Starting phenix.real_space_refine on Wed Sep 25 19:46:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofh_20046/09_2024/6ofh_20046_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofh_20046/09_2024/6ofh_20046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofh_20046/09_2024/6ofh_20046.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofh_20046/09_2024/6ofh_20046.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofh_20046/09_2024/6ofh_20046_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofh_20046/09_2024/6ofh_20046_neut.cif" } resolution = 3.7 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= 0.003 sd= 0.023 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 7353 2.51 5 N 1919 2.21 5 O 2356 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: 11628 Number of models: 1 Model: "" Number of chains: 1 Chain: "E" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Restraints were copied for chains: D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, V Time building chain proxies: 2.70, per 1000 atoms: 0.23 Number of scatterers: 11628 At special positions: 0 Unit cell: (93.94, 92.232, 153.72, 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 2356 8.00 N 1919 7.00 C 7353 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.3 seconds 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2888 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 0 sheets defined 88.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'D' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP D 17 " --> pdb=" O SER D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN D 77 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE U 16 " --> pdb=" O VAL U 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP U 17 " --> pdb=" O SER U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR U 28 " --> pdb=" O GLN U 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA U 36 " --> pdb=" O ASP U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA U 46 " --> pdb=" O ALA U 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU U 56 " --> pdb=" O SER U 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN U 77 " --> pdb=" O ALA U 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 20 removed outlier: 3.744A pdb=" N PHE V 16 " --> pdb=" O VAL V 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP V 17 " --> pdb=" O SER V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR V 28 " --> pdb=" O GLN V 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA V 46 " --> pdb=" O ALA V 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU V 56 " --> pdb=" O SER V 52 " (cutoff:3.500A) Processing helix chain 'V' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN V 77 " --> pdb=" O ALA V 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP E 17 " --> pdb=" O SER E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU E 56 " --> pdb=" O SER E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN E 77 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 20 removed outlier: 3.744A pdb=" N PHE F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP F 17 " --> pdb=" O SER F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 56 " --> pdb=" O SER F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 79 removed outlier: 4.576A pdb=" N GLN F 77 " --> pdb=" O ALA F 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE G 16 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP G 17 " --> pdb=" O SER G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA G 36 " --> pdb=" O ASP G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA G 46 " --> pdb=" O ALA G 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU G 56 " --> pdb=" O SER G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN G 77 " --> pdb=" O ALA G 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE H 16 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP H 17 " --> pdb=" O SER H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA H 36 " --> pdb=" O ASP H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA H 46 " --> pdb=" O ALA H 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 79 removed outlier: 4.574A pdb=" N GLN H 77 " --> pdb=" O ALA H 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE I 16 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP I 17 " --> pdb=" O SER I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA I 36 " --> pdb=" O ASP I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA I 46 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU I 56 " --> pdb=" O SER I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN I 77 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE J 16 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP J 17 " --> pdb=" O SER J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA J 36 " --> pdb=" O ASP J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA J 46 " --> pdb=" O ALA J 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU J 56 " --> pdb=" O SER J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN J 77 " --> pdb=" O ALA J 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE K 16 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP K 17 " --> pdb=" O SER K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR K 28 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA K 36 " --> pdb=" O ASP K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA K 46 " --> pdb=" O ALA K 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU K 56 " --> pdb=" O SER K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN K 77 " --> pdb=" O ALA K 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 20 removed outlier: 3.744A pdb=" N PHE L 16 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP L 17 " --> pdb=" O SER L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR L 28 " --> pdb=" O GLN L 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA L 36 " --> pdb=" O ASP L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA L 46 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU L 56 " --> pdb=" O SER L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 79 removed outlier: 4.576A pdb=" N GLN L 77 " --> pdb=" O ALA L 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 20 removed outlier: 3.742A pdb=" N PHE M 16 " --> pdb=" O VAL M 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP M 17 " --> pdb=" O SER M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR M 28 " --> pdb=" O GLN M 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA M 36 " --> pdb=" O ASP M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA M 46 " --> pdb=" O ALA M 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU M 56 " --> pdb=" O SER M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN M 77 " --> pdb=" O ALA M 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 20 removed outlier: 3.744A pdb=" N PHE N 16 " --> pdb=" O VAL N 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP N 17 " --> pdb=" O SER N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR N 28 " --> pdb=" O GLN N 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA N 46 " --> pdb=" O ALA N 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU N 56 " --> pdb=" O SER N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 79 removed outlier: 4.576A pdb=" N GLN N 77 " --> pdb=" O ALA N 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE O 16 " --> pdb=" O VAL O 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP O 17 " --> pdb=" O SER O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA O 36 " --> pdb=" O ASP O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA O 46 " --> pdb=" O ALA O 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU O 56 " --> pdb=" O SER O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN O 77 " --> pdb=" O ALA O 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 20 removed outlier: 3.742A pdb=" N PHE P 16 " --> pdb=" O VAL P 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP P 17 " --> pdb=" O SER P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA P 36 " --> pdb=" O ASP P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA P 46 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU P 56 " --> pdb=" O SER P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN P 77 " --> pdb=" O ALA P 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE Q 16 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP Q 17 " --> pdb=" O SER Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA Q 36 " --> pdb=" O ASP Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU Q 56 " --> pdb=" O SER Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN Q 77 " --> pdb=" O ALA Q 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE R 16 " --> pdb=" O VAL R 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP R 17 " --> pdb=" O SER R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR R 28 " --> pdb=" O GLN R 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA R 36 " --> pdb=" O ASP R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU R 56 " --> pdb=" O SER R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN R 77 " --> pdb=" O ALA R 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE S 16 " --> pdb=" O VAL S 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR S 28 " --> pdb=" O GLN S 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA S 36 " --> pdb=" O ASP S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA S 46 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU S 56 " --> pdb=" O SER S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 79 removed outlier: 4.576A pdb=" N GLN S 77 " --> pdb=" O ALA S 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE T 16 " --> pdb=" O VAL T 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP T 17 " --> pdb=" O SER T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR T 28 " --> pdb=" O GLN T 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA T 36 " --> pdb=" O ASP T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA T 46 " --> pdb=" O ALA T 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU T 56 " --> pdb=" O SER T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN T 77 " --> pdb=" O ALA T 74 " (cutoff:3.500A) 893 hydrogen bonds defined for protein. 