Starting phenix.real_space_refine on Thu Sep 26 02:42:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofe_20043/09_2024/6ofe_20043.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofe_20043/09_2024/6ofe_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofe_20043/09_2024/6ofe_20043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofe_20043/09_2024/6ofe_20043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofe_20043/09_2024/6ofe_20043.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofe_20043/09_2024/6ofe_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-5461/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: 3.39, per 1000 atoms: 0.28 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: 3.13 Conformation dependent library (CDL) restraints added in 1.6 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: 1.09 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: 3.24 Time building geometry restraints manager: 3.55 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 24.610 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.760 ------------------------------------------------------------------------------- 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= 0.374 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 1.180 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: 0.2362 time to fit residues: 142.1163 Evaluate side-chains 332 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 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= 0.149 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 *********************** 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 fitting. rotamer outliers: 18 poor density : 345 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 29 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7726 (mt-10) REVERT: Q 37 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8503 (ttmm) REVERT: T 39 SER cc_start: 0.9233 (m) cc_final: 0.8964 (p) REVERT: T 69 LYS cc_start: 0.8649 (tmtp) cc_final: 0.7473 (tttt) REVERT: K 37 LYS cc_start: 0.8604 (ttmt) cc_final: 0.7956 (tptt) REVERT: K 53 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6406 (mt-10) REVERT: K 55 ASN cc_start: 0.8331 (t0) cc_final: 0.7976 (t0) REVERT: L 25 THR cc_start: 0.9064 (m) cc_final: 0.8819 (p) REVERT: L 39 SER cc_start: 0.8702 (m) cc_final: 0.8399 (p) REVERT: L 70 ASP cc_start: 0.7958 (m-30) cc_final: 0.7724 (m-30) REVERT: N 39 SER cc_start: 0.8748 (m) cc_final: 0.8497 (p) REVERT: O 52 SER cc_start: 0.9007 (m) cc_final: 0.8755 (p) REVERT: F 37 LYS cc_start: 0.8631 (ttmt) cc_final: 0.7872 (tptp) REVERT: F 39 SER cc_start: 0.8634 (m) cc_final: 0.7553 (m) REVERT: G 37 LYS cc_start: 0.8553 (ttmt) cc_final: 0.7861 (tptt) REVERT: G 39 SER cc_start: 0.8807 (m) cc_final: 0.8207 (p) REVERT: H 37 LYS cc_start: 0.8295 (ttmt) cc_final: 0.7410 (tptt) REVERT: I 37 LYS cc_start: 0.8467 (ttmt) cc_final: 0.7723 (tptt) REVERT: J 37 LYS cc_start: 0.8376 (ttmt) cc_final: 0.7626 (tptt) REVERT: J 55 ASN cc_start: 0.8270 (t0) cc_final: 0.7987 (t0) REVERT: D 37 LYS cc_start: 0.8662 (ttmt) cc_final: 0.7488 (tptt) REVERT: A 24 GLN cc_start: 0.8312 (mp10) cc_final: 0.7854 (mp10) REVERT: A 33 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8633 (mtpt) REVERT: A 37 LYS cc_start: 0.8687 (ttmt) cc_final: 0.7517 (tptp) REVERT: A 53 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7997 (mm-30) REVERT: B 37 LYS cc_start: 0.8677 (ttmt) cc_final: 0.7761 (tptt) REVERT: B 57 TYR cc_start: 0.9382 (OUTLIER) cc_final: 0.8827 (t80) REVERT: C 37 LYS cc_start: 0.8842 (ttmt) cc_final: 0.7996 (tptt) REVERT: E 37 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8180 (tptp) REVERT: E 53 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7399 (mm-30) outliers start: 18 outliers final: 9 residues processed: 350 average time/residue: 0.2462 