8759 (t) REVERT: T 61 GLN cc_start: 0.8921 (tt0) cc_final: 0.8676 (tt0) REVERT: K 37 LYS cc_start: 0.8459 (ttmt) cc_final: 0.7809 (tptt) REVERT: K 53 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6449 (mt-10) REVERT: K 55 ASN cc_start: 0.8429 (t0) cc_final: 0.8126 (t0) REVERT: L 22 ASN cc_start: 0.7766 (p0) cc_final: 0.7463 (p0) REVERT: O 52 SER cc_start: 0.9114 (m) cc_final: 0.8718 (p) REVERT: F 37 LYS cc_start: 0.8644 (ttmt) cc_final: 0.7891 (tptp) REVERT: G 24 GLN cc_start: 0.8304 (mp10) cc_final: 0.8005 (mp10) REVERT: G 37 LYS cc_start: 0.8567 (ttmt) cc_final: 0.7838 (tptt) REVERT: H 37 LYS cc_start: 0.8344 (ttmt) cc_final: 0.7377 (tptt) REVERT: I 37 LYS cc_start: 0.8525 (ttmt) cc_final: 0.7653 (tptt) REVERT: I 55 ASN cc_start: 0.8424 (t0) cc_final: 0.8140 (t0) REVERT: J 37 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7490 (tptt) REVERT: J 55 ASN cc_start: 0.8327 (t0) cc_final: 0.8041 (t0) REVERT: D 37 LYS cc_start: 0.8764 (ttmt) cc_final: 0.7598 (tptt) REVERT: A 10 ASP cc_start: 0.8355 (m-30) cc_final: 0.8062 (m-30) REVERT: A 22 ASN cc_start: 0.8086 (p0) cc_final: 0.7886 (p0) REVERT: A 24 GLN cc_start: 0.8369 (mp10) cc_final: 0.7998 (mp10) REVERT: A 37 LYS cc_start: 0.8705 (ttmt) cc_final: 0.7580 (tptp) REVERT: B 37 LYS cc_start: 0.8703 (ttmt) cc_final: 0.7598 (tptt) REVERT: B 57 TYR cc_start: 0.9316 (OUTLIER) cc_final: 0.8937 (t80) REVERT: C 37 LYS cc_start: 0.8908 (ttmt) cc_final: 0.7911 (tptt) REVERT: E 37 LYS cc_start: 0.9075 (ttmt) cc_final: 0.8182 (tptp) outliers start: 30 outliers final: 21 residues processed: 339 average time/residue: 0.2422 time to fit residues: 119.2738 Evaluate side-chains 320 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 298 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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 L residue 24 GLN Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 39 SER 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 B residue 57 TYR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 79 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.089187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.078713 restraints weight = 21602.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.081079 restraints weight = 10856.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.082675 restraints weight = 6724.052| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12440 Z= 0.116 Angle : 0.430 5.889 16940 Z= 0.228 Chirality : 0.034 0.103 1940 Planarity : 0.003 0.030 2220 Dihedral : 3.667 15.441 1680 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.15 % Allowed : 21.92 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.21), residues: 1520 helix: 1.56 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.80 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 5 PHE 0.006 0.001 PHE N 16 TYR 0.010 0.001 TYR P 54 ARG 0.003 0.000 ARG J 80 Details of bonding type rmsd hydrogen bonds : bond 0.02851 ( 920) hydrogen bonds : angle 3.00145 ( 2640) covalent geometry : bond 0.00255 (12440) covalent geometry : angle 0.43006 (16940) *********************** 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 348 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 320 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7574 (mt-10) REVERT: Q 53 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8117 (mm-30) REVERT: T 62 SER cc_start: 0.9399 (t) cc_final: 0.8993 (t) REVERT: K 37 LYS cc_start: 0.8417 (ttmt) cc_final: 0.7749 (tptt) REVERT: K 55 ASN cc_start: 0.8388 (t0) cc_final: 0.8113 (t0) REVERT: K 57 TYR cc_start: 0.9215 (OUTLIER) cc_final: 0.8277 (t80) REVERT: L 22 ASN cc_start: 0.7853 (p0) cc_final: 0.7501 (p0) REVERT: O 52 SER cc_start: 0.9085 (m) cc_final: 0.8726 (p) REVERT: F 22 ASN cc_start: 0.8064 (p0) cc_final: 0.7612 (p0) REVERT: F 37 LYS cc_start: 0.8596 (ttmt) cc_final: 0.7817 (tptp) REVERT: G 24 GLN cc_start: 0.8252 (mp10) cc_final: 0.8047 (mp10) REVERT: G 37 LYS cc_start: 0.8501 (ttmt) cc_final: 0.7784 (tptt) REVERT: H 37 LYS cc_start: 0.8305 (ttmt) cc_final: 0.7433 (tptp) REVERT: I 37 LYS cc_start: 0.8428 (ttmt) cc_final: 0.7547 (tptt) REVERT: I 55 ASN cc_start: 0.8303 (t0) cc_final: 0.7996 (t0) REVERT: J 37 LYS cc_start: 0.8152 (ttmt) cc_final: 0.7442 (tptt) REVERT: J 55 ASN cc_start: 0.8301 (t0) cc_final: 0.8081 (t0) REVERT: D 37 LYS cc_start: 0.8775 (ttmt) cc_final: 0.7643 (tptt) REVERT: A 10 ASP cc_start: 0.8309 (m-30) cc_final: 0.8033 (m-30) REVERT: A 24 GLN cc_start: 0.8335 (mp10) cc_final: 0.8005 (mp10) REVERT: A 37 LYS cc_start: 0.8685 (ttmt) cc_final: 0.7563 (tptp) REVERT: B 37 LYS cc_start: 0.8736 (ttmt) cc_final: 0.7712 (tptt) REVERT: C 37 LYS cc_start: 0.8893 (ttmt) cc_final: 0.7793 (tptt) REVERT: E 37 LYS cc_start: 0.9068 (ttmt) cc_final: 0.8192 (tptp) outliers start: 28 outliers final: 23 residues processed: 339 average time/residue: 0.2284 time to fit residues: 111.3977 Evaluate side-chains 323 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 299 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 39 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 K residue 62 SER Chi-restraints excluded: chain M residue 53 GLU Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 21 ASP 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 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 62 SER Chi-restraints excluded: chain E residue 57 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 66 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 108 optimal weight: 0.0980 chunk 84 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 63 ASN ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN M 78 ASN ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 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 = 0.3125 r_free = 0.3125 target = 0.090017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.079533 restraints weight = 21676.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.081908 restraints weight = 10887.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.083522 restraints weight = 6737.849| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3307 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= 0.092 Angle : 0.411 5.804 16940 Z= 0.215 Chirality : 0.033 0.097 1940 Planarity : 0.003 0.030 2220 Dihedral : 3.507 14.130 1680 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.08 % Allowed : 22.69 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.21), residues: 1520 helix: 2.11 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.67 (0.49), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 5 PHE 0.005 0.001 PHE O 16 TYR 0.009 0.001 TYR T 54 ARG 0.003 0.000 ARG J 80 Details of bonding type rmsd hydrogen bonds : bond 0.02665 ( 920) hydrogen bonds : angle 2.86327 ( 2640) covalent geometry : bond 0.00194 (12440) covalent geometry : angle 0.41072 (16940) *********************** 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 342 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 315 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7577 (mt-10) REVERT: Q 53 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8093 (mm-30) REVERT: S 62 SER cc_start: 0.9177 (t) cc_final: 0.8967 (t) REVERT: T 62 SER cc_start: 0.9373 (t) cc_final: 0.8959 (t) REVERT: K 37 LYS cc_start: 0.8374 (ttmt) cc_final: 0.7759 (tptp) REVERT: K 55 ASN cc_start: 0.8368 (t0) cc_final: 0.8086 (t0) REVERT: K 57 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.8199 (t80) REVERT: L 22 ASN cc_start: 0.7760 (p0) cc_final: 0.7477 (p0) REVERT: M 47 TYR cc_start: 0.9101 (t80) cc_final: 0.8708 (t80) REVERT: O 52 SER cc_start: 0.9086 (m) cc_final: 0.8736 (p) REVERT: F 22 ASN cc_start: 0.8058 (p0) cc_final: 0.7590 (p0) REVERT: F 37 LYS cc_start: 0.8584 (ttmt) cc_final: 0.7743 (tptp) REVERT: G 37 LYS cc_start: 0.8398 (ttmt) cc_final: 0.7860 (tptp) REVERT: H 37 LYS cc_start: 0.8310 (ttmt) cc_final: 0.7484 (tptp) REVERT: I 55 ASN cc_start: 0.8256 (t0) cc_final: 0.7920 (t0) REVERT: J 17 ASP cc_start: 0.7973 (m-30) cc_final: 0.7763 (m-30) REVERT: J 37 LYS cc_start: 0.8095 (ttmt) cc_final: 0.7283 (tptt) REVERT: J 55 ASN cc_start: 0.8311 (t0) cc_final: 0.8023 (t0) REVERT: D 37 LYS cc_start: 0.8761 (ttmt) cc_final: 0.7540 (tptt) REVERT: A 24 GLN cc_start: 0.8375 (mp10) cc_final: 0.7976 (mp10) REVERT: A 37 LYS cc_start: 0.8603 (ttmt) cc_final: 0.7447 (tptp) REVERT: B 37 LYS cc_start: 0.8711 (ttmt) cc_final: 0.7694 (tptt) REVERT: C 37 LYS cc_start: 0.8774 (ttmt) cc_final: 0.7771 (tptt) REVERT: E 37 LYS cc_start: 0.9032 (ttmt) cc_final: 0.8170 (tptp) REVERT: E 55 ASN cc_start: 0.8532 (t0) cc_final: 0.8315 (t0) outliers start: 27 outliers final: 20 residues processed: 336 average time/residue: 0.2165 time to fit residues: 106.2723 Evaluate side-chains 318 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 297 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P 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 M residue 53 GLU 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 39 SER 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 J residue 77 GLN Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 57 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 63 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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** L 24 GLN N 24 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 = 0.3086 r_free = 0.3086 target = 0.087581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.077180 restraints weight = 22021.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.079452 restraints weight = 11396.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.081001 restraints weight = 7185.149| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12440 Z= 0.140 Angle : 0.452 6.126 16940 Z= 0.236 Chirality : 0.035 0.108 1940 Planarity : 0.003 0.025 2220 Dihedral : 3.631 16.997 1680 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.69 % Allowed : 22.92 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.21), residues: 1520 helix: 2.27 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.79 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 5 PHE 0.006 0.001 PHE G 68 TYR 0.011 0.001 TYR P 54 ARG 0.002 0.000 ARG J 80 Details of bonding type rmsd hydrogen bonds : bond 0.02814 ( 920) hydrogen bonds : angle 2.98846 ( 2640) covalent geometry : bond 0.00317 (12440) covalent geometry : angle 0.45244 (16940) *********************** 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 345 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 310 time to evaluate : 1.412 Fit side-chains revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7598 (mt-10) REVERT: Q 53 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7893 (mm-30) REVERT: S 62 SER cc_start: 0.9183 (t) cc_final: 0.8960 (t) REVERT: T 5 TRP cc_start: 0.8887 (t60) cc_final: 0.8619 (t60) REVERT: T 62 SER cc_start: 0.9390 (t) cc_final: 0.8981 (t) REVERT: K 37 LYS cc_start: 0.8384 (ttmt) cc_final: 0.7815 (tptp) REVERT: K 55 ASN cc_start: 0.8416 (t0) cc_final: 0.8127 (t0) REVERT: K 57 TYR cc_start: 0.9259 (OUTLIER) cc_final: 0.8413 (t80) REVERT: L 22 ASN cc_start: 0.7930 (p0) cc_final: 0.7663 (p0) REVERT: O 52 SER cc_start: 0.9089 (m) cc_final: 0.8771 (p) REVERT: F 22 ASN cc_start: 0.8184 (p0) cc_final: 0.7711 (p0) REVERT: F 37 LYS cc_start: 0.8594 (ttmt) cc_final: 0.7798 (tptp) REVERT: G 29 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7933 (mt-10) REVERT: G 37 LYS cc_start: 0.8472 (ttmt) cc_final: 0.7947 (tptp) REVERT: H 37 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7414 (tptp) REVERT: I 55 ASN cc_start: 0.8401 (t0) cc_final: 0.8096 (t0) REVERT: J 37 LYS cc_start: 0.8158 (ttmt) cc_final: 0.7436 (tptt) REVERT: J 55 ASN cc_start: 0.8381 (t0) cc_final: 0.8162 (t0) REVERT: D 37 LYS cc_start: 0.8795 (ttmt) cc_final: 0.7662 (tptt) REVERT: A 24 GLN cc_start: 0.8364 (mp10) cc_final: 0.8016 (mp10) REVERT: A 37 LYS cc_start: 0.8667 (ttmt) cc_final: 0.7507 (tptp) REVERT: B 37 LYS cc_start: 0.8721 (ttmt) cc_final: 0.7627 (tptt) REVERT: B 53 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7741 (mm-30) REVERT: E 37 LYS cc_start: 0.9073 (ttmt) cc_final: 0.8189 (tptp) outliers start: 35 outliers final: 27 residues processed: 334 average time/residue: 0.2395 time to fit residues: 116.3372 Evaluate side-chains 324 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 296 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 K residue 62 SER 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 A 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 37 optimal weight: 0.0870 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 129 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 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 = 0.3110 r_free = 0.3110 target = 0.089043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.078634 restraints weight = 21760.