2565 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: 3.48 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 2071 1.29 - 1.35: 1767 1.35 - 1.41: 1130 1.41 - 1.48: 1777 1.48 - 1.54: 5092 Bond restraints: 11837 Sorted by residual: bond pdb=" CB GLU M 53 " pdb=" CG GLU M 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" CB GLU R 53 " pdb=" CG GLU R 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" CB GLU F 53 " pdb=" CG GLU F 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" CB GLU J 53 " pdb=" CG GLU J 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" CB GLU L 53 " pdb=" CG GLU L 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.19e+00 ... (remaining 11832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 15378 1.64 - 3.28: 690 3.28 - 4.92: 25 4.92 - 6.56: 0 6.56 - 8.21: 19 Bond angle restraints: 16112 Sorted by residual: angle pdb=" CA LEU N 56 " pdb=" CB LEU N 56 " pdb=" CG LEU N 56 " ideal model delta sigma weight residual 116.30 108.09 8.21 3.50e+00 8.16e-02 5.50e+00 angle pdb=" CA LEU L 56 " pdb=" CB LEU L 56 " pdb=" CG LEU L 56 " ideal model delta sigma weight residual 116.30 108.10 8.20 3.50e+00 8.16e-02 5.49e+00 angle pdb=" CA LEU K 56 " pdb=" CB LEU K 56 " pdb=" CG LEU K 56 " ideal model delta sigma weight residual 116.30 108.10 8.20 3.50e+00 8.16e-02 5.48e+00 angle pdb=" CA PRO H 38 " pdb=" C PRO H 38 " pdb=" O PRO H 38 " ideal model delta sigma weight residual 121.38 119.58 1.80 7.70e-01 1.69e+00 5.47e+00 angle pdb=" CA LEU J 56 " pdb=" CB LEU J 56 " pdb=" CG LEU J 56 " ideal model delta sigma weight residual 116.30 108.12 8.18 3.50e+00 8.16e-02 5.47e+00 ... (remaining 16107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.17: 5624 6.17 - 12.34: 1119 12.34 - 18.51: 324 18.51 - 24.68: 77 24.68 - 30.85: 38 Dihedral angle restraints: 7182 sinusoidal: 2755 harmonic: 4427 Sorted by residual: dihedral pdb=" CA ASP D 70 " pdb=" C ASP D 70 " pdb=" N ILE D 71 " pdb=" CA ILE D 71 " ideal model delta harmonic sigma weight residual 180.00 164.46 15.54 0 5.00e+00 4.00e-02 9.66e+00 dihedral pdb=" CA ASP Q 70 " pdb=" C ASP Q 70 " pdb=" N ILE Q 71 " pdb=" CA ILE Q 71 " ideal model delta harmonic sigma weight residual 180.00 164.47 15.53 0 5.00e+00 4.00e-02 9.65e+00 dihedral pdb=" CA ASP S 70 " pdb=" C ASP S 70 " pdb=" N ILE S 71 " pdb=" CA ILE S 71 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.64e+00 ... (remaining 7179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.020: 423 0.020 - 0.041: 702 0.041 - 0.061: 378 0.061 - 0.082: 212 0.082 - 0.102: 128 Chirality restraints: 1843 Sorted by residual: chirality pdb=" CA SER N 39 " pdb=" N SER N 39 " pdb=" C SER N 39 " pdb=" CB SER N 39 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.60e-01 chirality pdb=" CA SER U 39 " pdb=" N SER U 39 " pdb=" C SER U 39 " pdb=" CB SER U 39 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.60e-01 chirality pdb=" CA PRO U 38 " pdb=" N PRO U 38 " pdb=" C PRO U 38 " pdb=" CB PRO U 38 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.56e-01 ... (remaining 1840 not shown) Planarity restraints: 2109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE P 76 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C ILE P 76 " -0.027 2.00e-02 2.50e+03 pdb=" O ILE P 76 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN P 77 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 76 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C ILE R 76 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE R 76 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN R 77 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE O 76 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C ILE O 76 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE O 76 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN O 77 " 0.009 2.00e-02 2.50e+03 ... (remaining 2106 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 106 2.66 - 3.22: 11323 3.22 - 3.78: 17158 3.78 - 4.34: 24963 4.34 - 4.90: 40716 Nonbonded interactions: 94266 Sorted by model distance: nonbonded pdb=" OD1 ASP D 10 " pdb=" OG SER H 49 " model vdw 2.097 3.040 nonbonded pdb=" NZ LYS G 66 " pdb=" OD2 ASP G 70 " model vdw 2.098 3.120 nonbonded pdb=" NZ LYS F 66 " pdb=" OD2 ASP F 70 " model vdw 2.098 3.120 nonbonded pdb=" NZ LYS P 66 " pdb=" OD2 ASP P 70 " model vdw 2.098 3.120 nonbonded pdb=" NZ LYS L 66 " pdb=" OD2 ASP L 70 " model vdw 2.098 3.120 ... (remaining 94261 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 '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' selection = chain 'U' selection = chain 'V' } 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: 0.050 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 22.890 Find NCS groups from input model: 0.420 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 : 0.008 0.035 11837 Z= 0.495 Angle : 0.752 8.205 16112 Z= 0.416 Chirality : 0.045 0.102 1843 Planarity : 0.005 0.028 2109 Dihedral : 7.705 30.854 4294 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -6.76 (0.10), residues: 1444 helix: -4.06 (0.06), residues: 1254 sheet: None (None), residues: 0 loop : -4.86 (0.27), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP G 5 PHE 0.020 0.004 PHE U 68 TYR 0.010 0.002 TYR D 57 ARG 0.004 0.001 ARG U 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 643 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 ASP cc_start: 0.7305 (m-30) cc_final: 0.7001 (m-30) REVERT: D 12 VAL cc_start: 0.9496 (t) cc_final: 0.9264 (t) REVERT: D 26 GLN cc_start: 0.7390 (mt0) cc_final: 0.7068 (mt0) REVERT: D 33 LYS cc_start: 0.8263 (mttt) cc_final: 0.7696 (mmtt) REVERT: D 54 TYR cc_start: 0.8293 (t80) cc_final: 0.8030 (t80) REVERT: U 15 LYS cc_start: 0.8811 (mttt) cc_final: 0.8488 (mmmm) REVERT: U 25 THR cc_start: 0.8574 (m) cc_final: 0.8034 (p) REVERT: U 28 THR cc_start: 0.8521 (m) cc_final: 0.8288 (p) REVERT: U 37 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7199 (tptt) REVERT: U 43 LEU cc_start: 0.9411 (mt) cc_final: 0.8678 (mt) REVERT: U 53 GLU cc_start: 0.8675 (tp30) cc_final: 0.8447 (tp30) REVERT: U 66 LYS cc_start: 0.8544 (tptp) cc_final: 0.7280 (mttt) REVERT: V 28 THR cc_start: 0.8981 (m) cc_final: 0.8129 (p) REVERT: V 33 LYS cc_start: 0.8265 (mttt) cc_final: 0.7499 (mtmt) REVERT: V 37 LYS cc_start: 0.9168 (ttmt) cc_final: 0.7889 (tptt) REVERT: V 47 TYR cc_start: 0.9134 (t80) cc_final: 0.8045 (t80) REVERT: V 53 GLU cc_start: 0.8174 (tp30) cc_final: 0.7797 (tp30) REVERT: E 28 THR cc_start: 0.7588 (m) cc_final: 0.7083 (p) REVERT: E 32 ASP cc_start: 0.7929 (m-30) cc_final: 0.7719 (m-30) REVERT: E 37 LYS cc_start: 0.7405 (ttmt) cc_final: 0.6675 (tptt) REVERT: F 28 THR cc_start: 0.9130 (m) cc_final: 0.8353 (p) REVERT: F 34 LEU cc_start: 0.9349 (tp) cc_final: 0.9102 (tt) REVERT: F 37 LYS cc_start: 0.8687 (ttmt) cc_final: 0.7915 (tptt) REVERT: F 39 SER cc_start: 0.9258 (m) cc_final: 0.8971 (t) REVERT: F 47 TYR cc_start: 0.9116 (t80) cc_final: 0.8106 (t80) REVERT: F 49 SER cc_start: 0.8330 (t) cc_final: 0.8086 (p) REVERT: F 63 ASN cc_start: 0.8789 (m-40) cc_final: 0.8179 (m-40) REVERT: F 66 LYS cc_start: 0.8562 (tptp) cc_final: 0.7287 (mttm) REVERT: G 8 TYR cc_start: 0.8726 (t80) cc_final: 0.8493 (t80) REVERT: G 11 ASP cc_start: 0.8244 (m-30) cc_final: 0.7717 (m-30) REVERT: G 23 LEU cc_start: 0.8811 (tp) cc_final: 0.8543 (tp) REVERT: G 37 LYS cc_start: 0.8371 (ttmt) cc_final: 0.7112 (tptt) REVERT: G 57 TYR cc_start: 0.8778 (t80) cc_final: 0.8165 (t80) REVERT: H 22 ASN cc_start: 0.8247 (p0) cc_final: 0.7969 (p0) REVERT: H 28 THR cc_start: 0.9268 (m) cc_final: 0.8613 (p) REVERT: H 32 ASP cc_start: 0.8001 (m-30) cc_final: 0.7663 (m-30) REVERT: H 37 LYS cc_start: 0.8567 (ttmt) cc_final: 0.7180 (tptt) REVERT: H 39 SER cc_start: 0.9287 (m) cc_final: 0.8695 (m) REVERT: I 28 THR cc_start: 0.9439 (m) cc_final: 0.9119 (m) REVERT: I 31 LEU cc_start: 0.9475 (tp) cc_final: 0.9100 (tp) REVERT: I 32 ASP cc_start: 0.8545 (m-30) cc_final: 0.8200 (m-30) REVERT: I 37 LYS cc_start: 0.8662 (ttmt) cc_final: 0.7393 (tptt) REVERT: I 47 TYR cc_start: 0.9254 (t80) cc_final: 0.8950 (t80) REVERT: I 49 SER cc_start: 0.9083 (t) cc_final: 0.8777 (t) REVERT: J 6 SER cc_start: 0.8989 (m) cc_final: 0.8766 (p) REVERT: J 24 GLN cc_start: 0.7828 (mp10) cc_final: 0.7618 (tp-100) REVERT: J 37 LYS cc_start: 0.8754 (ttmt) cc_final: 0.7266 (tptt) REVERT: J 47 TYR cc_start: 0.9064 (t80) cc_final: 0.8457 (t80) REVERT: J 49 SER cc_start: 0.9100 (t) cc_final: 0.8862 (t) REVERT: J 51 LEU cc_start: 0.8744 (tp) cc_final: 0.8259 (tt) REVERT: J 54 TYR cc_start: 0.8899 (t80) cc_final: 0.8495 (t80) REVERT: J 57 TYR cc_start: 0.8689 (t80) cc_final: 0.8452 (t80) REVERT: J 58 ARG cc_start: 0.8180 (mmt180) cc_final: 0.7880 (mmt180) REVERT: J 64 THR cc_start: 0.8630 (m) cc_final: 0.8232 (m) REVERT: K 9 LEU cc_start: 0.9230 (mt) cc_final: 0.8980 (mm) REVERT: K 37 LYS cc_start: 0.9113 (ttmt) cc_final: 0.7915 (tptp) REVERT: K 39 SER cc_start: 0.8861 (m) cc_final: 0.8641 (t) REVERT: K 47 TYR cc_start: 0.9029 (t80) cc_final: 0.8021 (t80) REVERT: K 54 TYR cc_start: 0.8955 (t80) cc_final: 0.8625 (t80) REVERT: K 61 GLN cc_start: 0.8940 (tt0) cc_final: 0.8709 (tt0) REVERT: L 23 LEU cc_start: 0.8841 (tp) cc_final: 0.8296 (tt) REVERT: L 26 GLN cc_start: 0.8671 (mt0) cc_final: 0.8421 (mt0) REVERT: L 37 LYS cc_start: 0.9006 (ttmt) cc_final: 0.7242 (tptt) REVERT: L 39 SER cc_start: 0.9050 (m) cc_final: 0.8790 (t) REVERT: L 53 GLU cc_start: 0.8349 (tp30) cc_final: 0.7778 (tp30) REVERT: M 28 THR cc_start: 0.9247 (m) cc_final: 0.8054 (p) REVERT: M 31 LEU cc_start: 0.9203 (tp) cc_final: 0.8779 (tt) REVERT: M 33 LYS cc_start: 0.9116 (mttt) cc_final: 0.8861 (mtmt) REVERT: M 39 SER cc_start: 0.9295 (m) cc_final: 0.8820 (p) REVERT: M 47 TYR cc_start: 0.9139 (t80) cc_final: 0.8715 (t80) REVERT: M 51 LEU cc_start: 0.9386 (tp) cc_final: 0.9087 (tp) REVERT: M 54 TYR cc_start: 0.9097 (t80) cc_final: 0.8803 (t80) REVERT: N 31 LEU cc_start: 0.9170 (tp) cc_final: 0.8881 (tt) REVERT: N 43 LEU cc_start: 0.9280 (mt) cc_final: 0.8975 (mt) REVERT: N 47 TYR cc_start: 0.9145 (t80) cc_final: 0.8732 (t80) REVERT: N 51 LEU cc_start: 0.9065 (tp) cc_final: 0.8697 (tt) REVERT: N 58 ARG cc_start: 0.8693 (mmt180) cc_final: 0.8489 (mmt180) REVERT: O 9 LEU cc_start: 0.9010 (mt) cc_final: 0.8703 (mt) REVERT: O 15 LYS cc_start: 0.8916 (mttt) cc_final: 0.8674 (tppt) REVERT: O 17 ASP cc_start: 0.7785 (m-30) cc_final: 0.7428 (t0) REVERT: O 22 ASN cc_start: 0.9063 (p0) cc_final: 0.7894 (p0) REVERT: O 25 THR cc_start: 0.8817 (m) cc_final: 0.8390 (m) REVERT: O 28 THR cc_start: 0.8657 (m) cc_final: 0.8345 (p) REVERT: O 33 LYS cc_start: 0.9062 (mttt) cc_final: 0.8847 (mmmm) REVERT: O 47 TYR cc_start: 0.8941 (t80) cc_final: 0.8642 (t80) REVERT: O 50 LYS cc_start: 0.9063 (mmtt) cc_final: 0.8834 (mmtm) REVERT: O 53 GLU cc_start: 0.8604 (tp30) cc_final: 0.8305 (tp30) REVERT: O 55 ASN cc_start: 0.9010 (t0) cc_final: 0.7921 (t0) REVERT: O 58 ARG cc_start: 0.8940 (mmt180) cc_final: 0.8618 (mmt-90) REVERT: O 59 ASN cc_start: 0.8739 (m-40) cc_final: 0.8134 (m110) REVERT: O 69 LYS cc_start: 0.8210 (tttm) cc_final: 0.7947 (tptt) REVERT: P 22 ASN cc_start: 0.9054 (p0) cc_final: 0.8649 (p0) REVERT: P 40 ASP cc_start: 0.7928 (t0) cc_final: 0.7707 (t0) REVERT: P 56 LEU cc_start: 0.9466 (mt) cc_final: 0.8965 (mp) REVERT: Q 33 LYS cc_start: 0.8819 (mttt) cc_final: 0.8523 (mttp) REVERT: Q 47 TYR cc_start: 0.9157 (t80) cc_final: 0.8888 (t80) REVERT: Q 51 LEU cc_start: 0.9225 (tp) cc_final: 0.8827 (tp) REVERT: Q 56 LEU cc_start: 0.9501 (mt) cc_final: 0.9244 (mm) REVERT: Q 57 TYR cc_start: 0.9030 (t80) cc_final: 0.8534 (t80) REVERT: Q 58 ARG cc_start: 0.8919 (mmt180) cc_final: 0.8668 (mmt-90) REVERT: Q 69 LYS cc_start: 0.8488 (tttm) cc_final: 0.7627 (tptt) REVERT: R 6 SER cc_start: 0.8532 (m) cc_final: 0.8202 (t) REVERT: R 22 ASN cc_start: 0.8994 (p0) cc_final: 0.7796 (p0) REVERT: R 25 THR cc_start: 0.8501 (m) cc_final: 0.7824 (p) REVERT: R 28 THR cc_start: 0.8689 (m) cc_final: 0.8055 (p) REVERT: R 39 SER cc_start: 0.9221 (m) cc_final: 0.8748 (t) REVERT: R 56 LEU cc_start: 0.9130 (mt) cc_final: 0.8747 (mt) REVERT: S 22 ASN cc_start: 0.8719 (p0) cc_final: 0.8454 (p0) REVERT: S 25 THR cc_start: 0.7755 (m) cc_final: 0.6977 (p) REVERT: S 31 LEU cc_start: 0.8716 (tp) cc_final: 0.8107 (tp) REVERT: S 33 LYS cc_start: 0.8394 (mttt) cc_final: 0.8104 (ttmm) REVERT: T 22 ASN cc_start: 0.8787 (p0) cc_final: 0.8096 (p0) REVERT: T 25 THR cc_start: 0.8429 (m) cc_final: 0.7695 (p) REVERT: T 26 GLN cc_start: 0.9243 (mt0) cc_final: 0.8906 (mt0) REVERT: T 28 THR cc_start: 0.8064 (m) cc_final: 