time to fit residues: 121.7770 Evaluate side-chains 313 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 303 time to evaluate : 1.478 ------------------------------------------------------------------------------- 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 70 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 C 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12440 Z= 0.149 Angle : 0.431 6.326 16940 Z= 0.229 Chirality : 0.033 0.103 1940 Planarity : 0.003 0.029 2220 Dihedral : 3.619 13.862 1680 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.85 % Allowed : 20.38 % 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: 0.53 (0.20), residues: 1520 helix: 0.72 (0.13), residues: 1360 sheet: None (None), residues: 0 loop : -2.22 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 5 PHE 0.006 0.001 PHE O 16 TYR 0.010 0.001 TYR O 54 ARG 0.004 0.000 ARG J 80 *********************** 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 337 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 313 time to evaluate : 1.568 Fit side-chains revert: symmetry clash REVERT: R 25 THR cc_start: 0.9118 (m) cc_final: 0.8814 (t) REVERT: K 37 LYS cc_start: 0.8483 (ttmt) cc_final: 0.7882 (tptt) REVERT: K 53 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6478 (mt-10) REVERT: K 55 ASN cc_start: 0.8305 (t0) cc_final: 0.8020 (t0) REVERT: L 22 ASN cc_start: 0.7607 (p0) cc_final: 0.7342 (p0) REVERT: N 39 SER cc_start: 0.8742 (m) cc_final: 0.8261 (p) REVERT: O 32 ASP cc_start: 0.8009 (m-30) cc_final: 0.7692 (m-30) REVERT: O 47 TYR cc_start: 0.9076 (t80) cc_final: 0.8867 (t80) REVERT: O 52 SER cc_start: 0.9116 (m) cc_final: 0.8710 (p) REVERT: F 37 LYS cc_start: 0.8618 (ttmt) cc_final: 0.7883 (tptp) REVERT: F 39 SER cc_start: 0.8658 (m) cc_final: 0.8145 (m) REVERT: G 24 GLN cc_start: 0.8282 (mp10) cc_final: 0.7953 (mp10) REVERT: G 37 LYS cc_start: 0.8513 (ttmt) cc_final: 0.7864 (tptt) REVERT: H 25 THR cc_start: 0.9135 (m) cc_final: 0.8902 (t) REVERT: H 37 LYS cc_start: 0.8364 (ttmt) cc_final: 0.7497 (tptt) REVERT: H 53 GLU cc_start: 0.8233 (tp30) cc_final: 0.8001 (tp30) REVERT: I 37 LYS cc_start: 0.8515 (ttmt) cc_final: 0.7653 (tptt) REVERT: I 55 ASN cc_start: 0.8329 (t0) cc_final: 0.8047 (t0) REVERT: J 37 LYS cc_start: 0.8262 (ttmt) cc_final: 0.7556 (tptt) REVERT: J 55 ASN cc_start: 0.8258 (t0) cc_final: 0.7933 (t0) REVERT: D 37 LYS cc_start: 0.8699 (ttmt) cc_final: 0.7468 (tptt) REVERT: A 24 GLN cc_start: 0.8304 (mp10) cc_final: 0.7950 (mp10) REVERT: A 37 LYS cc_start: 0.8665 (ttmt) cc_final: 0.7540 (tptp) REVERT: B 37 LYS cc_start: 0.8733 (ttmt) cc_final: 0.7807 (tptt) REVERT: C 37 LYS cc_start: 0.8863 (ttmt) cc_final: 0.7890 (tptt) REVERT: E 37 LYS cc_start: 0.9060 (ttmt) cc_final: 0.8179 (tptp) outliers start: 24 outliers final: 18 residues processed: 326 average time/residue: 0.2361 time to fit residues: 110.7723 Evaluate side-chains 307 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 289 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 62 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 N 55 ASN ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3044 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= 0.211 Angle : 0.454 5.917 16940 Z= 0.241 Chirality : 0.035 0.107 1940 Planarity : 0.003 0.028 2220 Dihedral : 3.691 15.969 1680 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.62 % Allowed : 21.31 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.82 (0.21), residues: 1520 helix: 1.53 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.74 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 5 PHE 0.007 0.001 PHE N 16 TYR 0.013 0.001 TYR P 54 ARG 0.003 0.000 ARG J 80 *********************** 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 358 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 324 time to