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.081003 restraints weight = 10934.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.082578 restraints weight = 6740.038| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12440 Z= 0.097 Angle : 0.433 5.660 16940 Z= 0.224 Chirality : 0.033 0.102 1940 Planarity : 0.003 0.026 2220 Dihedral : 3.521 15.045 1680 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.38 % Allowed : 23.62 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.21), residues: 1520 helix: 2.49 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.84 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP E 5 PHE 0.005 0.001 PHE L 16 TYR 0.010 0.001 TYR N 47 ARG 0.002 0.000 ARG J 80 Details of bonding type rmsd hydrogen bonds : bond 0.02640 ( 920) hydrogen bonds : angle 2.85059 ( 2640) covalent geometry : bond 0.00211 (12440) covalent geometry : angle 0.43323 (16940) *********************** 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 350 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 319 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7577 (mt-10) REVERT: Q 53 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7849 (mm-30) REVERT: R 62 SER cc_start: 0.9277 (t) cc_final: 0.8910 (t) REVERT: S 62 SER cc_start: 0.9320 (t) cc_final: 0.9095 (t) REVERT: T 5 TRP cc_start: 0.8872 (t60) cc_final: 0.8596 (t60) REVERT: T 62 SER cc_start: 0.9442 (t) cc_final: 0.9010 (t) REVERT: K 37 LYS cc_start: 0.8329 (ttmt) cc_final: 0.7730 (tptp) REVERT: K 55 ASN cc_start: 0.8385 (t0) cc_final: 0.8099 (t0) REVERT: K 57 TYR cc_start: 0.9221 (OUTLIER) cc_final: 0.8272 (t80) REVERT: L 22 ASN cc_start: 0.7876 (p0) cc_final: 0.7613 (p0) REVERT: L 61 GLN cc_start: 0.8785 (tt0) cc_final: 0.8533 (tt0) REVERT: O 47 TYR cc_start: 0.9175 (t80) cc_final: 0.8946 (t80) REVERT: O 52 SER cc_start: 0.9097 (m) cc_final: 0.8762 (p) REVERT: F 22 ASN cc_start: 0.8169 (p0) cc_final: 0.7657 (p0) REVERT: F 37 LYS cc_start: 0.8620 (ttmt) cc_final: 0.7757 (tptp) REVERT: G 29 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7918 (mt-10) REVERT: G 37 LYS cc_start: 0.8435 (ttmt) cc_final: 0.7872 (tptp) REVERT: H 37 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7439 (tptp) REVERT: I 55 ASN cc_start: 0.8307 (t0) cc_final: 0.8023 (t0) REVERT: J 37 LYS cc_start: 0.8139 (ttmt) cc_final: 0.7356 (tptt) REVERT: J 55 ASN cc_start: 0.8339 (t0) cc_final: 0.8136 (t0) REVERT: D 37 LYS cc_start: 0.8751 (ttmt) cc_final: 0.7459 (tptt) REVERT: D 53 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8107 (mm-30) REVERT: A 24 GLN cc_start: 0.8381 (mp10) cc_final: 0.8015 (mp10) REVERT: A 37 LYS cc_start: 0.8605 (ttmt) cc_final: 0.7418 (tptp) REVERT: B 37 LYS cc_start: 0.8709 (ttmt) cc_final: 0.7579 (tptt) REVERT: B 53 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7723 (mm-30) REVERT: E 37 LYS cc_start: 0.9020 (ttmt) cc_final: 0.8140 (tptp) REVERT: E 55 ASN cc_start: 0.8599 (t0) cc_final: 0.8378 (t0) outliers start: 31 outliers final: 24 residues processed: 342 average time/residue: 0.3067 time to fit residues: 155.2521 Evaluate side-chains 331 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 306 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 62 SER 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 K residue 57 TYR Chi-restraints excluded: chain M residue 53 GLU 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 I residue 57 TYR Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain C residue 80 ARG 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 56 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 94 optimal weight: 0.3980 chunk 28 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** L 24 GLN ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 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 = 0.3111 r_free = 0.3111 target = 0.088989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.078688 restraints weight = 21901.