0.7510 (p) REVERT: T 39 SER cc_start: 0.9144 (m) cc_final: 0.8937 (p) REVERT: T 43 LEU cc_start: 0.9287 (mt) cc_final: 0.8440 (mt) REVERT: T 47 TYR cc_start: 0.9026 (t80) cc_final: 0.8042 (t80) REVERT: T 50 LYS cc_start: 0.9094 (mmtt) cc_final: 0.8752 (mmtt) REVERT: T 57 TYR cc_start: 0.8561 (t80) cc_final: 0.7517 (t80) REVERT: T 58 ARG cc_start: 0.8754 (mmt180) cc_final: 0.6824 (mtt180) outliers start: 0 outliers final: 0 residues processed: 643 average time/residue: 0.2381 time to fit residues: 212.6715 Evaluate side-chains 527 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 527 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 GLN U 26 GLN F 77 GLN G 78 ASN I 63 ASN J 26 GLN K 63 ASN L 63 ASN M 61 GLN ** O 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 GLN R 63 ASN S 48 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11837 Z= 0.199 Angle : 0.549 5.509 16112 Z= 0.304 Chirality : 0.037 0.134 1843 Planarity : 0.004 0.021 2109 Dihedral : 4.212 15.244 1596 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.87 % Allowed : 11.48 % Favored : 85.65 % 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: -2.06 (0.18), residues: 1444 helix: -0.77 (0.12), residues: 1292 sheet: None (None), residues: 0 loop : -5.28 (0.25), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 5 PHE 0.010 0.001 PHE T 79 TYR 0.016 0.002 TYR O 54 ARG 0.005 0.000 ARG J 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 581 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8549 (mmmm) cc_final: 0.8209 (mmmt) REVERT: U 15 LYS cc_start: 0.8940 (mttt) cc_final: 0.8414 (mmmm) REVERT: U 37 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7233 (tptp) REVERT: U 53 GLU cc_start: 0.8349 (tp30) cc_final: 0.8035 (mm-30) REVERT: U 66 LYS cc_start: 0.8785 (tptp) cc_final: 0.6728 (mttt) REVERT: V 28 THR cc_start: 0.8696 (m) cc_final: 0.8276 (p) REVERT: V 37 LYS cc_start: 0.9251 (ttmt) cc_final: 0.7900 (tptt) REVERT: V 47 TYR cc_start: 0.9000 (t80) cc_final: 0.8220 (t80) REVERT: V 49 SER cc_start: 0.8645 (t) cc_final: 0.8295 (p) REVERT: V 53 GLU cc_start: 0.8388 (tp30) cc_final: 0.7932 (mm-30) REVERT: V 77 GLN cc_start: 0.8339 (tp40) cc_final: 0.7745 (tp-100) REVERT: E 32 ASP cc_start: 0.8093 (m-30) cc_final: 0.7855 (m-30) REVERT: E 37 LYS cc_start: 0.7799 (ttmt) cc_final: 0.7025 (tptt) REVERT: E 48 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8533 (tm-30) REVERT: E 57 TYR cc_start: 0.8339 (t80) cc_final: 0.7778 (t80) REVERT: F 28 THR cc_start: 0.8725 (m) cc_final: 0.8217 (p) REVERT: F 32 ASP cc_start: 0.7714 (m-30) cc_final: 0.7434 (m-30) REVERT: F 34 LEU cc_start: 0.9245 (tp) cc_final: 0.8985 (tt) REVERT: F 37 LYS cc_start: 0.8615 (ttmt) cc_final: 0.7919 (tptt) REVERT: F 39 SER cc_start: 0.8690 (m) cc_final: 0.8290 (t) REVERT: F 47 TYR cc_start: 0.8927 (t80) cc_final: 0.8184 (t80) REVERT: F 49 SER cc_start: 0.9237 (t) cc_final: 0.8833 (p) REVERT: F 53 GLU cc_start: 0.8392 (tp30) cc_final: 0.7486 (mm-30) REVERT: F 66 LYS cc_start: 0.8858 (tptp) cc_final: 0.7287 (mttm) REVERT: G 11 ASP cc_start: 0.8389 (m-30) cc_final: 0.7842 (m-30) REVERT: G 15 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8874 (ttmm) REVERT: G 37 LYS cc_start: 0.8416 (ttmt) cc_final: 0.7152 (tptt) REVERT: G 49 SER cc_start: 0.8765 (t) cc_final: 0.8219 (m) REVERT: G 69 LYS cc_start: 0.8586 (tttm) cc_final: 0.8356 (tttt) REVERT: H 28 THR cc_start: 0.9000 (m) cc_final: 0.8459 (p) REVERT: H 31 LEU cc_start: 0.8879 (tp) cc_final: 0.8614 (tt) REVERT: H 32 ASP cc_start: 0.8023 (m-30) cc_final: 0.7568 (m-30) REVERT: H 37 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7084 (tptt) REVERT: H 39 SER cc_start: 0.9101 (m) cc_final: 0.8866 (m) REVERT: H 47 TYR cc_start: 0.9170 (t80) cc_final: 0.7461 (t80) REVERT: H 51 LEU cc_start: 0.9238 (tp) cc_final: 0.8761 (tp) REVERT: I 28 THR cc_start: 0.9049 (m) cc_final: 0.8700 (p) REVERT: I 32 ASP cc_start: 0.8537 (m-30) cc_final: 0.8269 (m-30) REVERT: I 37 LYS cc_start: 0.8708 (ttmt) cc_final: 0.7326 (tptp) REVERT: I 47 TYR cc_start: 0.9265 (t80) cc_final: 0.8965 (t80) REVERT: J 24 GLN cc_start: 0.8193 (mp10) cc_final: 0.7828 (tp-100) REVERT: J 37 LYS cc_start: 0.8779 (ttmt) cc_final: 0.7301 (tptp) REVERT: J 47 TYR cc_start: 0.9236 (t80) cc_final: 0.8697 (t80) REVERT: J 49 SER cc_start: 0.9251 (t) cc_final: 0.8787 (p) REVERT: J 50 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8666 (mmtt) REVERT: K 37 LYS cc_start: 0.9108 (ttmt) cc_final: 0.7796 (tptt) REVERT: K 40 ASP cc_start: 0.8023 (t0) cc_final: 0.7795 (t70) REVERT: K 47 TYR cc_start: 0.9134 (t80) cc_final: 0.8227 (t80) REVERT: K 50 LYS cc_start: 0.9051 (mmtt) cc_final: 0.8838 (mmtp) REVERT: K 77 GLN cc_start: 0.8500 (tp40) cc_final: 0.8277 (tp-100) REVERT: L 23 LEU cc_start: 0.8793 (tp) cc_final: 0.8286 (tt) REVERT: L 26 GLN cc_start: 0.8510 (mt0) cc_final: 0.8300 (mt0) REVERT: L 31 LEU cc_start: 0.9149 (tp) cc_final: 0.8904 (tp) REVERT: L 37 LYS cc_start: 0.8746 (ttmt) cc_final: 0.7158 (tptt) REVERT: L 53 GLU cc_start: 0.8167 (tp30) cc_final: 0.7797 (tp30) REVERT: M 28 THR cc_start: 0.8759 (m) cc_final: 0.8310 (p) REVERT: M 31 LEU cc_start: 0.9098 (tp) cc_final: 0.8632 (tt) REVERT: M 32 ASP cc_start: 0.8371 (p0) cc_final: 0.8149 (p0) REVERT: M 39 SER cc_start: 0.9178 (m) cc_final: 0.8888 (p) REVERT: M 47 TYR cc_start: 0.9089 (t80) cc_final: 0.8617 (t80) REVERT: M 50 LYS cc_start: 0.9191 (mmtt) cc_final: 0.8825 (mmtt) REVERT: M 66 LYS cc_start: 0.8750 (tptt) cc_final: 0.8170 (tmtt) REVERT: N 47 TYR cc_start: 0.8953 (t80) cc_final: 0.8531 (t80) REVERT: N 49 SER cc_start: 0.9594 (m) cc_final: 0.9330 (t) REVERT: N 50 LYS cc_start: 0.9245 (mmtp) cc_final: 0.8739 (mmmt) REVERT: N 51 LEU cc_start: 0.9008 (tp) cc_final: 0.8763 (tt) REVERT: N 53 GLU cc_start: 0.8343 (tp30) cc_final: 0.7840 (tp30) REVERT: N 58 ARG cc_start: 0.8408 (mmt180) cc_final: 0.8067 (mmt180) REVERT: O 17 ASP cc_start: 0.7920 (m-30) cc_final: 0.7165 (t0) REVERT: O 22 ASN cc_start: 0.9207 (p0) cc_final: 0.8357 (p0) REVERT: O 25 THR cc_start: 0.9064 (m) cc_final: 0.8710 (m) REVERT: O 28 THR cc_start: 0.8586 (m) cc_final: 0.7243 (p) REVERT: O 33 LYS cc_start: 0.9147 (mttt) cc_final: 0.8461 (mtmm) REVERT: O 47 TYR cc_start: 0.9138 (t80) cc_final: 0.8853 (t80) REVERT: O 49 SER cc_start: 0.9469 (m) cc_final: 0.9173 (t) REVERT: O 58 ARG cc_start: 0.8655 (mmt180) cc_final: 0.8383 (mmt-90) REVERT: O 59 ASN cc_start: 0.8552 (m-40) cc_final: 0.7830 (m110) REVERT: O 69 LYS cc_start: 0.8382 (tttm) cc_final: 0.7846 (tttt) REVERT: P 22 ASN cc_start: 0.9178 (p0) cc_final: 0.8871 (p0) REVERT: Q 28 THR cc_start: 0.8242 (m) cc_final: 0.8005 (p) REVERT: Q 40 ASP cc_start: 0.8344 (t0) cc_final: 0.7914 (t0) REVERT: Q 54 TYR cc_start: 0.8454 (t80) cc_final: 0.7875 (t80) REVERT: Q 57 TYR cc_start: 0.8984 (t80) cc_final: 0.8552 (t80) REVERT: Q 69 LYS cc_start: 0.8586 (tttm) cc_final: 0.8151 (ttmt) REVERT: Q 76 ILE cc_start: 0.8214 (mm) cc_final: 0.7953 (tt) REVERT: R 22 ASN cc_start: 0.8925 (p0) cc_final: 0.8173 (p0) REVERT: R 24 GLN cc_start: 0.8313 (mp10) cc_final: 0.8061 (pm20) REVERT: R 25 THR cc_start: 0.8609 (m) cc_final: 0.8064 (p) REVERT: R 29 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8072 (tm-30) REVERT: R 33 LYS cc_start: 0.8986 (ttmt) cc_final: 0.8539 (mtmt) REVERT: S 25 THR cc_start: 0.8157 (m) cc_final: 0.7813 (p) REVERT: S 39 SER cc_start: 0.8948 (m) cc_final: 0.8090 (m) REVERT: T 22 ASN cc_start: 0.8591 (p0) cc_final: 0.8068 (p0) REVERT: T 31 LEU cc_start: 0.8887 (tp) cc_final: 0.8644 (tp) REVERT: T 39 SER cc_start: 0.9084 (m) cc_final: 0.8775 (p) REVERT: T 40 ASP cc_start: 0.8316 (t0) cc_final: 0.7926 (t0) REVERT: T 48 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8818 (tm-30) REVERT: T 50 LYS cc_start: 0.9009 (mmtt) cc_final: 0.8747 (mmmt) REVERT: T 66 LYS cc_start: 0.9067 (tptp) cc_final: 0.8730 (tppt) REVERT: T 69 LYS cc_start: 0.7163 (tttm) cc_final: 0.6802 (ttmt) outliers start: 36 outliers final: 24 residues processed: 594 average time/residue: 0.2426 time to fit residues: 202.2688 Evaluate side-chains 561 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 536 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 10 ASP Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 GLN D 77 GLN U 26 GLN K 24 GLN M 26 GLN ** O 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 GLN S 26 GLN T 24 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11837 Z= 0.193 Angle : 0.496 6.997 16112 Z= 0.265 Chirality : 0.037 0.110 1843 Planarity : 0.003 0.020 2109 Dihedral : 3.845 17.569 1596 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.75 % Allowed : 15.95 % Favored : 80.30 % 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: 0.18 (0.21), residues: 1444 helix: 0.75 (0.13), residues: 1292 sheet: None (None), residues: 0 loop : -5.04 (0.25), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 5 PHE 0.006 0.001 PHE T 79 TYR 0.018 0.002 TYR N 57 ARG 0.004 0.000 ARG J 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 559 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8661 (mmmm) cc_final: 0.8338 (mmmt) REVERT: D 22 ASN cc_start: 0.7173 (p0) cc_final: 0.6915 (p0) REVERT: D 76 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8987 (mt) REVERT: U 15 LYS cc_start: 0.8970 (mttt) cc_final: 0.8474 (mmmm) REVERT: U 37 LYS cc_start: 0.8222 (ttmt) cc_final: 0.7295 (tptp) REVERT: U 66 LYS cc_start: 0.8758 (tptp) cc_final: 0.6557 (mttt) REVERT: V 37 LYS cc_start: 0.9168 (ttmt) cc_final: 0.7731 (tptt) REVERT: V 47 TYR cc_start: 0.9049 (t80) cc_final: 0.8290 (t80) REVERT: V 49 SER cc_start: 0.8639 (t) cc_final: 0.8277 (p) REVERT: V 53 GLU cc_start: 0.8037 (tp30) cc_final: 0.7836 (mm-30) REVERT: V 77 GLN cc_start: 0.8580 (tp40) cc_final: 0.7889 (tp-100) REVERT: E 11 ASP cc_start: 0.8148 (m-30) cc_final: 0.7602 (m-30) REVERT: E 37 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7250 (tptt) REVERT: E 54 TYR cc_start: 0.8595 (t80) cc_final: 0.8326 (t80) REVERT: E 66 LYS cc_start: 0.7909 (tptp) cc_final: 0.5961 (mttt) REVERT: E 69 LYS cc_start: 0.7791 (tttm) cc_final: 0.7517 (tptp) REVERT: F 28 THR cc_start: 0.8711 (m) cc_final: 0.8129 (p) REVERT: F 32 ASP cc_start: 0.7761 (m-30) cc_final: 0.7459 (m-30) REVERT: F 34 LEU cc_start: 0.9209 (tp) cc_final: 0.8936 (tt) REVERT: F 37 LYS cc_start: 0.8383 (ttmt) cc_final: 0.7735 (tptt) REVERT: F 39 SER cc_start: 0.8763 (m) cc_final: 0.8217 (t) REVERT: F 47 TYR cc_start: 0.8883 (t80) cc_final: 0.8228 (t80) REVERT: F 49 SER cc_start: 0.9300 (t) cc_final: 0.8973 (p) REVERT: F 53 GLU cc_start: 0.8340 (tp30) cc_final: 0.7804 (mm-30) REVERT: F 63 ASN cc_start: 0.9160 (m-40) cc_final: 0.8804 (m110) REVERT: F 66 LYS cc_start: 0.8829 (tptp) cc_final: 0.7323 (mttm) REVERT: G 11 ASP cc_start: 0.8392 (m-30) cc_final: 0.7969 (t0) REVERT: G 15 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8749 (ttmm) REVERT: G 37 LYS cc_start: 0.8432 (ttmt) cc_final: 0.7214 (tptt) REVERT: G 49 SER cc_start: 0.8726 (t) cc_final: 0.8209 (m) REVERT: G 69 LYS cc_start: 0.8725 (tttm) cc_final: 0.8390 (tttt) REVERT: H 23 LEU cc_start: 0.8826 (tp) cc_final: 0.8581 (tt) REVERT: H 28 THR cc_start: 0.8959 (m) cc_final: 0.8422 (p) REVERT: H 31 LEU cc_start: 0.8798 (tp) cc_final: 0.8592 (tt) REVERT: H 32 ASP cc_start: 0.7809 (m-30) cc_final: 0.7380 (m-30) REVERT: H 37 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7085 (tptt) REVERT: H 47 TYR cc_start: 0.9151 (t80) cc_final: 0.7411 (t80) REVERT: H 51 LEU cc_start: 0.9277 (tp) cc_final: 0.8757 (tp) REVERT: H 77 GLN cc_start: 0.8566 (tp40) cc_final: 0.8362 (tp40) REVERT: I 28 THR cc_start: 0.9046 (m) cc_final: 0.8713 (p) REVERT: I 32 ASP cc_start: 0.8521 (m-30) cc_final: 0.8274 (m-30) REVERT: I 37 LYS cc_start: 0.8664 (ttmt) cc_final: 0.7313 (tptp) REVERT: I 47 TYR cc_start: 0.9271 (t80) cc_final: 0.8934 (t80) REVERT: J 17 ASP cc_start: 0.7933 (m-30) cc_final: 0.7595 (m-30) REVERT: J 22 ASN cc_start: 0.8051 (p0) cc_final: 0.7479 (p0) REVERT: J 24 GLN cc_start: 0.7906 (mp10) cc_final: 0.7646 (tp-100) REVERT: J 37 LYS cc_start: 0.8767 (ttmt) cc_final: 0.7329 (tptt) REVERT: J 47 TYR cc_start: 0.9165 (t80) cc_final: 0.8690 (t80) REVERT: J 49 SER cc_start: 0.9235 (t) cc_final: 0.8833 (p) REVERT: J 80 ARG cc_start: 0.7809 (ttp80) cc_final: 0.7547 (ttp80) REVERT: K 33 LYS cc_start: 0.9198 (mttt) cc_final: 0.8821 (mtpp) REVERT: K 37 LYS cc_start: 0.9118 (ttmt) cc_final: 0.7760 (tptt) REVERT: K 47 TYR cc_start: 0.9124 (t80) cc_final: 0.7813 (t80) REVERT: K 63 ASN cc_start: 0.8572 (m-40) cc_final: 0.8277 (m110) REVERT: L 23 LEU cc_start: 0.8572 (tp) cc_final: 0.8245 (tt) REVERT: L 26 GLN cc_start: 0.8568 (mt0) cc_final: 0.8361 (tt0) REVERT: L 37 LYS cc_start: 0.8709 (ttmt) cc_final: 0.6958 (tptt) REVERT: L 53 GLU cc_start: 0.8155 (tp30) cc_final: 0.7862 (tp30) REVERT: M 28 THR cc_start: 0.8807 (m) cc_final: 0.8237 (p) REVERT: M 31 LEU cc_start: 0.9229 (tp) cc_final: 0.8731 (tt) REVERT: M 32 ASP cc_start: 0.8376 (p0) cc_final: 0.8112 (p0) REVERT: M 33 LYS cc_start: 0.9099 (mttt) cc_final: 0.8861 (mtpt) REVERT: M 39 SER cc_start: 0.9124 (m) cc_final: 0.8603 (p) REVERT: M 47 TYR cc_start: 0.9229 (t80) cc_final: 0.8645 (t80) REVERT: M 66 LYS cc_start: 0.8794 (tptt) cc_final: 0.8116 (tmtt) REVERT: N 15 LYS cc_start: 0.8595 (ttmm) cc_final: 0.8307 (ttmm) REVERT: N 24 GLN cc_start: 0.8809 (mp10) cc_final: 0.8100 (tm-30) REVERT: N 32 ASP cc_start: 0.8253 (m-30) cc_final: 0.8021 (m-30) REVERT: N 47 TYR cc_start: 0.8871 (t80) cc_final: 0.8542 (t80) REVERT: N 49 SER cc_start: 0.9515 (m) cc_final: 0.9263 (t) REVERT: N 50 LYS cc_start: 0.9037 (mmtp) cc_final: 0.8428 (mmmt) REVERT: N 51 LEU cc_start: 0.8984 (tp) cc_final: 0.8660 (tt) REVERT: N 53 GLU cc_start: 0.8269 (tp30) cc_final: 0.7714 (tp30) REVERT: O 17 ASP cc_start: 0.7944 (m-30) cc_final: 0.7260 (t0) REVERT: O 22 ASN cc_start: 0.9223 (p0) cc_final: 0.7761 (p0) REVERT: O 25 THR cc_start: 0.9091 (m) cc_final: 0.8400 (p) REVERT: O 28 THR cc_start: 0.8409 (m) cc_final: 0.8091 (p) REVERT: O 33 LYS cc_start: 0.9129 (mttt) cc_final: 0.8418 (mtmm) REVERT: O 47 TYR cc_start: 0.9116 (t80) cc_final: 0.8684 (t80) REVERT: O 49 SER cc_start: 0.9326 (m) cc_final: 0.9031 (t) REVERT: O 52 SER cc_start: 0.9013 (m) cc_final: 0.8768 (t) REVERT: O 59 ASN cc_start: 0.8540 (m-40) cc_final: 0.7730 (m110) REVERT: O 69 LYS cc_start: 0.8097 (tttm) cc_final: 0.7820 (ttmt) REVERT: O 77 GLN cc_start: 0.8591 (tp-100) cc_final: 0.8346 (tp-100) REVERT: P 22 ASN cc_start: 0.9240 (p0) cc_final: 0.8687 (p0) REVERT: P 24 GLN cc_start: 0.8180 (mp10) cc_final: 0.7941 (mp10) REVERT: P 26 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8954 (tt0) REVERT: P 56 LEU cc_start: 0.9314 (mt) cc_final: 0.9093 (mp) REVERT: Q 17 ASP cc_start: 0.7749 (m-30) cc_final: 0.7429 (m-30) REVERT: Q 25 THR cc_start: 0.8819 (m) cc_final: 0.8191 (p) REVERT: Q 28 THR cc_start: 0.8239 (m) cc_final: 0.7983 (p) REVERT: Q 40 ASP cc_start: 0.8211 (t0) cc_final: 0.7657 (t0) REVERT: Q 54 TYR cc_start: 0.8453 (t80) cc_final: 0.7977 (t80) REVERT: Q 57 TYR cc_start: 0.9022 (t80) cc_final: 0.8520 (t80) REVERT: Q 69 LYS cc_start: 0.8585 (tttm) cc_final: 0.8086 (ttmt) REVERT: R 22 ASN cc_start: 0.8934 (p0) cc_final: 0.8197 (p0) REVERT: R 24 GLN cc_start: 0.8332 (mp10) cc_final: 0.8107 (pm20) REVERT: R 33 LYS cc_start: 0.9025 (ttmt) cc_final: 0.8469 (mtmt) REVERT: S 25 THR cc_start: 0.8024 (m) cc_final: 0.7766 (p) REVERT: S 31 LEU cc_start: 0.8941 (tp) cc_final: 0.8504 (tp) REVERT: S 33 LYS cc_start: 0.8811 (mttp) cc_final: 0.8154 (mtpp) REVERT: S 39 SER cc_start: 0.9160 (m) cc_final: 0.8263 (m) REVERT: S 59 ASN cc_start: 0.8637 (m-40) cc_final: 0.8023 (m110) REVERT: S 76 ILE cc_start: 0.7902 (mt) cc_final: 0.7571 (tt) REVERT: T 22 ASN cc_start: 0.8610 (p0) cc_final: 0.8184 (p0) REVERT: T 25 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8353 (p) REVERT: T 48 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8817 (tm-30) REVERT: T 50 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8785 (mmmt) REVERT: T 69 LYS cc_start: 0.7188 (tttm) cc_final: 0.6709 (ttmt) outliers start: 47 outliers final: 28 residues processed: 573 average time/residue: 0.2238 time to fit residues: 181.0673 Evaluate side-chains 562 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 530 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 26 GLN Chi-restraints excluded: chain P residue 33 LYS Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 GLN D 77 GLN ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 ASN T 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 11837 Z= 0.290 Angle : 0.541 7.882 16112 Z= 0.286 Chirality : 0.040 0.114 1843 Planarity : 0.003 0.016 2109 Dihedral : 3.884 21.536 1596 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.23 % Allowed : 18.02 % Favored : 77.75 % 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: 1.01 (0.22), residues: 1444 helix: 1.31 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.89 (0.28), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 5 PHE 0.011 0.002 PHE N 68 TYR 0.014 0.002 TYR G 57 ARG 0.003 0.001 ARG J 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 569 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8480 (mmmt) REVERT: D 23 LEU cc_start: 0.8128 (tp) cc_final: 0.7761 (tt) REVERT: D 76 ILE cc_start: 0.9223 (mt) cc_final: 0.8904 (mt) REVERT: U 15 LYS cc_start: 0.9085 (mttt) cc_final: 0.8747 (mmtp) REVERT: U 37 LYS cc_start: 0.8164 (ttmt) cc_final: 0.7247 (tptt) REVERT: U 66 LYS cc_start: 0.8680 (tptp) cc_final: 0.7060 (mttt) REVERT: V 37 LYS cc_start: 0.8707 (ttmt) cc_final: 0.7464 (tptt) REVERT: V 47 TYR cc_start: 0.9160 (t80) cc_final: 0.8355 (t80) REVERT: V 49 SER cc_start: 0.8646 (t) cc_final: 0.8259 (p) REVERT: V 51 LEU cc_start: 0.9178 (tp) cc_final: 0.8960 (tp) REVERT: V 53 GLU cc_start: 0.8010 (tp30) cc_final: 0.7742 (mm-30) REVERT: V 77 GLN cc_start: 0.8740 (tp40) cc_final: 0.8036 (tp-100) REVERT: E 23 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7212 (tp) REVERT: E 37 LYS cc_start: 0.8709 (ttmt) cc_final: 0.7392 (tptt) REVERT: E 47 TYR cc_start: 0.8988 (t80) cc_final: 0.8605 (t80) REVERT: E 53 GLU cc_start: 0.8823 (tp30) cc_final: 0.8222 (mm-30) REVERT: E 66 LYS cc_start: 0.8142 (tptp) cc_final: 0.6638 (mttt) REVERT: F 28 THR cc_start: 0.8740 (m) cc_final: 0.8121 (p) REVERT: F 32 ASP cc_start: 0.7823 (m-30) cc_final: 0.7496 (m-30) REVERT: F 34 LEU cc_start: 0.9223 (tp) cc_final: 0.8964 (tt) REVERT: F 37 LYS cc_start: 0.8469 (ttmt) cc_final: 0.7806 (tptt) REVERT: F 39 SER cc_start: 0.8863 (m) cc_final: 0.8221 (t) REVERT: F 47 TYR cc_start: 0.8999 (t80) cc_final: 0.8372 (t80) REVERT: F 49 SER cc_start: 0.9295 (t) cc_final: 0.8907 (p) REVERT: F 53 GLU cc_start: 0.8345 (tp30) cc_final: 0.7740 (mm-30) REVERT: F 66 LYS cc_start: 0.8659 (tptp) cc_final: 0.7315 (mttm) REVERT: G 11 ASP cc_start: 0.8243 (m-30) cc_final: 0.7948 (t0) REVERT: G 15 LYS cc_start: 0.9121 (ttmt) cc_final: 0.8735 (ttmm) REVERT: G 33 LYS cc_start: 0.9082 (mtpp) cc_final: 0.8855 (mtpp) REVERT: G 37 LYS cc_start: 0.8441 (ttmt) cc_final: 0.7154 (tptt) REVERT: G 66 LYS cc_start: 0.9133 (tppt) cc_final: 0.8486 (tppt) REVERT: G 69 LYS cc_start: 0.8723 (tttm) cc_final: 0.8386 (tttt) REVERT: H 23 LEU cc_start: 0.8853 (tp) cc_final: 0.8590 (tt) REVERT: H 28 THR cc_start: 0.8995 (m) cc_final: 0.8293 (p) REVERT: H 32 ASP cc_start: 0.7960 (m-30) cc_final: 0.7620 (m-30) REVERT: H 37 LYS cc_start: 0.8137 (ttmt) cc_final: 0.6882 (tptt) REVERT: H 47 TYR cc_start: 0.9173 (t80) cc_final: 0.7388 (t80) REVERT: H 51 LEU cc_start: 0.9334 (tp) cc_final: 0.8693 (tp) REVERT: H 77 GLN cc_start: 0.8565 (tp40) cc_final: 0.8349 (tp40) REVERT: I 28 THR cc_start: 0.9087 (m) cc_final: 0.8720 (p) REVERT: I 32 ASP cc_start: 0.8438 (m-30) cc_final: 0.8197 (m-30) REVERT: I 37 LYS cc_start: 0.8731 (ttmt) cc_final: 0.7381 (tptp) REVERT: I 47 TYR cc_start: 0.9303 (t80) cc_final: 0.8960 (t80) REVERT: I 77 GLN cc_start: 0.8628 (tp40) cc_final: 0.8412 (tp40) REVERT: J 17 ASP cc_start: 0.7951 (m-30) cc_final: 0.7698 (m-30) REVERT: J 22 ASN cc_start: 0.8264 (p0) cc_final: 0.7672 (p0) REVERT: J 37 LYS cc_start: 0.8842 (ttmt) cc_final: 0.7324 (tptt) REVERT: J 47 TYR cc_start: 0.9221 (t80) cc_final: 0.8539 (t80) REVERT: J 49 SER cc_start: 0.9220 (t) cc_final: 0.8864 (p) REVERT: J 54 TYR cc_start: 0.8952 (t80) cc_final: 0.8573 (t80) REVERT: K 33 LYS cc_start: 0.9208 (mttt) cc_final: 0.8847 (mtpp) REVERT: K 37 LYS cc_start: 0.9106 (ttmt) cc_final: 0.7712 (tptt) REVERT: K 47 TYR cc_start: 0.9169 (t80) cc_final: 0.7755 (t80) REVERT: K 53 GLU cc_start: 0.8298 (tp30) cc_final: 0.8082 (mm-30) REVERT: K 63 ASN cc_start: 0.8670 (m-40) cc_final: 0.8221 (m110) REVERT: L 23 LEU cc_start: 0.8678 (tp) cc_final: 0.8350 (tp) REVERT: L 26 GLN cc_start: 0.8713 (mt0) cc_final: 0.8403 (tt0) REVERT: L 37 LYS cc_start: 0.8759 (ttmt) cc_final: 0.6993 (tptt) REVERT: L 48 GLN cc_start: 0.8752 (tt0) cc_final: 0.8070 (tt0) REVERT: L 53 GLU cc_start: 0.8251 (tp30) cc_final: 0.7840 (tp30) REVERT: M 28 THR cc_start: 0.8849 (m) cc_final: 0.8194 (p) REVERT: M 31 LEU cc_start: 0.9243 (tp) cc_final: 0.8771 (tt) REVERT: M 32 ASP cc_start: 0.8335 (p0) cc_final: 0.8017 (p0) REVERT: M 39 SER cc_start: 0.9257 (m) cc_final: 0.8976 (p) REVERT: M 47 TYR cc_start: 0.9216 (t80) cc_final: 0.8639 (t80) REVERT: M 66 LYS cc_start: 0.8557 (tptt) cc_final: 0.8038 (tmtt) REVERT: N 15 LYS cc_start: 0.8625 (ttmm) cc_final: 0.8149 (ttmm) REVERT: N 24 GLN cc_start: 0.8768 (mp10) cc_final: 0.7965 (tm-30) REVERT: N 32 ASP cc_start: 0.8237 (m-30) cc_final: 0.7960 (m-30) REVERT: N 49 SER cc_start: 0.9470 (m) cc_final: 0.9203 (t) REVERT: N 50 LYS cc_start: 0.8963 (mmtp) cc_final: 0.8429 (mmmt) REVERT: N 51 LEU cc_start: 0.9002 (tp) cc_final: 0.8714 (tt) REVERT: N 53 GLU cc_start: 0.8323 (tp30) cc_final: 0.7733 (tp30) REVERT: O 15 LYS cc_start: 0.8869 (tppt) cc_final: 0.8545 (tptp) REVERT: O 17 ASP cc_start: 0.7937 (m-30) cc_final: 0.7234 (t0) REVERT: O 22 ASN cc_start: 0.9254 (p0) cc_final: 0.8029 (p0) REVERT: O 25 THR cc_start: 0.9017 (m) cc_final: 0.8410 (p) REVERT: O 28 THR cc_start: 0.8344 (m) cc_final: 0.8053 (p) REVERT: O 33 LYS cc_start: 0.9134 (mttt) cc_final: 0.8398 (mtmm) REVERT: O 47 TYR cc_start: 0.9050 (t80) cc_final: 0.8746 (t80) REVERT: O 49 SER cc_start: 0.9253 (m) cc_final: 0.9009 (t) REVERT: O 52 SER cc_start: 0.9073 (m) cc_final: 0.8689 (t) REVERT: O 59 ASN cc_start: 0.8513 (m-40) cc_final: 0.7896 (m110) REVERT: O 69 LYS cc_start: 0.8211 (tttm) cc_final: 0.7859 (ttmt) REVERT: O 77 GLN cc_start: 0.8764 (tp-100) cc_final: 0.8514 (tp-100) REVERT: P 22 ASN cc_start: 0.9334 (p0) cc_final: 0.8897 (p0) REVERT: P 31 LEU cc_start: 0.8842 (tp) cc_final: 0.8620 (tt) REVERT: P 32 ASP cc_start: 0.8125 (m-30) cc_final: 0.7845 (m-30) REVERT: P 69 LYS cc_start: 0.8133 (tttm) cc_final: 0.7807 (ttmt) REVERT: Q 25 THR cc_start: 0.8835 (m) cc_final: 0.8225 (p) REVERT: Q 28 THR cc_start: 0.8241 (m) cc_final: 0.7973 (p) REVERT: Q 