evaluate : 1.488 Fit side-chains REVERT: Q 29 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7608 (mt-10) REVERT: Q 37 LYS cc_start: 0.8674 (ttmm) cc_final: 0.8437 (ttmm) REVERT: T 61 GLN cc_start: 0.8884 (tt0) cc_final: 0.8574 (tt0) REVERT: K 37 LYS cc_start: 0.8447 (ttmt) cc_final: 0.7802 (tptt) REVERT: K 55 ASN cc_start: 0.8423 (t0) cc_final: 0.8133 (t0) REVERT: K 57 TYR cc_start: 0.9204 (OUTLIER) cc_final: 0.8368 (t80) REVERT: O 52 SER cc_start: 0.9120 (m) cc_final: 0.8759 (p) REVERT: F 37 LYS cc_start: 0.8614 (ttmt) cc_final: 0.7852 (tptp) REVERT: G 24 GLN cc_start: 0.8271 (mp10) cc_final: 0.8055 (mp10) REVERT: G 37 LYS cc_start: 0.8559 (ttmt) cc_final: 0.7911 (tptt) REVERT: H 37 LYS cc_start: 0.8354 (ttmt) cc_final: 0.7466 (tptp) REVERT: I 37 LYS cc_start: 0.8473 (ttmt) cc_final: 0.7612 (tptt) REVERT: I 55 ASN cc_start: 0.8410 (t0) cc_final: 0.8169 (t0) REVERT: J 17 ASP cc_start: 0.8128 (m-30) cc_final: 0.7873 (m-30) REVERT: J 37 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7480 (tptt) REVERT: J 53 GLU cc_start: 0.8403 (tp30) cc_final: 0.8028 (mm-30) REVERT: J 55 ASN cc_start: 0.8357 (t0) cc_final: 0.8124 (t0) REVERT: D 37 LYS cc_start: 0.8772 (ttmt) cc_final: 0.7636 (tptt) REVERT: A 10 ASP cc_start: 0.8362 (m-30) cc_final: 0.8016 (m-30) REVERT: A 24 GLN cc_start: 0.8313 (mp10) cc_final: 0.7997 (mp10) REVERT: A 37 LYS cc_start: 0.8699 (ttmt) cc_final: 0.7543 (tptp) REVERT: B 37 LYS cc_start: 0.8731 (ttmt) cc_final: 0.7699 (tptt) REVERT: B 53 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7825 (mm-30) REVERT: B 57 TYR cc_start: 0.9355 (OUTLIER) cc_final: 0.8976 (t80) REVERT: C 37 LYS cc_start: 0.8936 (ttmt) cc_final: 0.7852 (tptt) REVERT: E 37 LYS cc_start: 0.9079 (ttmt) cc_final: 0.8184 (tptp) outliers start: 34 outliers final: 26 residues processed: 347 average time/residue: 0.2267 time to fit residues: 113.7148 Evaluate side-chains 328 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 300 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain S residue 57 TYR Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 39 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 62 SER Chi-restraints excluded: chain N residue 25 THR 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 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 B residue 62 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3271 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= 0.174 Angle : 0.435 5.869 16940 Z= 0.229 Chirality : 0.034 0.103 1940 Planarity : 0.003 0.031 2220 Dihedral : 3.627 17.255 1680 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.69 % Allowed : 22.31 % Favored : 75.00 % 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: 2.47 (0.21), residues: 1520 helix: 1.99 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.74 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 5 PHE 0.005 0.001 PHE O 16 TYR 0.010 0.001 TYR O 54 ARG 0.002 0.000 ARG J 80 *********************** 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 353 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 318 time to evaluate : 1.318 Fit side-chains REVERT: Q 29 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7572 (mt-10) REVERT: Q 37 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8413 (ttmm) REVERT: Q 53 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8084 (mm-30) REVERT: T 62 SER cc_start: 0.9387 (t) cc_final: 0.8994 (t) REVERT: K 37 LYS cc_start: 0.8414 (ttmt) cc_final: 0.7779 (tptt) REVERT: K 55 ASN cc_start: 0.8397 (t0) cc_final: 0.8111 (t0) REVERT: K 57 TYR cc_start: 0.9203 (OUTLIER) cc_final: 0.8292 (t80) REVERT: L 22 ASN cc_start: 0.7872 (p0) cc_final: 0.7513 (p0) REVERT: M 53 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8016 (tp30) REVERT: O 52 SER cc_start: 0.9099 (m) cc_final: 0.8749 (p) REVERT: F 22 ASN cc_start: 