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.080974 restraints weight = 11292.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.082522 restraints weight = 7089.640| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12440 Z= 0.102 Angle : 0.436 5.215 16940 Z= 0.226 Chirality : 0.033 0.101 1940 Planarity : 0.003 0.026 2220 Dihedral : 3.481 14.953 1680 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.38 % Allowed : 23.69 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.21), residues: 1520 helix: 2.59 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.82 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 5 PHE 0.004 0.001 PHE K 16 TYR 0.011 0.001 TYR D 47 ARG 0.002 0.000 ARG J 80 Details of bonding type rmsd hydrogen bonds : bond 0.02608 ( 920) hydrogen bonds : angle 2.84123 ( 2640) covalent geometry : bond 0.00223 (12440) covalent geometry : angle 0.43638 (16940) *********************** 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 339 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 308 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7588 (mt-10) REVERT: Q 53 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7818 (mm-30) REVERT: R 62 SER cc_start: 0.9291 (t) cc_final: 0.8940 (t) REVERT: S 5 TRP cc_start: 0.8656 (t60) cc_final: 0.8394 (t60) REVERT: S 62 SER cc_start: 0.9331 (t) cc_final: 0.9111 (t) REVERT: T 5 TRP cc_start: 0.8844 (t60) cc_final: 0.8591 (t60) REVERT: T 62 SER cc_start: 0.9444 (t) cc_final: 0.9028 (t) REVERT: K 37 LYS cc_start: 0.8325 (ttmt) cc_final: 0.7767 (tptp) REVERT: K 55 ASN cc_start: 0.8381 (t0) cc_final: 0.8099 (t0) REVERT: K 57 TYR cc_start: 0.9227 (OUTLIER) cc_final: 0.8301 (t80) REVERT: L 22 ASN cc_start: 0.7910 (p0) cc_final: 0.7661 (p0) REVERT: L 61 GLN cc_start: 0.8769 (tt0) cc_final: 0.8556 (tt0) REVERT: O 47 TYR cc_start: 0.9179 (t80) cc_final: 0.8955 (t80) REVERT: O 52 SER cc_start: 0.9129 (m) cc_final: 0.8778 (p) REVERT: F 22 ASN cc_start: 0.8101 (p0) cc_final: 0.7797 (p0) REVERT: F 37 LYS cc_start: 0.8666 (ttmt) cc_final: 0.7835 (tptp) REVERT: G 24 GLN cc_start: 0.8187 (mp10) cc_final: 0.7927 (mp10) REVERT: G 37 LYS cc_start: 0.8418 (ttmt) cc_final: 0.7878 (tptp) REVERT: H 37 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7478 (tptp) REVERT: I 55 ASN cc_start: 0.8321 (t0) cc_final: 0.8035 (t0) REVERT: J 37 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7442 (tptt) REVERT: J 55 ASN cc_start: 0.8326 (t0) cc_final: 0.8122 (t0) REVERT: D 37 LYS cc_start: 0.8787 (ttmt) cc_final: 0.7522 (tptt) REVERT: A 24 GLN cc_start: 0.8381 (mp10) cc_final: 0.7995 (mp10) REVERT: A 37 LYS cc_start: 0.8614 (ttmt) cc_final: 0.7443 (tptp) REVERT: B 37 LYS cc_start: 0.8707 (ttmt) cc_final: 0.7518 (tptt) REVERT: B 53 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7674 (mm-30) REVERT: E 37 LYS cc_start: 0.9036 (ttmt) cc_final: 0.8174 (tptp) outliers start: 31 outliers final: 26 residues processed: 329 average time/residue: 0.2324 time to fit residues: 110.9018 Evaluate side-chains 336 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 309 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 21 ASP 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 53 GLU Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 77 GLN Chi-restraints excluded: chain M residue 53 GLU 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 I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain B residue 62 SER 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 65 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** L 24 GLN ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3097 r_free = 0.3097 target = 0.088242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.077834 restraints weight = 21783.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.080169 restraints weight = 11014.