40 ASP cc_start: 0.8347 (t0) cc_final: 0.8102 (t0) REVERT: Q 54 TYR cc_start: 0.8550 (t80) cc_final: 0.7903 (t80) REVERT: Q 57 TYR cc_start: 0.8912 (t80) cc_final: 0.8532 (t80) REVERT: Q 69 LYS cc_start: 0.8614 (tttm) cc_final: 0.7763 (tttt) REVERT: R 22 ASN cc_start: 0.9095 (p0) cc_final: 0.8611 (p0) REVERT: R 24 GLN cc_start: 0.8226 (mp10) cc_final: 0.7849 (pm20) REVERT: R 29 GLU cc_start: 0.8711 (tm-30) cc_final: 0.7998 (tm-30) REVERT: R 33 LYS cc_start: 0.9106 (ttmt) cc_final: 0.8482 (mtmt) REVERT: S 5 TRP cc_start: 0.8367 (t60) cc_final: 0.7771 (t60) REVERT: S 17 ASP cc_start: 0.6964 (m-30) cc_final: 0.6686 (m-30) REVERT: S 25 THR cc_start: 0.8298 (m) cc_final: 0.8003 (p) REVERT: S 31 LEU cc_start: 0.9003 (tp) cc_final: 0.8739 (tp) REVERT: S 39 SER cc_start: 0.9265 (m) cc_final: 0.8377 (m) REVERT: S 59 ASN cc_start: 0.8757 (m-40) cc_final: 0.7742 (m110) REVERT: S 69 LYS cc_start: 0.7858 (tttm) cc_final: 0.7534 (ttmt) REVERT: S 76 ILE cc_start: 0.8487 (mt) cc_final: 0.8218 (tt) REVERT: T 22 ASN cc_start: 0.8722 (p0) cc_final: 0.8333 (p0) REVERT: T 25 THR cc_start: 0.8696 (p) cc_final: 0.8211 (t) REVERT: T 48 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8862 (tm-30) REVERT: T 50 LYS cc_start: 0.8862 (mmtt) cc_final: 0.8649 (mmtt) REVERT: T 69 LYS cc_start: 0.6984 (tttm) cc_final: 0.6484 (tttt) outliers start: 53 outliers final: 42 residues processed: 584 average time/residue: 0.2249 time to fit residues: 186.1581 Evaluate side-chains 588 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 545 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain V residue 71 ILE Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 33 LYS Chi-restraints excluded: chain P residue 64 THR Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 GLN D 77 GLN ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 GLN N 48 GLN ** O 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN P 26 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11837 Z= 0.263 Angle : 0.534 9.446 16112 Z= 0.280 Chirality : 0.040 0.189 1843 Planarity : 0.003 0.019 2109 Dihedral : 3.849 22.592 1596 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.39 % Allowed : 19.46 % Favored : 76.16 % 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: 1.47 (0.22), residues: 1444 helix: 1.61 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.68 (0.30), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 5 PHE 0.009 0.001 PHE O 16 TYR 0.013 0.002 TYR P 57 ARG 0.003 0.001 ARG G 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 557 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8966 (mmmm) cc_final: 0.8626 (mmmt) REVERT: D 63 ASN cc_start: 0.8355 (m-40) cc_final: 0.7910 (m-40) REVERT: D 66 LYS cc_start: 0.9181 (tptp) cc_final: 0.7448 (mttt) REVERT: U 15 LYS cc_start: 0.9142 (mttt) cc_final: 0.8869 (mmtp) REVERT: U 37 LYS cc_start: 0.8174 (ttmt) cc_final: 0.7219 (tptt) REVERT: U 66 LYS cc_start: 0.8682 (tptp) cc_final: 0.7033 (mttt) REVERT: V 37 LYS cc_start: 0.8705 (ttmt) cc_final: 0.7467 (tptt) REVERT: V 47 TYR cc_start: 0.9195 (t80) cc_final: 0.8319 (t80) REVERT: V 49 SER cc_start: 0.8622 (t) cc_final: 0.8236 (p) REVERT: V 51 LEU cc_start: 0.9191 (tp) cc_final: 0.8952 (tp) REVERT: V 53 GLU cc_start: 0.8079 (tp30) cc_final: 0.7862 (mm-30) REVERT: V 77 GLN cc_start: 0.8733 (tp40) cc_final: 0.8202 (tp40) REVERT: E 15 LYS cc_start: 0.8701 (mmmm) cc_final: 0.8467 (mmmt) REVERT: E 22 ASN cc_start: 0.7777 (p0) cc_final: 0.7118 (p0) REVERT: E 37 LYS cc_start: 0.8643 (ttmt) cc_final: 0.7327 (tptt) REVERT: E 47 TYR cc_start: 0.9036 (t80) cc_final: 0.8742 (t80) REVERT: E 53 GLU cc_start: 0.8773 (tp30) cc_final: 0.8288 (mm-30) REVERT: E 66 LYS cc_start: 0.8159 (tptp) cc_final: 0.6716 (mttt) REVERT: E 69 LYS cc_start: 0.8233 (tttp) cc_final: 0.7852 (tttp) REVERT: F 28 THR cc_start: 0.8722 (m) cc_final: 0.8061 (p) REVERT: F 32 ASP cc_start: 0.7786 (m-30) cc_final: 0.7440 (m-30) REVERT: F 34 LEU cc_start: 0.9214 (tp) cc_final: 0.8930 (tt) REVERT: F 37 LYS cc_start: 0.8532 (ttmt) cc_final: 0.7850 (tptt) REVERT: F 39 SER cc_start: 0.8884 (m) cc_final: 0.8252 (t) REVERT: F 47 TYR cc_start: 0.9006 (t80) cc_final: 0.8539 (t80) REVERT: F 49 SER cc_start: 0.9294 (t) cc_final: 0.8900 (p) REVERT: F 51 LEU cc_start: 0.9196 (tp) cc_final: 0.8904 (tp) REVERT: F 53 GLU cc_start: 0.8369 (tp30) cc_final: 0.7749 (mm-30) REVERT: F 66 LYS cc_start: 0.8616 (tptp) cc_final: 0.7342 (mttm) REVERT: G 11 ASP cc_start: 0.8257 (m-30) cc_final: 0.7941 (t0) REVERT: G 15 LYS cc_start: 0.9110 (ttmt) cc_final: 0.8777 (ttmm) REVERT: G 33 LYS cc_start: 0.9081 (mtpp) cc_final: 0.8863 (mtpp) REVERT: G 37 LYS cc_start: 0.8433 (ttmt) cc_final: 0.7134 (tptt) REVERT: G 55 ASN cc_start: 0.8503 (t0) cc_final: 0.7736 (t0) REVERT: G 66 LYS cc_start: 0.9119 (tppt) cc_final: 0.8527 (tppt) REVERT: G 69 LYS cc_start: 0.8707 (tttm) cc_final: 0.8387 (tttt) REVERT: H 28 THR cc_start: 0.8988 (m) cc_final: 0.8324 (p) REVERT: H 32 ASP cc_start: 0.7983 (m-30) cc_final: 0.7656 (m-30) REVERT: H 37 LYS cc_start: 0.8229 (ttmt) cc_final: 0.6994 (tptt) REVERT: H 47 TYR cc_start: 0.9163 (t80) cc_final: 0.7353 (t80) REVERT: H 51 LEU cc_start: 0.9339 (tp) cc_final: 0.8743 (tp) REVERT: H 77 GLN cc_start: 0.8555 (tp40) cc_final: 0.8348 (tp40) REVERT: I 28 THR cc_start: 0.9123 (m) cc_final: 0.8662 (p) REVERT: I 37 LYS cc_start: 0.8729 (ttmt) cc_final: 0.7367 (tptp) REVERT: I 47 TYR cc_start: 0.9225 (t80) cc_final: 0.8915 (t80) REVERT: J 17 ASP cc_start: 0.7702 (m-30) cc_final: 0.7430 (m-30) REVERT: J 22 ASN cc_start: 0.8181 (p0) cc_final: 0.7587 (p0) REVERT: J 37 LYS cc_start: 0.8897 (ttmt) cc_final: 0.7325 (tptt) REVERT: J 39 SER cc_start: 0.8966 (t) cc_final: 0.8759 (t) REVERT: J 47 TYR cc_start: 0.9224 (t80) cc_final: 0.8497 (t80) REVERT: J 49 SER cc_start: 0.9257 (t) cc_final: 0.8938 (p) REVERT: J 54 TYR cc_start: 0.8875 (t80) cc_final: 0.8674 (t80) REVERT: K 33 LYS cc_start: 0.9224 (mttt) cc_final: 0.8845 (mtpp) REVERT: K 37 LYS cc_start: 0.9035 (ttmt) cc_final: 0.7527 (tptt) REVERT: K 47 TYR cc_start: 0.9198 (t80) cc_final: 0.7721 (t80) REVERT: K 63 ASN cc_start: 0.8666 (m-40) cc_final: 0.8330 (m110) REVERT: L 26 GLN cc_start: 0.8775 (mt0) cc_final: 0.8349 (tt0) REVERT: L 48 GLN cc_start: 0.8749 (tt0) cc_final: 0.8032 (tt0) REVERT: L 53 GLU cc_start: 0.8272 (tp30) cc_final: 0.7928 (tp30) REVERT: M 28 THR cc_start: 0.8844 (m) cc_final: 0.8113 (p) REVERT: M 31 LEU cc_start: 0.9285 (tp) cc_final: 0.8967 (tp) REVERT: M 32 ASP cc_start: 0.8365 (p0) cc_final: 0.7981 (p0) REVERT: M 47 TYR cc_start: 0.9140 (t80) cc_final: 0.8546 (t80) REVERT: M 66 LYS cc_start: 0.8581 (tptt) cc_final: 0.8085 (tmtt) REVERT: M 69 LYS cc_start: 0.8609 (tttp) cc_final: 0.7832 (ttpt) REVERT: N 24 GLN cc_start: 0.8729 (mp10) cc_final: 0.7943 (tm-30) REVERT: N 32 ASP cc_start: 0.8231 (m-30) cc_final: 0.7961 (m-30) REVERT: N 49 SER cc_start: 0.9445 (m) cc_final: 0.9169 (t) REVERT: N 50 LYS cc_start: 0.8949 (mmtp) cc_final: 0.8433 (mmmt) REVERT: N 51 LEU cc_start: 0.9198 (tp) cc_final: 0.8794 (tt) REVERT: N 53 GLU cc_start: 0.8295 (tp30) cc_final: 0.7669 (tp30) REVERT: O 15 LYS cc_start: 0.8841 (tppt) cc_final: 0.8576 (tptp) REVERT: O 17 ASP cc_start: 0.8216 (m-30) cc_final: 0.7481 (t0) REVERT: O 22 ASN cc_start: 0.9258 (p0) cc_final: 0.8058 (p0) REVERT: O 25 THR cc_start: 0.9023 (m) cc_final: 0.8384 (p) REVERT: O 28 THR cc_start: 0.8364 (m) cc_final: 0.8061 (p) REVERT: O 33 LYS cc_start: 0.9121 (mttt) cc_final: 0.8386 (mtmm) REVERT: O 47 TYR cc_start: 0.9070 (t80) cc_final: 0.8762 (t80) REVERT: O 49 SER cc_start: 0.9238 (m) cc_final: 0.8971 (t) REVERT: O 52 SER cc_start: 0.9071 (m) cc_final: 0.8836 (t) REVERT: O 59 ASN cc_start: 0.8517 (m-40) cc_final: 0.7771 (m110) REVERT: O 69 LYS cc_start: 0.8187 (tttm) cc_final: 0.7777 (ttmt) REVERT: O 77 GLN cc_start: 0.8898 (tp-100) cc_final: 0.8610 (tp-100) REVERT: P 22 ASN cc_start: 0.9254 (p0) cc_final: 0.8513 (p0) REVERT: P 31 LEU cc_start: 0.8756 (tp) cc_final: 0.8517 (tt) REVERT: P 32 ASP cc_start: 0.8010 (m-30) cc_final: 0.7775 (m-30) REVERT: P 56 LEU cc_start: 0.9153 (mp) cc_final: 0.8895 (mp) REVERT: P 69 LYS cc_start: 0.8089 (tttm) cc_final: 0.7784 (ttmt) REVERT: Q 25 THR cc_start: 0.8840 (m) cc_final: 0.8228 (p) REVERT: Q 28 THR cc_start: 0.8223 (m) cc_final: 0.7997 (p) REVERT: Q 40 ASP cc_start: 0.8232 (t0) cc_final: 0.7681 (t0) REVERT: Q 54 TYR cc_start: 0.8562 (t80) cc_final: 0.7923 (t80) REVERT: Q 57 TYR cc_start: 0.8792 (t80) cc_final: 0.8557 (t80) REVERT: Q 69 LYS cc_start: 0.8414 (tttm) cc_final: 0.7733 (tttt) REVERT: R 22 ASN cc_start: 0.9076 (p0) cc_final: 0.8620 (p0) REVERT: R 24 GLN cc_start: 0.8178 (mp10) cc_final: 0.7816 (pm20) REVERT: R 29 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8201 (tm-30) REVERT: R 33 LYS cc_start: 0.9082 (ttmt) cc_final: 0.8695 (ttmt) REVERT: R 50 LYS cc_start: 0.8307 (mmtt) cc_final: 0.8090 (mmmt) REVERT: S 5 TRP cc_start: 0.8547 (t60) cc_final: 0.7926 (t60) REVERT: S 17 ASP cc_start: 0.7241 (m-30) cc_final: 0.6950 (m-30) REVERT: S 39 SER cc_start: 0.9292 (m) cc_final: 0.8173 (m) REVERT: S 59 ASN cc_start: 0.8594 (m-40) cc_final: 0.7494 (m110) REVERT: S 69 LYS cc_start: 0.7729 (tttm) cc_final: 0.7388 (ttmt) REVERT: T 22 ASN cc_start: 0.8719 (p0) cc_final: 0.8325 (p0) REVERT: T 25 THR cc_start: 0.8684 (p) cc_final: 0.8195 (t) REVERT: T 48 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8876 (tm-30) REVERT: T 69 LYS cc_start: 0.7034 (tttm) cc_final: 0.6492 (tttt) outliers start: 55 outliers final: 46 residues processed: 574 average time/residue: 0.2248 time to fit residues: 183.5844 Evaluate side-chains 589 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 543 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 21 ASP Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 26 GLN Chi-restraints excluded: chain P residue 64 THR Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 40 ASP Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 0.0970 chunk 115 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN M 26 GLN M 77 GLN ** O 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11837 Z= 0.143 Angle : 0.483 7.460 16112 Z= 0.252 Chirality : 0.036 0.137 1843 Planarity : 0.002 0.017 2109 Dihedral : 3.601 23.353 1596 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.23 % Allowed : 23.52 % Favored : 74.24 % 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: 2.03 (0.22), residues: 1444 helix: 1.98 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.53 (0.33), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 5 PHE 0.003 0.000 PHE N 16 TYR 0.013 0.001 TYR G 47 ARG 0.002 0.000 ARG E 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 570 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8785 (mmmm) cc_final: 0.8455 (mmmt) REVERT: D 63 ASN cc_start: 0.8025 (m-40) cc_final: 0.7418 (m-40) REVERT: D 66 LYS cc_start: 0.9185 (tptp) cc_final: 0.7406 (mttt) REVERT: U 15 LYS cc_start: 0.9109 (mttt) cc_final: 0.8836 (mmtp) REVERT: U 37 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7180 (tptp) REVERT: U 66 LYS cc_start: 0.8713 (tptp) cc_final: 0.6655 (mttp) REVERT: V 37 LYS cc_start: 0.8669 (ttmt) cc_final: 0.7428 (tptt) REVERT: V 47 TYR cc_start: 0.9144 (t80) cc_final: 0.8244 (t80) REVERT: V 49 SER cc_start: 0.8677 (t) cc_final: 0.8264 (p) REVERT: V 77 GLN cc_start: 0.8732 (tp40) cc_final: 0.8224 (tp40) REVERT: E 22 ASN cc_start: 0.7635 (p0) cc_final: 0.6993 (p0) REVERT: E 37 LYS cc_start: 