0.8096 (p0) cc_final: 0.7600 (p0) REVERT: F 37 LYS cc_start: 0.8601 (ttmt) cc_final: 0.7816 (tptp) REVERT: G 37 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8039 (tptp) REVERT: H 37 LYS cc_start: 0.8326 (ttmt) cc_final: 0.7494 (tptp) REVERT: I 22 ASN cc_start: 0.8229 (p0) cc_final: 0.7889 (p0) REVERT: I 55 ASN cc_start: 0.8283 (t0) cc_final: 0.7967 (t0) REVERT: J 17 ASP cc_start: 0.8164 (m-30) cc_final: 0.7954 (m-30) REVERT: J 37 LYS cc_start: 0.8144 (ttmt) cc_final: 0.7381 (tptt) REVERT: J 53 GLU cc_start: 0.8386 (tp30) cc_final: 0.8008 (mm-30) REVERT: J 55 ASN cc_start: 0.8352 (t0) cc_final: 0.8141 (t0) REVERT: D 37 LYS cc_start: 0.8768 (ttmt) cc_final: 0.7633 (tptt) REVERT: A 24 GLN cc_start: 0.8354 (mp10) cc_final: 0.7971 (mp10) REVERT: A 37 LYS cc_start: 0.8662 (ttmt) cc_final: 0.7489 (tptp) REVERT: B 37 LYS cc_start: 0.8759 (ttmt) cc_final: 0.7737 (tptt) REVERT: B 53 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7727 (mm-30) REVERT: C 37 LYS cc_start: 0.8927 (ttmt) cc_final: 0.7839 (tptt) REVERT: E 37 LYS cc_start: 0.9073 (ttmt) cc_final: 0.8188 (tptp) outliers start: 35 outliers final: 26 residues processed: 344 average time/residue: 0.2261 time to fit residues: 112.5910 Evaluate side-chains 326 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 299 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 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 57 TYR Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain L residue 77 GLN Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 77 GLN Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 62 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 135 optimal weight: 0.6980 chunk 112 optimal weight: 0.1980 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3418 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= 0.122 Angle : 0.415 5.676 16940 Z= 0.216 Chirality : 0.033 0.100 1940 Planarity : 0.003 0.026 2220 Dihedral : 3.489 14.794 1680 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.62 % Allowed : 23.00 % Favored : 75.38 % 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: 2.96 (0.21), residues: 1520 helix: 2.35 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.77 (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 0.009 0.001 TYR M 47 ARG 0.002 0.000 ARG J 80 *********************** 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 338 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 317 time to evaluate : 1.294 Fit side-chains REVERT: Q 29 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7595 (mt-10) REVERT: Q 37 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8424 (ttmm) REVERT: Q 53 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8122 (mm-30) REVERT: R 62 SER cc_start: 0.9172 (t) cc_final: 0.8786 (t) REVERT: S 62 SER cc_start: 0.9219 (t) cc_final: 0.8949 (t) REVERT: T 62 SER cc_start: 0.9386 (t) cc_final: 0.8977 (t) REVERT: K 37 LYS cc_start: 0.8333 (ttmt) cc_final: 0.7763 (tptp) REVERT: K 55 ASN cc_start: 0.8357 (t0) cc_final: 0.8076 (t0) REVERT: L 22 ASN cc_start: 0.7894 (p0) cc_final: 0.7533 (p0) REVERT: L 61 GLN cc_start: 0.8803 (tt0) cc_final: 0.8524 (tt0) REVERT: M 47 TYR cc_start: 0.9095 (t80) cc_final: 0.8697 (t80) REVERT: O 47 TYR cc_start: 0.9137 (t80) cc_final: 0.8916 (t80) REVERT: O 52 SER cc_start: 0.9109 (m) cc_final: 0.8748 (p) REVERT: F 22 ASN cc_start: 0.8107 (p0) cc_final: 0.7639 (p0) REVERT: F 37 LYS cc_start: 0.8585 (ttmt) cc_final: 0.7774 (tptp) REVERT: G 37 LYS cc_start: 0.8503 (ttmt) cc_final: 0.8002 (tptp) REVERT: H 37 LYS cc_start: 0.8263 (ttmt) cc_final: 0.7481 (tptp) REVERT: I 22 ASN cc_start: 0.8171 (p0) cc_final: 0.7853 (t0) REVERT: I 55 ASN cc_start: 0.8245 (t0) cc_final: 0.7936 (t0) REVERT: J 17 ASP cc_start: 0.8146 (m-30) cc_final: 0.7936 (m-30) REVERT: J 37 LYS cc_start: 0.8126 (ttmt) cc_final: 