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.081711 restraints weight = 6830.756| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12440 Z= 0.114 Angle : 0.452 6.398 16940 Z= 0.234 Chirality : 0.034 0.102 1940 Planarity : 0.003 0.026 2220 Dihedral : 3.497 14.867 1680 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.31 % Allowed : 24.08 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.21), residues: 1520 helix: 2.69 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.82 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 5 PHE 0.004 0.001 PHE D 16 TYR 0.012 0.001 TYR T 54 ARG 0.002 0.000 ARG J 80 Details of bonding type rmsd hydrogen bonds : bond 0.02648 ( 920) hydrogen bonds : angle 2.87326 ( 2640) covalent geometry : bond 0.00255 (12440) covalent geometry : angle 0.45218 (16940) *********************** 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 338 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 308 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7568 (mt-10) REVERT: Q 53 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7754 (mm-30) REVERT: R 62 SER cc_start: 0.9299 (t) cc_final: 0.8962 (t) REVERT: S 5 TRP cc_start: 0.8669 (t60) cc_final: 0.8364 (t60) REVERT: S 62 SER cc_start: 0.9326 (t) cc_final: 0.9096 (t) REVERT: T 5 TRP cc_start: 0.8861 (t60) cc_final: 0.8572 (t60) REVERT: T 62 SER cc_start: 0.9436 (t) cc_final: 0.9008 (t) REVERT: K 37 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7719 (tptp) REVERT: K 55 ASN cc_start: 0.8427 (t0) cc_final: 0.8135 (t0) REVERT: K 57 TYR cc_start: 0.9227 (OUTLIER) cc_final: 0.8307 (t80) REVERT: L 22 ASN cc_start: 0.7948 (p0) cc_final: 0.7696 (p0) REVERT: L 61 GLN cc_start: 0.8816 (tt0) cc_final: 0.8549 (tt0) REVERT: O 47 TYR cc_start: 0.9184 (t80) cc_final: 0.8953 (t80) REVERT: O 52 SER cc_start: 0.9195 (m) cc_final: 0.8806 (p) REVERT: F 22 ASN cc_start: 0.8122 (p0) cc_final: 0.7814 (p0) REVERT: F 37 LYS cc_start: 0.8705 (ttmt) cc_final: 0.7857 (tptp) REVERT: G 24 GLN cc_start: 0.8220 (mp10) cc_final: 0.7999 (mp10) REVERT: G 37 LYS cc_start: 0.8463 (ttmt) cc_final: 0.7863 (tptp) REVERT: H 37 LYS cc_start: 0.8301 (ttmt) cc_final: 0.7485 (tptp) REVERT: I 55 ASN cc_start: 0.8365 (t0) cc_final: 0.8072 (t0) REVERT: J 37 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7344 (tptt) REVERT: J 55 ASN cc_start: 0.8355 (t0) cc_final: 0.8151 (t0) REVERT: D 37 LYS cc_start: 0.8790 (ttmt) cc_final: 0.7496 (tptt) REVERT: A 24 GLN cc_start: 0.8422 (mp10) cc_final: 0.8030 (mp10) REVERT: A 37 LYS cc_start: 0.8594 (ttmt) cc_final: 0.7368 (tptp) REVERT: B 37 LYS cc_start: 0.8671 (ttmt) cc_final: 0.7425 (tptt) REVERT: B 53 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7807 (mm-30) REVERT: E 37 LYS cc_start: 0.9032 (ttmt) cc_final: 0.8141 (tptp) outliers start: 30 outliers final: 27 residues processed: 330 average time/residue: 0.2242 time to fit residues: 107.7220 Evaluate side-chains 336 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 308 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 53 GLU Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 77 GLN Chi-restraints excluded: chain M residue 53 GLU 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 I residue 67 VAL Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 62 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 97 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** L 24 GLN ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3115 r_free = 0.3115 target = 0.089443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.079313 restraints weight = 21724.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.081600 restraints weight = 11172.