0.8696 (ttmt) cc_final: 0.7436 (tptt) REVERT: E 53 GLU cc_start: 0.8522 (tp30) cc_final: 0.8071 (mm-30) REVERT: E 66 LYS cc_start: 0.8108 (tptp) cc_final: 0.6621 (mttt) REVERT: E 69 LYS cc_start: 0.8104 (tttp) cc_final: 0.7877 (tttp) REVERT: F 28 THR cc_start: 0.8692 (m) cc_final: 0.8100 (p) REVERT: F 32 ASP cc_start: 0.7755 (m-30) cc_final: 0.7412 (m-30) REVERT: F 34 LEU cc_start: 0.9177 (tp) cc_final: 0.8909 (tt) REVERT: F 37 LYS cc_start: 0.8528 (ttmt) cc_final: 0.7791 (tptt) REVERT: F 39 SER cc_start: 0.8855 (m) cc_final: 0.8206 (t) REVERT: F 47 TYR cc_start: 0.8906 (t80) cc_final: 0.8254 (t80) REVERT: F 49 SER cc_start: 0.9242 (t) cc_final: 0.8802 (p) REVERT: F 53 GLU cc_start: 0.8080 (tp30) cc_final: 0.7549 (mm-30) REVERT: F 63 ASN cc_start: 0.9178 (m-40) cc_final: 0.8950 (m110) REVERT: F 66 LYS cc_start: 0.8619 (tptp) cc_final: 0.7598 (ttmt) REVERT: G 11 ASP cc_start: 0.8118 (m-30) cc_final: 0.7895 (t0) REVERT: G 15 LYS cc_start: 0.9088 (ttmt) cc_final: 0.8796 (ttmm) REVERT: G 33 LYS cc_start: 0.9284 (mtpp) cc_final: 0.9014 (mtpp) REVERT: G 37 LYS cc_start: 0.8481 (ttmt) cc_final: 0.7211 (tptt) REVERT: G 66 LYS cc_start: 0.9056 (tppt) cc_final: 0.8493 (tppt) REVERT: G 69 LYS cc_start: 0.8718 (tttm) cc_final: 0.8409 (tttt) REVERT: H 28 THR cc_start: 0.8956 (m) cc_final: 0.8388 (p) REVERT: H 32 ASP cc_start: 0.7925 (m-30) cc_final: 0.7611 (m-30) REVERT: H 37 LYS cc_start: 0.8234 (ttmt) cc_final: 0.6920 (tptt) REVERT: H 47 TYR cc_start: 0.9104 (t80) cc_final: 0.7352 (t80) REVERT: H 51 LEU cc_start: 0.9315 (tp) cc_final: 0.8740 (tp) REVERT: H 77 GLN cc_start: 0.8514 (tp40) cc_final: 0.8308 (tp40) REVERT: I 37 LYS cc_start: 0.8629 (ttmt) cc_final: 0.7237 (tptp) REVERT: I 47 TYR cc_start: 0.9173 (t80) cc_final: 0.8847 (t80) REVERT: I 79 PHE cc_start: 0.9108 (m-10) cc_final: 0.8892 (m-10) REVERT: J 22 ASN cc_start: 0.8083 (p0) cc_final: 0.7536 (p0) REVERT: J 37 LYS cc_start: 0.8805 (ttmt) cc_final: 0.7297 (tptt) REVERT: J 47 TYR cc_start: 0.9123 (t80) cc_final: 0.8513 (t80) REVERT: J 49 SER cc_start: 0.9270 (t) cc_final: 0.8922 (p) REVERT: J 80 ARG cc_start: 0.7888 (ttp80) cc_final: 0.7633 (ttp80) REVERT: K 33 LYS cc_start: 0.9213 (mttt) cc_final: 0.8805 (mtpp) REVERT: K 37 LYS cc_start: 0.8986 (ttmt) cc_final: 0.7558 (tptp) REVERT: K 47 TYR cc_start: 0.9106 (t80) cc_final: 0.7732 (t80) REVERT: K 63 ASN cc_start: 0.8505 (m-40) cc_final: 0.8154 (m110) REVERT: K 77 GLN cc_start: 0.8707 (tp40) cc_final: 0.8091 (tp-100) REVERT: L 26 GLN cc_start: 0.8667 (mt0) cc_final: 0.8323 (tt0) REVERT: L 28 THR cc_start: 0.8983 (m) cc_final: 0.8600 (p) REVERT: L 37 LYS cc_start: 0.8691 (ttmt) cc_final: 0.6980 (tptt) REVERT: L 53 GLU cc_start: 0.8181 (tp30) cc_final: 0.7871 (tp30) REVERT: L 77 GLN cc_start: 0.8405 (tp-100) cc_final: 0.8057 (tp40) REVERT: M 22 ASN cc_start: 0.8550 (p0) cc_final: 0.8092 (p0) REVERT: M 28 THR cc_start: 0.8819 (m) cc_final: 0.8068 (p) REVERT: M 31 LEU cc_start: 0.9291 (tp) cc_final: 0.8982 (tp) REVERT: M 32 ASP cc_start: 0.8386 (p0) cc_final: 0.8027 (p0) REVERT: M 47 TYR cc_start: 0.9189 (t80) cc_final: 0.8559 (t80) REVERT: M 50 LYS cc_start: 0.9114 (mmtt) cc_final: 0.8839 (mmtt) REVERT: M 66 LYS cc_start: 0.8674 (tptt) cc_final: 0.8140 (tmtt) REVERT: M 69 LYS cc_start: 0.8573 (tttp) cc_final: 0.7816 (ttpt) REVERT: N 15 LYS cc_start: 0.8473 (ttmm) cc_final: 0.8099 (ttmm) REVERT: N 24 GLN cc_start: 0.8658 (mp10) cc_final: 0.7889 (tm-30) REVERT: N 32 ASP cc_start: 0.8257 (m-30) cc_final: 0.8001 (m-30) REVERT: N 47 TYR cc_start: 0.8880 (t80) cc_final: 0.8542 (t80) REVERT: N 49 SER cc_start: 0.9410 (m) cc_final: 0.9093 (t) REVERT: N 53 GLU cc_start: 0.8216 (tp30) cc_final: 0.7584 (tp30) REVERT: O 15 LYS cc_start: 0.8827 (tppt) cc_final: 0.8556 (tptp) REVERT: O 17 ASP cc_start: 0.8188 (m-30) cc_final: 0.7439 (t0) REVERT: O 22 ASN cc_start: 0.9194 (p0) cc_final: 0.7975 (p0) REVERT: O 25 THR cc_start: 0.8985 (m) cc_final: 0.8416 (p) REVERT: O 28 THR cc_start: 0.8365 (m) cc_final: 0.8056 (p) REVERT: O 33 LYS cc_start: 0.9104 (mttt) cc_final: 0.8343 (mtmm) REVERT: O 47 TYR cc_start: 0.9011 (t80) cc_final: 0.8741 (t80) REVERT: O 49 SER cc_start: 0.9174 (m) cc_final: 0.8917 (t) REVERT: O 52 SER cc_start: 0.9168 (m) cc_final: 0.8934 (t) REVERT: O 59 ASN cc_start: 0.8410 (m-40) cc_final: 0.7676 (m110) REVERT: O 69 LYS cc_start: 0.8217 (tttm) cc_final: 0.7695 (ttmt) REVERT: O 77 GLN cc_start: 0.8737 (tp-100) cc_final: 0.8244 (tp-100) REVERT: P 22 ASN cc_start: 0.9320 (p0) cc_final: 0.8797 (p0) REVERT: P 23 LEU cc_start: 0.8770 (tp) cc_final: 0.8335 (tt) REVERT: P 29 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: P 32 ASP cc_start: 0.7823 (m-30) cc_final: 0.7536 (m-30) REVERT: P 49 SER cc_start: 0.9217 (m) cc_final: 0.8922 (p) REVERT: P 69 LYS cc_start: 0.8142 (tttm) cc_final: 0.7615 (ttmt) REVERT: Q 25 THR cc_start: 0.8787 (m) cc_final: 0.8226 (p) REVERT: Q 31 LEU cc_start: 0.8745 (tp) cc_final: 0.8538 (tp) REVERT: Q 40 ASP cc_start: 0.8094 (t0) cc_final: 0.7858 (t0) REVERT: Q 54 TYR cc_start: 0.8473 (t80) cc_final: 0.7938 (t80) REVERT: Q 69 LYS cc_start: 0.8360 (tttm) cc_final: 0.7699 (tttp) REVERT: R 17 ASP cc_start: 0.7399 (m-30) cc_final: 0.7175 (m-30) REVERT: R 22 ASN cc_start: 0.9087 (p0) cc_final: 0.8660 (p0) REVERT: R 24 GLN cc_start: 0.8200 (mp10) cc_final: 0.7589 (pm20) REVERT: R 29 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8130 (tm-30) REVERT: R 69 LYS cc_start: 0.8119 (tttm) cc_final: 0.7065 (mttt) REVERT: S 5 TRP cc_start: 0.8473 (t60) cc_final: 0.7872 (t60) REVERT: S 17 ASP cc_start: 0.7255 (m-30) cc_final: 0.6929 (m-30) REVERT: S 33 LYS cc_start: 0.8823 (mttp) cc_final: 0.8224 (mtmt) REVERT: S 39 SER cc_start: 0.9238 (m) cc_final: 0.8249 (m) REVERT: S 59 ASN cc_start: 0.8682 (m-40) cc_final: 0.7568 (m110) REVERT: S 69 LYS cc_start: 0.7691 (tttm) cc_final: 0.7334 (ttmt) REVERT: T 22 ASN cc_start: 0.8643 (p0) cc_final: 0.8250 (p0) REVERT: T 25 THR cc_start: 0.8570 (p) cc_final: 0.8095 (t) REVERT: T 48 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8467 (tm-30) REVERT: T 50 LYS cc_start: 0.8929 (mmtt) cc_final: 0.8689 (mmmt) REVERT: T 69 LYS cc_start: 0.7015 (tttm) cc_final: 0.6466 (tttt) outliers start: 28 outliers final: 19 residues processed: 575 average time/residue: 0.2228 time to fit residues: 181.9756 Evaluate side-chains 569 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 549 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 77 GLN Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 40 ASP Chi-restraints excluded: chain T residue 13 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 73 optimal weight: 0.0570 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN M 77 GLN ** O 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11837 Z= 0.257 Angle : 0.552 8.053 16112 Z= 0.284 Chirality : 0.040 0.126 1843 Planarity : 0.003 0.020 2109 Dihedral : 3.706 26.884 1596 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.11 % Allowed : 24.00 % Favored : 72.89 % 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: 2.05 (0.22), residues: 1444 helix: 1.98 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.38 (0.35), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 5 PHE 0.009 0.001 PHE J 16 TYR 0.012 0.002 TYR E 57 ARG 0.003 0.000 ARG V 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 568 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8846 (mmmm) cc_final: 0.8518 (mmmt) REVERT: D 66 LYS cc_start: 0.9033 (tptp) cc_final: 0.7509 (mttt) REVERT: U 15 LYS cc_start: 0.9081 (mttt) cc_final: 0.8835 (mmtp) REVERT: U 37 LYS cc_start: 0.8176 (ttmt) cc_final: 0.7227 (tptt) REVERT: U 66 LYS cc_start: 0.8734 (tptp) cc_final: 0.6494 (mttt) REVERT: V 15 LYS cc_start: 0.9219 (tppp) cc_final: 0.8999 (mmtp) REVERT: V 37 LYS cc_start: 0.8743 (ttmt) cc_final: 0.7544 (tptt) REVERT: V 47 TYR cc_start: 0.9222 (t80) cc_final: 0.8379 (t80) REVERT: V 49 SER cc_start: 0.8663 (t) cc_final: 0.8304 (p) REVERT: V 77 GLN cc_start: 0.8748 (tp40) cc_final: 0.8216 (tp40) REVERT: E 37 LYS cc_start: 0.8695 (ttmt) cc_final: 0.7344 (tptt) REVERT: E 53 GLU cc_start: 0.8638 (tp30) cc_final: 0.8151 (mm-30) REVERT: E 66 LYS cc_start: 0.8219 (tptp) cc_final: 0.6726 (mttt) REVERT: F 28 THR cc_start: 0.8734 (m) cc_final: 0.8076 (p) REVERT: F 32 ASP cc_start: 0.7782 (m-30) cc_final: 0.7425 (m-30) REVERT: F 34 LEU cc_start: 0.9200 (tp) cc_final: 0.8917 (tt) REVERT: F 37 LYS cc_start: 0.8619 (ttmt) cc_final: 0.7821 (tptt) REVERT: F 39 SER cc_start: 0.8867 (m) cc_final: 0.8215 (t) REVERT: F 47 TYR cc_start: 0.9042 (t80) cc_final: 0.8542 (t80) REVERT: F 49 SER cc_start: 0.9290 (t) cc_final: 0.8882 (p) REVERT: F 51 LEU cc_start: 0.9182 (tp) cc_final: 0.8922 (tp) REVERT: F 53 GLU cc_start: 0.8338 (tp30) cc_final: 0.7721 (mm-30) REVERT: F 63 ASN cc_start: 0.9165 (m-40) cc_final: 0.8804 (m110) REVERT: F 66 LYS cc_start: 0.8639 (tptp) cc_final: 0.7534 (ttmt) REVERT: G 11 ASP cc_start: 0.8266 (m-30) cc_final: 0.7928 (t0) REVERT: G 15 LYS cc_start: 0.9094 (ttmt) cc_final: 0.8781 (ttmm) REVERT: G 33 LYS cc_start: 0.9276 (mtpp) cc_final: 0.9036 (mtpp) REVERT: G 37 LYS cc_start: 0.8422 (ttmt) cc_final: 0.7127 (tptt) REVERT: G 66 LYS cc_start: 0.8981 (tppt) cc_final: 0.8483 (tppt) REVERT: G 69 LYS cc_start: 0.8734 (tttm) cc_final: 0.8384 (tttt) REVERT: H 28 THR cc_start: 0.8981 (m) cc_final: 0.8372 (p) REVERT: H 32 ASP cc_start: 0.7860 (m-30) cc_final: 0.7525 (m-30) REVERT: H 37 LYS cc_start: 0.8091 (ttmt) cc_final: 0.6787 (tptt) REVERT: H 47 TYR cc_start: 0.9138 (t80) cc_final: 0.7369 (t80) REVERT: H 51 LEU cc_start: 0.9281 (tp) cc_final: 0.8618 (tp) REVERT: H 77 GLN cc_start: 0.8562 (tp40) cc_final: 0.8305 (tp-100) REVERT: I 37 LYS cc_start: 0.8742 (ttmt) cc_final: 0.7326 (tptp) REVERT: I 47 TYR cc_start: 0.9112 (t80) cc_final: 0.8749 (t80) REVERT: J 22 ASN cc_start: 0.8204 (p0) cc_final: 0.7633 (p0) REVERT: J 37 LYS cc_start: 0.8879 (ttmt) cc_final: 0.7389 (tptt) REVERT: J 39 SER cc_start: 0.8928 (t) cc_final: 0.8717 (t) REVERT: J 47 TYR cc_start: 0.9179 (t80) cc_final: 0.8463 (t80) REVERT: J 49 SER cc_start: 0.9250 (t) cc_final: 0.8915 (p) REVERT: J 54 TYR cc_start: 0.8830 (t80) cc_final: 0.8606 (t80) REVERT: K 33 LYS cc_start: 0.9212 (mttt) cc_final: 0.8825 (mtpp) REVERT: K 37 LYS cc_start: 0.9007 (ttmt) cc_final: 0.7562 (tptp) REVERT: K 47 TYR cc_start: 0.9142 (t80) cc_final: 0.7806 (t80) REVERT: L 23 LEU cc_start: 0.8641 (tp) cc_final: 0.8251 (tp) REVERT: L 26 GLN cc_start: 0.8746 (mt0) cc_final: 0.8418 (mt0) REVERT: L 53 GLU cc_start: 0.8280 (tp30) cc_final: 0.7916 (tp30) REVERT: L 77 GLN cc_start: 0.8516 (tp-100) cc_final: 0.8117 (tp40) REVERT: M 22 ASN cc_start: 0.8654 (p0) cc_final: 0.8215 (p0) REVERT: M 26 GLN cc_start: 0.8902 (mt0) cc_final: 0.8638 (mt0) REVERT: M 28 THR cc_start: 0.8807 (m) cc_final: 0.8060 (p) REVERT: M 31 LEU cc_start: 0.9311 (tp) cc_final: 0.8998 (tp) REVERT: M 32 ASP cc_start: 0.8375 (p0) cc_final: 0.8038 (p0) REVERT: M 47 TYR cc_start: 0.9291 (t80) cc_final: 0.8677 (t80) REVERT: M 66 LYS cc_start: 0.8543 (tptt) cc_final: 0.8006 (tmtt) REVERT: M 69 LYS cc_start: 0.8613 (tttp) cc_final: 0.7890 (ttpt) REVERT: N 23 LEU cc_start: 0.9021 (tp) cc_final: 0.8470 (tp) REVERT: N 24 GLN cc_start: 0.8657 (mp10) cc_final: 0.7896 (tm-30) REVERT: N 32 ASP cc_start: 0.8321 (m-30) cc_final: 0.8053 (m-30) REVERT: N 49 SER cc_start: 0.9429 (m) cc_final: 0.9151 (t) REVERT: N 50 LYS cc_start: 0.8927 (mmtp) cc_final: 0.8432 (mmmt) REVERT: N 51 LEU cc_start: 