0.7485 (tptt) REVERT: J 53 GLU cc_start: 0.8422 (tp30) cc_final: 0.8017 (mm-30) REVERT: J 55 ASN cc_start: 0.8295 (t0) cc_final: 0.8071 (t0) REVERT: D 10 ASP cc_start: 0.8451 (m-30) cc_final: 0.8203 (m-30) REVERT: D 37 LYS cc_start: 0.8743 (ttmt) cc_final: 0.7467 (tptt) REVERT: A 24 GLN cc_start: 0.8351 (mp10) cc_final: 0.7997 (mp10) REVERT: A 37 LYS cc_start: 0.8612 (ttmt) cc_final: 0.7463 (tptp) REVERT: B 37 LYS cc_start: 0.8726 (ttmt) cc_final: 0.7738 (tptt) REVERT: B 53 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7688 (mm-30) REVERT: E 37 LYS cc_start: 0.9026 (ttmt) cc_final: 0.8180 (tptp) REVERT: E 55 ASN cc_start: 0.8592 (t0) cc_final: 0.8364 (t0) outliers start: 21 outliers final: 16 residues processed: 334 average time/residue: 0.2112 time to fit residues: 102.4014 Evaluate side-chains 315 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 299 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 M residue 62 SER Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 77 GLN Chi-restraints excluded: chain D 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 15 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 82 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 GLN N 24 GLN ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12440 Z= 0.139 Angle : 0.431 6.721 16940 Z= 0.222 Chirality : 0.034 0.101 1940 Planarity : 0.003 0.027 2220 Dihedral : 3.467 14.531 1680 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.92 % Allowed : 23.38 % Favored : 74.69 % 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: 3.20 (0.21), residues: 1520 helix: 2.52 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.80 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 5 PHE 0.005 0.001 PHE C 16 TYR 0.010 0.001 TYR N 47 ARG 0.002 0.000 ARG J 80 *********************** 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 336 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 311 time to evaluate : 1.169 Fit side-chains REVERT: Q 29 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7600 (mt-10) REVERT: Q 37 LYS cc_start: 0.8674 (ttmm) cc_final: 0.8395 (ttmm) REVERT: Q 53 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8075 (mm-30) REVERT: R 62 SER cc_start: 0.9290 (t) cc_final: 0.8950 (t) REVERT: S 62 SER cc_start: 0.9344 (t) cc_final: 0.9101 (t) REVERT: T 5 TRP cc_start: 0.8870 (t60) cc_final: 0.8617 (t60) REVERT: T 62 SER cc_start: 0.9376 (t) cc_final: 0.8978 (t) REVERT: K 37 LYS cc_start: 0.8311 (ttmt) cc_final: 0.7719 (tptp) REVERT: K 55 ASN cc_start: 0.8372 (t0) cc_final: 0.8074 (t0) REVERT: K 57 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.8221 (t80) REVERT: L 22 ASN cc_start: 0.7876 (p0) cc_final: 0.7572 (p0) REVERT: L 61 GLN cc_start: 0.8793 (tt0) cc_final: 0.8514 (tt0) REVERT: M 47 TYR cc_start: 0.9117 (t80) cc_final: 0.8722 (t80) REVERT: O 47 TYR cc_start: 0.9147 (t80) cc_final: 0.8915 (t80) REVERT: O 52 SER cc_start: 0.9138 (m) cc_final: 0.8764 (p) REVERT: F 22 ASN cc_start: 0.8143 (p0) cc_final: 0.7812 (p0) REVERT: F 24 GLN cc_start: 0.8335 (mp10) cc_final: 0.8101 (mp10) REVERT: F 37 LYS cc_start: 0.8621 (ttmt) cc_final: 0.7783 (tptp) REVERT: G 24 GLN cc_start: 0.8276 (mp10) cc_final: 0.8022 (mp10) REVERT: G 37 LYS cc_start: 0.8478 (ttmt) cc_final: 0.7969 (tptp) REVERT: H 37 LYS cc_start: 0.8268 (ttmt) cc_final: 0.7484 (tptp) REVERT: I 22 ASN cc_start: 0.8200 (p0) cc_final: 0.7860 (t0) REVERT: I 55 ASN cc_start: 0.8341 (t0) cc_final: 0.8048 (t0) REVERT: J 17 ASP cc_start: 0.8164 (m-30) cc_final: 0.7950 (m-30) REVERT: J 37 LYS cc_start: 0.8150 (ttmt) cc_final: 0.7465 (tptt) REVERT: J 53 GLU cc_start: 0.8427 (tp30) cc_final: 0.8066 (mm-30) REVERT: D 37 LYS cc_start: 0.8733 (ttmt) cc_final: 0.7464 (tptt) REVERT: A 24 GLN cc_start: 0.8311 (mp10) cc_final: 0.7957 (mp10) REVERT: A 37 LYS cc_start: 0.8615 (ttmt) cc_final: 0.7454 (tptp) REVERT: B 37 LYS cc_start: 0.8718 (ttmt) cc_final: 0.7652 (tptt) REVERT: B 53 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7771 (mm-30) REVERT: E 37 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8159 (tptp) REVERT: E 55 ASN cc_start: 0.8571 (t0) cc_final: 0.8357 (t0) outliers start: 25 outliers final: 19 residues processed: 330 average time/residue: 0.2200 time to fit residues: 105.2558 Evaluate side-chains 321 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 301 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 0.1980 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3573 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= 0.135 Angle : 0.433 6.033 16940 Z= 0.223 Chirality : 0.033 0.099 1940 Planarity : 0.003 0.026 2220 Dihedral : 3.439 14.704 1680 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.62 % Allowed : 23.54 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.37 (0.21), residues: 1520 helix: 2.64 (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 0.005 0.001 PHE D 16 TYR 0.010 0.001 TYR D 47 ARG 0.002 0.000 ARG J 80 *********************** 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 330 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 309 time to evaluate : 1.251 Fit side-chains REVERT: Q 29 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7560 (mt-10) REVERT: Q 37 LYS cc_start: 0.8646 (ttmm) cc_final: 0.8417 (ttmm) REVERT: Q 53 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8025 (mm-30) REVERT: R 62 SER cc_start: 0.9305 (t) cc_final: 0.8955 (t) REVERT: S 5 TRP cc_start: 0.8591 (t60) cc_final: 0.8390 (t60) REVERT: S 62 SER cc_start: 0.9340 (t) cc_final: 0.9096 (t) REVERT: T 5 TRP cc_start: 0.8864 (t60) cc_final: 0.8608 (t60) REVERT: T 62 SER cc_start: 0.9448 (t) cc_final: 0.9021 (t) REVERT: K 37 LYS cc_start: 0.8342 (ttmt) cc_final: 0.7740 (tptp) REVERT: K 55 ASN cc_start: 0.8366 (t0) cc_final: 0.8079 (t0) REVERT: K 57 TYR cc_start: 0.9177 (OUTLIER) cc_final: 0.8229 (t80) REVERT: L 22 ASN cc_start: 0.7894 (p0) cc_final: 0.7595 (p0) REVERT: L 61 GLN cc_start: 0.8783 (tt0) cc_final: 0.8536 (tt0) REVERT: M 47 TYR cc_start: 0.9096 (t80) cc_final: 0.8709 (t80) REVERT: O 47 TYR cc_start: 0.9150 (t80) cc_final: 0.8923 (t80) REVERT: O 52 SER cc_start: 0.9161 (m) cc_final: 0.8764 (p) REVERT: F 22 ASN cc_start: 0.8101 (p0) cc_final: 0.7758 (p0) REVERT: F 24 GLN cc_start: 0.8375 (mp10) cc_final: 0.8151 (mp10) REVERT: F 37 LYS cc_start: 0.8666 (ttmt) cc_final: 0.7840 (tptp) REVERT: G 37 LYS cc_start: 0.8400 (ttmt) cc_final: 0.7886 (tptp) REVERT: H 37 LYS cc_start: 0.8268 (ttmt) cc_final: 0.7479 (tptp) REVERT: I 22 ASN cc_start: 0.8189 (p0) cc_final: 0.7862 (t0) REVERT: I 55 ASN cc_start: 0.8321 (t0) cc_final: 0.8026 (t0) REVERT: J 17 ASP cc_start: 0.8189 (m-30) cc_final: 0.7973 (m-30) REVERT: J 37 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7451 (tptt) REVERT: J 53 GLU cc_start: 0.8413 (tp30) cc_final: 0.8056 (mm-30) REVERT: D 37 LYS cc_start: 0.8737 (ttmt) cc_final: 0.7464 (tptt) REVERT: A 24 GLN cc_start: 0.8364 (mp10) cc_final: 0.7979 (mp10) REVERT: A 37 LYS cc_start: 0.8600 (ttmt) cc_final: 0.7407 (tptp) REVERT: B 37 LYS cc_start: 0.8712 (ttmt) cc_final: 0.7635 (tptt) REVERT: B 53 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7782 (mm-30) REVERT: E 37 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8195 (tptp) REVERT: E 55 ASN cc_start: 0.8608 (t0) cc_final: 0.8372 (t0) outliers start: 21 outliers final: 17 residues processed: 326 average time/residue: 0.2237 time to fit residues: 105.8620 Evaluate side-chains 326 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 308 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 77 GLN Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR 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 117 