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.083123 restraints weight = 6964.974| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12440 Z= 0.101 Angle : 0.439 5.142 16940 Z= 0.228 Chirality : 0.033 0.102 1940 Planarity : 0.003 0.026 2220 Dihedral : 3.449 14.998 1680 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.08 % Allowed : 24.23 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.21), residues: 1520 helix: 2.86 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.76 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP E 5 PHE 0.005 0.001 PHE N 16 TYR 0.014 0.001 TYR S 47 ARG 0.002 0.000 ARG J 80 Details of bonding type rmsd hydrogen bonds : bond 0.02607 ( 920) hydrogen bonds : angle 2.83978 ( 2640) covalent geometry : bond 0.00220 (12440) covalent geometry : angle 0.43941 (16940) ********************** 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 341 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 314 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7549 (mt-10) REVERT: Q 53 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7812 (mm-30) REVERT: R 62 SER cc_start: 0.9409 (t) cc_final: 0.9118 (t) REVERT: S 5 TRP cc_start: 0.8639 (t60) cc_final: 0.8379 (t60) REVERT: S 62 SER cc_start: 0.9359 (t) cc_final: 0.9135 (t) REVERT: T 5 TRP cc_start: 0.8810 (t60) cc_final: 0.8565 (t60) REVERT: T 62 SER cc_start: 0.9470 (t) cc_final: 0.9056 (t) REVERT: K 37 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7692 (tptp) REVERT: K 55 ASN cc_start: 0.8376 (t0) cc_final: 0.8093 (t0) REVERT: K 57 TYR cc_start: 0.9221 (OUTLIER) cc_final: 0.8294 (t80) REVERT: L 22 ASN cc_start: 0.7910 (p0) cc_final: 0.7666 (p0) REVERT: L 61 GLN cc_start: 0.8768 (tt0) cc_final: 0.8546 (tt0) REVERT: O 47 TYR cc_start: 0.9180 (t80) cc_final: 0.8958 (t80) REVERT: F 22 ASN cc_start: 0.8103 (p0) cc_final: 0.7801 (p0) REVERT: F 37 LYS cc_start: 0.8721 (ttmt) cc_final: 0.7992 (tptp) REVERT: G 24 GLN cc_start: 0.8153 (mp10) cc_final: 0.7928 (mp10) REVERT: G 37 LYS cc_start: 0.8470 (ttmt) cc_final: 0.7912 (tptp) REVERT: H 37 LYS cc_start: 0.8346 (ttmt) cc_final: 0.7527 (tptp) REVERT: I 55 ASN cc_start: 0.8319 (t0) cc_final: 0.8037 (t0) REVERT: J 37 LYS cc_start: 0.8136 (ttmt) cc_final: 0.7463 (tptt) REVERT: J 55 ASN cc_start: 0.8317 (t0) cc_final: 0.8116 (t0) REVERT: D 37 LYS cc_start: 0.8810 (ttmt) cc_final: 0.7544 (tptt) REVERT: A 24 GLN cc_start: 0.8358 (mp10) cc_final: 0.7985 (mp10) REVERT: A 37 LYS cc_start: 0.8607 (ttmt) cc_final: 0.7432 (tptp) REVERT: B 37 LYS cc_start: 0.8675 (ttmt) cc_final: 0.7477 (tptt) REVERT: E 37 LYS cc_start: 0.9037 (ttmt) cc_final: 0.8227 (tptp) REVERT: E 55 ASN cc_start: 0.8633 (t0) cc_final: 0.8212 (t0) outliers start: 27 outliers final: 23 residues processed: 334 average time/residue: 0.2341 time to fit residues: 113.1671 Evaluate side-chains 331 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 307 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 21 ASP 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 M residue 53 GLU 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 I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 62 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 28 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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** L 24 GLN M 24 GLN ** N 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 = 0.3102 r_free = 0.3102 target = 0.088698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.078461 restraints weight = 21806.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.080767 restraints weight = 11259.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.082303 restraints weight = 7018.679| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12440 Z= 0.116 Angle : 0.457 5.704 16940 Z= 0.236 Chirality : 0.034 0.103 1940 Planarity : 0.003 0.026 2220 Dihedral : 3.480 14.841 1680 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.92 % Allowed : 24.38 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.21), residues: 1520 helix: 2.92 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.75 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 5 PHE 0.005 0.001 PHE N 16 TYR 0.016 0.001 TYR K 47 ARG 0.002 0.000 ARG J 80 Details of bonding type rmsd hydrogen bonds : bond 0.02663 ( 920) hydrogen bonds : angle 2.88465 ( 2640) covalent geometry : bond 0.00259 (12440) covalent geometry : angle 0.45656 (16940) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3804.38 seconds wall clock time: 68 minutes 40.64 seconds (4120.64 seconds total)