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 113 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3631 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= 0.138 Angle : 0.437 6.409 16940 Z= 0.225 Chirality : 0.034 0.100 1940 Planarity : 0.003 0.026 2220 Dihedral : 3.425 14.756 1680 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.62 % Allowed : 23.69 % Favored : 74.69 % 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: 3.55 (0.21), residues: 1520 helix: 2.77 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.84 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 5 PHE 0.006 0.001 PHE O 16 TYR 0.011 0.001 TYR T 54 ARG 0.002 0.000 ARG J 80 *********************** 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 330 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 309 time to evaluate : 1.388 Fit side-chains REVERT: Q 29 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7584 (mt-10) REVERT: Q 37 LYS cc_start: 0.8639 (ttmm) cc_final: 0.8410 (ttmm) REVERT: Q 53 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8013 (mm-30) REVERT: R 62 SER cc_start: 0.9412 (t) cc_final: 0.9104 (t) REVERT: S 5 TRP cc_start: 0.8641 (t60) cc_final: 0.8422 (t60) REVERT: S 62 SER cc_start: 0.9354 (t) cc_final: 0.9117 (t) REVERT: T 5 TRP cc_start: 0.8857 (t60) cc_final: 0.8596 (t60) REVERT: T 62 SER cc_start: 0.9495 (t) cc_final: 0.9096 (t) REVERT: K 37 LYS cc_start: 0.8352 (ttmt) cc_final: 0.7770 (tptp) REVERT: K 55 ASN cc_start: 0.8373 (t0) cc_final: 0.8082 (t0) REVERT: K 57 TYR cc_start: 0.9181 (OUTLIER) cc_final: 0.8230 (t80) REVERT: L 61 GLN cc_start: 0.8776 (tt0) cc_final: 0.8527 (tt0) REVERT: O 47 TYR cc_start: 0.9155 (t80) cc_final: 0.8924 (t80) REVERT: O 52 SER cc_start: 0.9158 (m) cc_final: 0.8775 (p) REVERT: F 22 ASN cc_start: 0.8128 (p0) cc_final: 0.7791 (p0) REVERT: F 24 GLN cc_start: 0.8380 (mp10) cc_final: 0.8159 (mp10) REVERT: F 37 LYS cc_start: 0.8656 (ttmt) cc_final: 0.7913 (tptp) REVERT: G 24 GLN cc_start: 0.8216 (mp10) cc_final: 0.7963 (mp10) REVERT: G 37 LYS cc_start: 0.8412 (ttmt) cc_final: 0.7879 (tptp) REVERT: H 37 LYS cc_start: 0.8329 (ttmt) cc_final: 0.7546 (tptp) REVERT: I 22 ASN cc_start: 0.8240 (p0) cc_final: 0.7916 (t0) REVERT: I 55 ASN cc_start: 0.8344 (t0) cc_final: 0.8046 (t0) REVERT: J 17 ASP cc_start: 0.8187 (m-30) cc_final: 0.7986 (m-30) REVERT: J 37 LYS cc_start: 0.8163 (ttmt) cc_final: 0.7430 (tptt) REVERT: J 53 GLU cc_start: 0.8423 (tp30) cc_final: 0.8075 (mm-30) REVERT: D 37 LYS cc_start: 0.8763 (ttmt) cc_final: 0.7485 (tptt) REVERT: A 24 GLN cc_start: 0.8364 (mp10) cc_final: 0.7983 (mp10) REVERT: A 37 LYS cc_start: 0.8599 (ttmt) cc_final: 0.7405 (tptp) REVERT: B 37 LYS cc_start: 0.8760 (ttmt) cc_final: 0.7640 (tptt) REVERT: E 37 LYS cc_start: 0.9019 (ttmt) cc_final: 0.8192 (tptp) REVERT: E 55 ASN cc_start: 0.8612 (t0) cc_final: 0.8375 (t0) outliers start: 21 outliers final: 19 residues processed: 327 average time/residue: 0.2215 time to fit residues: 105.6651 Evaluate side-chains 324 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 304 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain R residue 13 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 53 GLU Chi-restraints excluded: chain K residue 57 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** M 24 GLN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12440 Z= 0.213 Angle : 0.475 7.369 16940 Z= 0.246 Chirality : 0.035 0.106 1940 Planarity : 0.003 0.026 2220 Dihedral : 3.587 17.436 1680 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.85 % Allowed : 23.69 % Favored : 74.46 % 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: 3.52 (0.21), residues: 1520 helix: 2.76 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.88 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 5 PHE 0.006 0.001 PHE G 68 TYR 0.013 0.001 TYR T 54 ARG 0.002 0.000 ARG J 80 ********************** 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 340 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 316 time to evaluate : 1.427 Fit side-chains REVERT: Q 29 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7534 (mt-10) REVERT: Q 53 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7889 (mm-30) REVERT: R 62 SER cc_start: 0.9321 (t) cc_final: 0.8989 (t) REVERT: S 5 TRP cc_start: 0.8670 (t60) cc_final: 0.8394 (t60) REVERT: S 62 SER cc_start: 0.9332 (t) cc_final: 0.9096 (t) REVERT: T 5 TRP cc_start: 0.8895 (t60) cc_final: 0.8580 (t60) REVERT: T 62 SER cc_start: 0.9437 (t) cc_final: 0.9010 (t) REVERT: K 37 LYS cc_start: 0.8392 (ttmt) cc_final: 0.7860 (tptt) REVERT: K 55 ASN cc_start: 0.8443 (t0) cc_final: 0.8128 (t0) REVERT: K 57 TYR cc_start: 0.9245 (OUTLIER) cc_final: 0.8344 (t80) REVERT: L 22 ASN cc_start: 0.8080 (p0) cc_final: 0.7784 (p0) REVERT: O 47 TYR cc_start: 0.9185 (t80) cc_final: 0.8951 (t80) REVERT: O 52 SER cc_start: 0.9185 (m) cc_final: 0.8791 (p) REVERT: F 22 ASN cc_start: 0.8206 (p0) cc_final: 0.7875 (p0) REVERT: F 24 GLN cc_start: 0.8426 (mp10) cc_final: 0.8220 (mp10) REVERT: F 37 LYS cc_start: 0.8652 (ttmt) cc_final: 0.7771 (tptp) REVERT: G 24 GLN cc_start: 0.8215 (mp10) cc_final: 0.7958 (mp10) REVERT: G 29 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7925 (mt-10) REVERT: G 37 LYS cc_start: 0.8496 (ttmt) cc_final: 0.7940 (tptp) REVERT: H 37 LYS cc_start: 0.8345 (ttmt) cc_final: 0.7535 (tptp) REVERT: I 22 ASN cc_start: 0.8320 (p0) cc_final: 0.7958 (t0) REVERT: I 55 ASN cc_start: 0.8424 (t0) cc_final: 0.8149 (t0) REVERT: J 17 ASP cc_start: 0.8250 (m-30) cc_final: 0.8018 (m-30) REVERT: J 37 LYS cc_start: 0.8176 (ttmt) cc_final: 0.7473 (tptt) REVERT: J 53 GLU cc_start: 0.8413 (tp30) cc_final: 0.8097 (mm-30) REVERT: D 37 LYS cc_start: 0.8807 (ttmt) cc_final: 0.7678 (tptt) REVERT: A 24 GLN cc_start: 0.8376 (mp10) cc_final: 0.8004 (mp10) REVERT: A 37 LYS cc_start: 0.8655 (ttmt) cc_final: 0.7419 (tptp) REVERT: B 37 LYS cc_start: 0.8687 (ttmt) cc_final: 0.7485 (tptt) REVERT: E 37 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8165 (tptp) outliers start: 24 outliers final: 20 residues processed: 335 average time/residue: 0.2106 time to fit residues: 103.6314 Evaluate side-chains 332 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 311 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain R residue 13 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 33 LYS Chi-restraints excluded: chain K residue 53 GLU Chi-restraints excluded: chain K residue 57 TYR 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 77 GLN 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 34 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 61 GLN ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.087695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.077257 restraints weight = 21977.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.079622 restraints weight = 11037.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.081188 restraints weight = 6795.745| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3713 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= 0.155 Angle : 0.463 9.283 16940 Z= 0.238 Chirality : 0.034 0.102 1940 Planarity : 0.003 0.026 2220 Dihedral : 3.551 16.500 1680 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.62 % Allowed : 24.54 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.73 (0.21), residues: 1520 helix: 2.91 (0.13), residues: 1320 sheet: None (None), residues: 0 loop : -0.88 (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 O 16 TYR 0.011 0.001 TYR T 54 ARG 0.002 0.000 ARG J 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2567.11 seconds wall clock time: 48 minutes 37.36 seconds (2917.36 seconds total)