0.9194 (tp) cc_final: 0.8771 (tt) REVERT: N 53 GLU cc_start: 0.8318 (tp30) cc_final: 0.7746 (tp30) REVERT: O 15 LYS cc_start: 0.8826 (tppt) cc_final: 0.8591 (tptp) REVERT: O 17 ASP cc_start: 0.8273 (m-30) cc_final: 0.7459 (t0) REVERT: O 22 ASN cc_start: 0.9215 (p0) cc_final: 0.7991 (p0) REVERT: O 25 THR cc_start: 0.9070 (m) cc_final: 0.8453 (p) REVERT: O 28 THR cc_start: 0.8352 (m) cc_final: 0.8052 (p) REVERT: O 33 LYS cc_start: 0.9124 (mttt) cc_final: 0.8374 (mtmm) REVERT: O 49 SER cc_start: 0.9224 (m) cc_final: 0.8947 (t) REVERT: O 52 SER cc_start: 0.9056 (m) cc_final: 0.8810 (t) REVERT: O 59 ASN cc_start: 0.8501 (m-40) cc_final: 0.7766 (m110) REVERT: O 69 LYS cc_start: 0.8132 (tttm) cc_final: 0.7576 (ttmt) REVERT: O 77 GLN cc_start: 0.8801 (tp-100) cc_final: 0.8445 (tp-100) REVERT: P 22 ASN cc_start: 0.9327 (p0) cc_final: 0.8708 (p0) REVERT: P 23 LEU cc_start: 0.8818 (tp) cc_final: 0.8383 (tt) REVERT: P 29 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: P 32 ASP cc_start: 0.8054 (m-30) cc_final: 0.7700 (m-30) REVERT: Q 25 THR cc_start: 0.8675 (m) cc_final: 0.8379 (p) REVERT: Q 40 ASP cc_start: 0.8202 (t0) cc_final: 0.7714 (t70) REVERT: Q 54 TYR cc_start: 0.8566 (t80) cc_final: 0.7963 (t80) REVERT: Q 69 LYS cc_start: 0.8422 (tttm) cc_final: 0.7964 (ttmt) REVERT: R 17 ASP cc_start: 0.7483 (m-30) cc_final: 0.7245 (m-30) REVERT: R 22 ASN cc_start: 0.9085 (p0) cc_final: 0.8824 (p0) REVERT: R 24 GLN cc_start: 0.8195 (mp10) cc_final: 0.7534 (pm20) REVERT: R 50 LYS cc_start: 0.8408 (mmtt) cc_final: 0.8160 (mmmt) REVERT: R 69 LYS cc_start: 0.8176 (tttm) cc_final: 0.6902 (mttt) REVERT: S 17 ASP cc_start: 0.7767 (m-30) cc_final: 0.7318 (m-30) REVERT: S 33 LYS cc_start: 0.8825 (mttp) cc_final: 0.8242 (mtmt) REVERT: S 39 SER cc_start: 0.9306 (m) cc_final: 0.8360 (m) REVERT: S 58 ARG cc_start: 0.9002 (mmt180) cc_final: 0.8741 (mmt90) REVERT: S 59 ASN cc_start: 0.8559 (m-40) cc_final: 0.7420 (m110) REVERT: T 22 ASN cc_start: 0.8806 (p0) cc_final: 0.8432 (p0) REVERT: T 25 THR cc_start: 0.8638 (p) cc_final: 0.8153 (t) REVERT: T 48 GLN cc_start: 0.9107 (tm-30) cc_final: 0.8510 (tm-30) REVERT: T 50 LYS cc_start: 0.8880 (mmtt) cc_final: 0.8619 (mmmt) REVERT: T 69 LYS cc_start: 0.7045 (tttm) cc_final: 0.6465 (tttt) outliers start: 39 outliers final: 34 residues processed: 580 average time/residue: 0.2358 time to fit residues: 194.8119 Evaluate side-chains 589 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 554 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain J residue 21 ASP Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 38 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 87 optimal weight: 0.0060 chunk 63 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN J 24 GLN K 55 ASN ** O 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11837 Z= 0.145 Angle : 0.504 8.144 16112 Z= 0.261 Chirality : 0.036 0.127 1843 Planarity : 0.003 0.018 2109 Dihedral : 3.468 22.155 1596 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.07 % Allowed : 25.76 % Favored : 72.17 % 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: 2.37 (0.22), residues: 1444 helix: 2.18 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.25 (0.37), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 5 PHE 0.005 0.000 PHE J 16 TYR 0.026 0.001 TYR E 47 ARG 0.002 0.000 ARG R 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 561 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8763 (mmmm) cc_final: 0.8481 (mmmt) REVERT: D 37 LYS cc_start: 0.8530 (ttmt) cc_final: 0.7435 (tptt) REVERT: U 15 LYS cc_start: 0.9039 (mttt) cc_final: 0.8773 (mmtp) REVERT: U 37 LYS cc_start: 0.8141 (ttmt) cc_final: 0.7203 (tptp) REVERT: U 66 LYS cc_start: 0.8687 (tptp) cc_final: 0.6668 (mttt) REVERT: V 37 LYS cc_start: 0.8616 (ttmt) cc_final: 0.7403 (tptt) REVERT: V 47 TYR cc_start: 0.9111 (t80) cc_final: 0.8285 (t80) REVERT: V 49 SER cc_start: 0.8609 (t) cc_final: 0.8253 (p) REVERT: V 77 GLN cc_start: 0.8743 (tp40) cc_final: 0.8265 (tp40) REVERT: E 22 ASN cc_start: 0.7899 (p0) cc_final: 0.7229 (p0) REVERT: E 37 LYS cc_start: 0.8703 (ttmt) cc_final: 0.7362 (tptt) REVERT: E 66 LYS cc_start: 0.8312 (tptp) cc_final: 0.6530 (mttt) REVERT: F 28 THR cc_start: 0.8700 (m) cc_final: 0.8075 (p) REVERT: F 32 ASP cc_start: 0.7743 (m-30) cc_final: 0.7394 (m-30) REVERT: F 34 LEU cc_start: 0.9177 (tp) cc_final: 0.8902 (tt) REVERT: F 37 LYS cc_start: 0.8599 (ttmt) cc_final: 0.7693 (tptt) REVERT: F 39 SER cc_start: 0.8819 (m) cc_final: 0.8163 (t) REVERT: F 47 TYR cc_start: 0.9074 (t80) cc_final: 0.8579 (t80) REVERT: F 49 SER cc_start: 0.9235 (t) cc_final: 0.8781 (p) REVERT: F 53 GLU cc_start: 0.8032 (tp30) cc_final: 0.7650 (mm-30) REVERT: F 66 LYS cc_start: 0.8627 (tptp) cc_final: 0.7513 (ttmt) REVERT: G 11 ASP cc_start: 0.8113 (m-30) cc_final: 0.7867 (t0) REVERT: G 15 LYS cc_start: 0.9074 (ttmt) cc_final: 0.8641 (ttmm) REVERT: G 33 LYS cc_start: 0.9307 (mtpp) cc_final: 0.9052 (mtpp) REVERT: G 37 LYS cc_start: 0.8456 (ttmt) cc_final: 0.7192 (tptt) REVERT: G 66 LYS cc_start: 0.8970 (tppt) cc_final: 0.8459 (tppt) REVERT: G 69 LYS cc_start: 0.8795 (tttm) cc_final: 0.8583 (tttt) REVERT: H 28 THR cc_start: 0.8955 (m) cc_final: 0.8400 (p) REVERT: H 32 ASP cc_start: 0.7906 (m-30) cc_final: 0.7601 (m-30) REVERT: H 37 LYS cc_start: 0.8139 (ttmt) cc_final: 0.7070 (tptp) REVERT: H 44 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8717 (mt) REVERT: H 47 TYR cc_start: 0.9070 (t80) cc_final: 0.7409 (t80) REVERT: H 51 LEU cc_start: 0.9248 (tp) cc_final: 0.8734 (tp) REVERT: H 77 GLN cc_start: 0.8543 (tp40) cc_final: 0.8330 (tp40) REVERT: I 37 LYS cc_start: 0.8463 (ttmt) cc_final: 0.6825 (tptp) REVERT: I 47 TYR cc_start: 0.9152 (t80) cc_final: 0.8692 (t80) REVERT: J 22 ASN cc_start: 0.8157 (p0) cc_final: 0.7634 (p0) REVERT: J 37 LYS cc_start: 0.8761 (ttmt) cc_final: 0.7432 (tptt) REVERT: J 39 SER cc_start: 0.8854 (t) cc_final: 0.8613 (t) REVERT: K 15 LYS cc_start: 0.8921 (tptm) cc_final: 0.8706 (tptm) REVERT: K 33 LYS cc_start: 0.9275 (mttt) cc_final: 0.8882 (mtpp) REVERT: K 37 LYS cc_start: 0.8939 (ttmt) cc_final: 0.7421 (tptt) REVERT: K 47 TYR cc_start: 0.9025 (t80) cc_final: 0.7812 (t80) REVERT: K 63 ASN cc_start: 0.8579 (m-40) cc_final: 0.8178 (m110) REVERT: L 23 LEU cc_start: 0.8562 (tp) cc_final: 0.8301 (tp) REVERT: L 26 GLN cc_start: 0.8692 (mt0) cc_final: 0.8309 (tt0) REVERT: L 28 THR cc_start: 0.8939 (m) cc_final: 0.8608 (p) REVERT: L 48 GLN cc_start: 0.7854 (tt0) cc_final: 0.7585 (tt0) REVERT: L 77 GLN cc_start: 0.8379 (tp-100) cc_final: 0.8073 (tp40) REVERT: M 22 ASN cc_start: 0.8544 (p0) cc_final: 0.8169 (p0) REVERT: M 28 THR cc_start: 0.8781 (m) cc_final: 0.8004 (p) REVERT: M 31 LEU cc_start: 0.9257 (tp) cc_final: 0.8936 (tp) REVERT: M 32 ASP cc_start: 0.8381 (p0) cc_final: 0.8008 (p0) REVERT: M 47 TYR cc_start: 0.9166 (t80) cc_final: 0.8513 (t80) REVERT: M 66 LYS cc_start: 0.8666 (tptt) cc_final: 0.8145 (tmtt) REVERT: M 69 LYS cc_start: 0.8532 (tttp) cc_final: 0.7780 (ttpt) REVERT: N 24 GLN cc_start: 0.8581 (mp10) cc_final: 0.7861 (tm-30) REVERT: N 32 ASP cc_start: 0.8312 (m-30) cc_final: 0.8060 (m-30) REVERT: N 47 TYR cc_start: 0.8900 (t80) cc_final: 0.8605 (t80) REVERT: N 49 SER cc_start: 0.9385 (m) cc_final: 0.9064 (t) REVERT: N 53 GLU cc_start: 0.8299 (tp30) cc_final: 0.7712 (tp30) REVERT: O 15 LYS cc_start: 0.8849 (tppt) cc_final: 0.8604 (tptp) REVERT: O 17 ASP cc_start: 0.8249 (m-30) cc_final: 0.7412 (t0) REVERT: O 22 ASN cc_start: 0.9116 (p0) cc_final: 0.7861 (p0) REVERT: O 25 THR cc_start: 0.9024 (m) cc_final: 0.8488 (p) REVERT: O 28 THR cc_start: 0.8402 (m) cc_final: 0.8071 (p) REVERT: O 33 LYS cc_start: 0.9085 (mttt) cc_final: 0.8195 (mtmm) REVERT: O 47 TYR cc_start: 0.8976 (t80) cc_final: 0.8643 (t80) REVERT: O 49 SER cc_start: 0.9108 (m) cc_final: 0.8810 (t) REVERT: O 59 ASN cc_start: 0.8378 (m-40) cc_final: 0.7727 (m110) REVERT: O 69 LYS cc_start: 0.8060 (tttm) cc_final: 0.7528 (ttmt) REVERT: O 77 GLN cc_start: 0.8754 (tp-100) cc_final: 0.8412 (tp-100) REVERT: P 22 ASN cc_start: 0.9278 (p0) cc_final: 0.8673 (p0) REVERT: P 23 LEU cc_start: 0.8743 (tp) cc_final: 0.8333 (tt) REVERT: P 29 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: Q 25 THR cc_start: 0.8622 (m) cc_final: 0.8384 (p) REVERT: Q 40 ASP cc_start: 0.8020 (t0) cc_final: 0.7756 (t0) REVERT: Q 54 TYR cc_start: 0.8408 (t80) cc_final: 0.7941 (t80) REVERT: Q 69 LYS cc_start: 0.8370 (tttm) cc_final: 0.7907 (ttmt) REVERT: R 17 ASP cc_start: 0.7378 (m-30) cc_final: 0.7150 (m-30) REVERT: R 22 ASN cc_start: 0.9084 (p0) cc_final: 0.8826 (p0) REVERT: R 24 GLN cc_start: 0.8189 (mp10) cc_final: 0.7845 (pm20) REVERT: R 33 LYS cc_start: 0.9120 (ttmt) cc_final: 0.8911 (mtmt) REVERT: R 59 ASN cc_start: 0.8368 (m-40) cc_final: 0.7094 (m110) REVERT: R 69 LYS cc_start: 0.8147 (tttm) cc_final: 0.6822 (mttt) REVERT: S 17 ASP cc_start: 0.7614 (m-30) cc_final: 0.7190 (m-30) REVERT: S 33 LYS cc_start: 0.8778 (mttp) cc_final: 0.8232 (mtmt) REVERT: S 39 SER cc_start: 0.9298 (m) cc_final: 0.8341 (m) REVERT: S 59 ASN cc_start: 0.8655 (m-40) cc_final: 0.7531 (m110) REVERT: T 17 ASP cc_start: 0.8511 (m-30) cc_final: 0.8282 (m-30) REVERT: T 22 ASN cc_start: 0.8647 (p0) cc_final: 0.8227 (p0) REVERT: T 25 THR cc_start: 0.8526 (p) cc_final: 0.8049 (t) REVERT: T 48 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8479 (tm-30) REVERT: T 50 LYS cc_start: 0.8897 (mmtt) cc_final: 0.8628 (mmmt) REVERT: T 69 LYS cc_start: 0.7010 (tttm) cc_final: 0.6571 (ttmt) outliers start: 26 outliers final: 17 residues processed: 568 average time/residue: 0.2209 time to fit residues: 178.7446 Evaluate side-chains 565 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 546 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 62 SER Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 33 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 52 optimal weight: 0.4980 chunk 93 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 GLN D 77 GLN U 78 ASN F 77 GLN ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN K 55 ASN N 55 ASN O 55 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11837 Z= 0.256 Angle : 0.567 9.487 16112 Z= 0.292 Chirality : 0.040 0.173 1843 Planarity : 0.003 0.019 2109 Dihedral : 3.642 26.847 1596 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.39 % Allowed : 26.24 % Favored : 71.37 % 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: 2.31 (0.22), residues: 1444 helix: 2.14 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.11 (0.38), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 5 PHE 0.010 0.001 PHE I 79 TYR 0.026 0.002 TYR E 47 ARG 0.002 0.000 ARG V 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 562 time to evaluate : 1.331 Fit side-chains REVERT: D 15 LYS cc_start: 0.8824 (mmmm) cc_final: 0.8561 (mmmt) REVERT: D 37 LYS cc_start: 0.8658 (ttmt) cc_final: 0.7584 (tptt) REVERT: D 56 LEU cc_start: 0.8960 (mt) cc_final: 0.8721 (mt) REVERT: U 15 LYS cc_start: 0.9086 (mttt) cc_final: 0.8836 (mmtp) REVERT: U 37 LYS cc_start: 0.8198 (ttmt) cc_final: 0.7254 (tptt) REVERT: U 66 LYS cc_start: 0.8731 (tptp) cc_final: 0.6573 (mttt) REVERT: V 37 LYS cc_start: 0.8700 (ttmt) cc_final: 0.7556 (tptt) REVERT: V 47 TYR cc_start: 0.9220 (t80) cc_final: 0.8375 (t80) REVERT: V 49 SER cc_start: 0.8636 (t) cc_final: 0.8266 (p) REVERT: V 77 GLN cc_start: 0.8767 (tp40) cc_final: 0.8192 (tp40) REVERT: E 15 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8520 (ttmm) REVERT: E 22 ASN cc_start: 0.8238 (p0) cc_final: 0.7516 (p0) REVERT: E 37 LYS cc_start: 0.8743 (ttmt) cc_final: 0.7370 (tptt) REVERT: E 53 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8278 (mm-30) REVERT: E 66 LYS cc_start: 0.8250 (tptp) cc_final: 0.6613 (mttt) REVERT: F 28 THR cc_start: 0.8729 (m) cc_final: 0.8518 (p) REVERT: F 34 LEU cc_start: 0.9203 (tp) cc_final: 0.8923 (tt) REVERT: F 37 LYS cc_start: 0.8656 (ttmt) cc_final: 0.7715 (tptt) REVERT: F 39 SER cc_start: 0.8847 (m) cc_final: 0.8221 (t) REVERT: F 47 TYR cc_start: 0.9056 (t80) cc_final: 0.8585 (t80) REVERT: F 49 SER cc_start: 0.9287 (t) cc_final: 0.8881 (p) REVERT: F 51 LEU cc_start: 0.9175 (tp) cc_final: 0.8925 (tp) REVERT: F 53 GLU cc_start: 0.8393 (tp30) cc_final: 0.7857 (mm-30) REVERT: F 66 LYS cc_start: 0.8643 (tptp) cc_final: 0.7304 (mttm) REVERT: G 11 ASP cc_start: 0.8166 (m-30) cc_final: 0.7905 (t0) REVERT: G 15 LYS cc_start: 0.9082 (ttmt) cc_final: 0.8756 (ttmm) REVERT: G 37 LYS cc_start: 0.8420 (ttmt) cc_final: 0.7147 (tptt) REVERT: G 66 LYS cc_start: 0.8967 (tppt) cc_final: 0.8497 (tppt) REVERT: G 69 LYS cc_start: 0.8649 (tttm) cc_final: 0.8310 (tttt) REVERT: H 28 THR cc_start: 0.8966 (m) cc_final: 0.8359 (p) REVERT: H 32 ASP cc_start: 0.7901 (m-30) cc_final: 0.7589 (m-30) REVERT: H 37 LYS cc_start: 0.8260 (ttmt) cc_final: 0.6918 (tptt) REVERT: H 47 TYR cc_start: 0.9111 (t80) cc_final: 0.7383 (t80) REVERT: H 51 LEU cc_start: 0.9276 (tp) cc_final: 0.8700 (tp) REVERT: H 77 GLN cc_start: 0.8711 (tp40) cc_final: 0.8470 (tp-100) REVERT: I 37 LYS cc_start: 0.8594 (ttmt) cc_final: 0.6995 (tptp) REVERT: J 22 ASN cc_start: 0.8246 (p0) cc_final: 0.7684 (p0) REVERT: J 37 LYS cc_start: 0.8753 (ttmt) cc_final: 0.7312 (tptt) REVERT: J 39 SER cc_start: 0.8900 (t) cc_final: 0.8662 (t) REVERT: J 47 TYR cc_start: 0.9173 (t80) cc_final: 0.8361 (t80) REVERT: J 54 TYR cc_start: 0.8873 (t80) cc_final: 0.8651 (t80) REVERT: K 33 LYS cc_start: 0.9277 (mttt) cc_final: 0.8885 (mtpp) REVERT: K 37 LYS cc_start: 0.8992 (ttmt) cc_final: 0.7536 (tptp) REVERT: K 47 TYR cc_start: 0.9056 (t80) cc_final: 0.7830 (t80) REVERT: L 23 LEU cc_start: 0.8651 (tp) cc_final: 0.8340 (tp) REVERT: L 26 GLN cc_start: 0.8938 (mt0) cc_final: 0.8411 (tt0) REVERT: L 28 THR cc_start: 0.8941 (m) cc_final: 0.8631 (p) REVERT: L 53 GLU cc_start: 0.8256 (tp30) cc_final: 0.7917 (tp30) REVERT: L 77 GLN cc_start: 0.8522 (tp-100) cc_final: 0.8167 (tp40) REVERT: M 22 ASN cc_start: 0.8630 (p0) cc_final: 0.8246 (p0) REVERT: M 28 THR cc_start: 0.8776 (m) cc_final: 0.8002 (p) REVERT: M 31 LEU cc_start: 0.9258 (tp) cc_final: 0.8926 (tp) REVERT: M 32 ASP cc_start: 0.8370 (p0) cc_final: 0.8021 (p0) REVERT: M 47 TYR cc_start: 0.9292 (t80) cc_final: 0.8641 (t80) REVERT: M 66 LYS cc_start: 0.8717 (tptt) cc_final: 0.8190 (tmtt) REVERT: M 69 LYS cc_start: 0.8609 (tttp) cc_final: 0.7908 (ttpt) REVERT: N 23 LEU cc_start: 0.9005 (tp) cc_final: 0.8787 (tp) REVERT: N 24 GLN cc_start: 0.8576 (mp10) cc_final: 0.7838 (tm-30) REVERT: N 32 ASP cc_start: 0.8343 (m-30) cc_final: 0.8074 (m-30) REVERT: N 49 SER cc_start: 0.9431 (m) cc_final: 0.9151 (t) REVERT: N 50 LYS cc_start: 0.8934 (mmtp) cc_final: 0.8457 (mmmt) REVERT: N 51 LEU cc_start: 0.9201 (tp) cc_final: 0.8772 (tt) REVERT: N 53 GLU cc_start: 0.8344 (tp30) cc_final: 0.7704 (tp30) REVERT: O 15 LYS cc_start: 0.8839 (tppt) cc_final: 0.8611 (tptp) REVERT: O 17 ASP cc_start: 0.8291 (m-30) cc_final: 0.7439 (t0) REVERT: O 22 ASN cc_start: 0.9159 (p0) cc_final: 0.7937 (p0) REVERT: O 25 THR cc_start: 0.9051 (m) cc_final: 0.8508 (p) REVERT: O 28 THR cc_start: 0.8417 (m) cc_final: 0.8089 (p) REVERT: O 33 LYS cc_start: 0.9135 (mttt) cc_final: 0.8405 (mtmm) REVERT: O 49 SER cc_start: 0.9234 (m) cc_final: 0.8710 (t) REVERT: O 59 ASN cc_start: 0.8436 (m-40) cc_final: 0.7786 (m110) REVERT: O 69 LYS cc_start: 0.8125 (tttm) cc_final: 0.7558 (ttmt) REVERT: O 77 GLN cc_start: 0.8868 (tp-100) cc_final: 0.8553 (tp-100) REVERT: P 22 ASN cc_start: 0.9258 (p0) cc_final: 0.8693 (p0) REVERT: P 23 LEU cc_start: 0.8837 (tp) cc_final: 0.8456 (tt) REVERT: P 29 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7826 (mp0) REVERT: Q 25 THR cc_start: 0.8687 (m) cc_final: 0.8418 (p) REVERT: Q 40 ASP cc_start: 0.8183 (t0) cc_final: 0.7696 (t70) REVERT: Q 54 TYR cc_start: 0.8548 (t80) cc_final: 0.8058 (t80) REVERT: Q 69 LYS cc_start: 0.8426 (tttm) cc_final: 0.7957 (ttmt) REVERT: R 24 GLN cc_start: 0.8186 (mp10) cc_final: 0.7524 (pm20) REVERT: R 29 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8136 (tm-30) REVERT: R 50 LYS cc_start: 0.8394 (mmtt) cc_final: 0.8152 (mmmt) REVERT: R 59 ASN cc_start: 0.8457 (m-40) cc_final: 0.7429 (m110) REVERT: R 69 LYS cc_start: 0.8190 (tttm) cc_final: 0.7275 (ttmt) REVERT: S 17 ASP cc_start: 0.7784 (m-30) cc_final: 0.7331 (m-30) REVERT: S 33 LYS cc_start: 0.8883 (mttp) cc_final: 0.8357 (mtmt) REVERT: S 39 SER cc_start: 0.9360 (m) cc_final: 0.8364 (m) REVERT: S 58 ARG cc_start: 0.9018 (mmt180) cc_final: 0.8802 (mmt90) REVERT: S 59 ASN cc_start: 0.8736 (m-40) cc_final: 0.7554 (m110) REVERT: T 17 ASP cc_start: 0.8038 (m-30) cc_final: 0.7810 (m-30) REVERT: T 22 ASN cc_start: 0.8789 (p0) cc_final: 0.8415 (p0) REVERT: T 25 THR cc_start: 0.8615 (p) cc_final: 0.8147 (t) REVERT: T 48 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8586 (tm-30) REVERT: T 50 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8605 (mmmt) REVERT: T 69 LYS cc_start: 0.7066 (tttm) cc_final: 0.6516 (tttt) outliers start: 30 outliers final: 27 residues processed: 572 average time/residue: 0.2310 time to fit residues: 187.3120 Evaluate side-chains 578 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 550 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain U residue 62 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 33 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 20.0000 chunk 59 optimal weight: 0.3980 chunk 87 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 105 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 112 optimal weight: 20.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11837 Z= 0.206 Angle : 0.550 8.271 16112 Z= 0.284 Chirality : 0.039 0.178 1843 Planarity : 0.003 0.021 2109 Dihedral : 3.633 25.317 1596 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.31 % Allowed : 27.03 % Favored : 70.65 % 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: 2.56 (0.22), residues: 1444 helix: 2.25 (0.14), residues: 1273 sheet: None (None), residues: 0 loop : -2.87 (0.43), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 5 PHE 0.009 0.001 PHE E 79 TYR 0.025 0.002 TYR E 47 ARG 0.002 0.000 ARG U 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 556 time to evaluate : 1.322 Fit side-chains REVERT: D 15 LYS cc_start: 0.8772 (mmmm) cc_final: 0.8520 (mmmt) REVERT: D 37 LYS cc_start: 0.8584 (ttmt) cc_final: 0.7578 (tptt) REVERT: U 15 LYS cc_start: 0.9083 (mttt) cc_final: 0.8836 (mmtp) REVERT: U 37 LYS cc_start: 0.8194 (ttmt) cc_final: 0.7244 (tptt) REVERT: U 66 LYS cc_start: 0.8693 (tptp) cc_final: 0.6657 (mttt) REVERT: V 15 LYS cc_start: 0.9216 (tppp) cc_final: 0.9001 (mmtp) REVERT: V 37 LYS cc_start: 0.8698 (ttmt) cc_final: 0.7536 (tptt) REVERT: V 47 TYR cc_start: 0.9207 (t80) cc_final: 0.8315 (t80) REVERT: V 49 SER cc_start: 0.8607 (t) cc_final: 0.8235 (p) REVERT: V 77 GLN cc_start: 0.8732 (tp40) cc_final: 0.8169 (tp40) REVERT: E 22 ASN cc_start: 0.8210 (p0) cc_final: 0.7568 (p0) REVERT: E 37 LYS cc_start: 0.8747 (ttmt) cc_final: 0.7360 (tptt) REVERT: E 53 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8069 (mm-30) REVERT: E 66 LYS cc_start: 0.8204 (tptp) cc_final: 0.6555 (mttt) REVERT: F 34 LEU cc_start: 0.9191 (tp) cc_final: 0.8928 (tt) REVERT: F 37 LYS cc_start: 0.8688 (ttmt) cc_final: 0.7622 (tptt) REVERT: F 39 SER cc_start: 0.8845 (m) cc_final: 0.8211 (t) REVERT: F 47 TYR cc_start: 0.9080 (t80) cc_final: 0.8412 (t80) REVERT: F 49 SER cc_start: 0.9273 (t) cc_final: 0.8851 (p) REVERT: F 53 GLU cc_start: 0.8199 (tp30) cc_final: 0.7896 (mm-30) REVERT: F 66 LYS cc_start: 0.8622 (tptp) cc_final: 0.7491 (ttmt) REVERT: F 77 GLN cc_start: 0.8684 (tp40) cc_final: 0.8466 (tp-100) REVERT: G 11 ASP cc_start: 0.8150 (m-30) cc_final: 0.7899 (t0) REVERT: G 15 LYS cc_start: 0.9072 (ttmt) cc_final: 0.8739 (ttmm) REVERT: G 37 LYS cc_start: 0.8422 (ttmt) cc_final: 0.7128 (tptt) REVERT: G 66 LYS cc_start: 0.8949 (tppt) cc_final: 0.8672 (tppt) REVERT: G 69 LYS cc_start: 0.8623 (tttm) cc_final: 0.8277 (tttt) REVERT: H 28 THR cc_start: 0.8949 (m) cc_final: 0.8437 (p) REVERT: H 32 ASP cc_start: 0.7839 (m-30) cc_final: 0.7489 (m-30) REVERT: H 37 LYS cc_start: 0.8228 (ttmt) cc_final: 0.6918 (tptt) REVERT: H 47 TYR cc_start: 0.9106 (t80) cc_final: 0.7259 (t80) REVERT: H 51 LEU cc_start: 0.9280 (tp) cc_final: 0.8697 (tt) REVERT: H 54 TYR cc_start: 0.9003 (t80) cc_final: 0.8705 (t80) REVERT: H 77 GLN cc_start: 0.8598 (tp40) cc_final: 0.8364 (tp-100) REVERT: I 37 LYS cc_start: 0.8615 (ttmt) cc_final: 0.7018 (tptp) REVERT: J 22 ASN cc_start: 0.8230 (p0) cc_final: 0.7685 (p0) REVERT: J 37 LYS cc_start: 0.8758 (ttmt) cc_final: 0.7421 (tptt) REVERT: J 39 SER cc_start: 0.8875 (t) cc_final: 0.8634 (t) REVERT: J 47 TYR cc_start: 0.9164 (t80) cc_final: 0.8363 (t80) REVERT: J 54 TYR cc_start: 0.8872 (t80) cc_final: 0.8618 (t80) REVERT: K 15 LYS cc_start: 0.8946 (tptm) cc_final: 0.8716 (tptp) REVERT: K 33 LYS cc_start: 0.9279 (mttt) cc_final: 0.8879 (mtpp) REVERT: K 37 LYS cc_start: 0.8975 (ttmt) cc_final: 0.7522 (tptp) REVERT: K 47 TYR cc_start: 0.9034 (t80) cc_final: 0.7791 (t80) REVERT: K 63 ASN cc_start: 0.8619 (m-40) cc_final: 0.8305 (m110) REVERT: L 23 LEU cc_start: 0.8638 (tp) cc_final: 0.8296 (tp) REVERT: L 26 GLN cc_start: 0.8934 (mt0) cc_final: 0.8376 (tt0) REVERT: L 28 THR cc_start: 0.8939 (m) cc_final: 0.8619 (p) REVERT: L 53 GLU cc_start: 0.8253 (tp30) cc_final: 0.7912 (tp30) REVERT: L 77 GLN cc_start: 0.8700 (tp-100) cc_final: 0.8395 (tp40) REVERT: M 22 ASN cc_start: 0.8633 (p0) cc_final: 0.8290 (p0) REVERT: M 28 THR cc_start: 0.8766 (m) cc_final: 0.7983 (p) REVERT: M 31 LEU cc_start: 0.9270 (tp) cc_final: 0.8933 (tp) REVERT: M 32 ASP cc_start: 0.8369 (p0) cc_final: 0.8007 (p0) REVERT: M 47 TYR cc_start: 0.9286 (t80) cc_final: 0.8656 (t80) REVERT: M 66 LYS cc_start: 0.8717 (tptt) cc_final: 0.8201 (tmtt) REVERT: M 69 LYS cc_start: 0.8586 (tttp) cc_final: 0.7863 (ttpt) REVERT: N 24 GLN cc_start: 0.8580 (mp10) cc_final: 0.8267 (tp40) REVERT: N 32 ASP cc_start: 0.8357 (m-30) cc_final: 0.8078 (m-30) REVERT: N 49 SER cc_start: 0.9419 (m) cc_final: 0.9148 (t) REVERT: N 50 LYS cc_start: 0.8922 (mmtp) cc_final: 0.8452 (mmmt) REVERT: N 51 LEU cc_start: 0.9193 (tp) cc_final: 0.8767 (tt) REVERT: N 53 GLU cc_start: 0.8281 (tp30) cc_final: 0.7950 (tp30) REVERT: O 15 LYS cc_start: 0.8807 (tppt) cc_final: 0.8581 (tptp) REVERT: O 17 ASP cc_start: 0.8282 (m-30) cc_final: 0.7439 (t0) REVERT: O 22 ASN cc_start: 0.9139 (p0) cc_final: 0.7889 (p0) REVERT: O 25 THR cc_start: 0.9036 (m) cc_final: 0.8500 (p) REVERT: O 28 THR cc_start: 0.8373 (m) cc_final: 0.8088 (p) REVERT: O 33 LYS cc_start: 0.9132 (mttt) cc_final: 0.8403 (mtmm) REVERT: O 49 SER cc_start: 0.9210 (m) cc_final: 0.8693 (t) REVERT: O 59 ASN cc_start: 0.8443 (m-40) cc_final: 0.7828 (m110) REVERT: O 69 LYS cc_start: 0.8101 (tttm) cc_final: 0.7526 (ttmt) REVERT: O 77 GLN cc_start: 0.8853 (tp-100) cc_final: 0.8547 (tp-100) REVERT: P 22 ASN cc_start: 0.9303 (p0) cc_final: 0.8702 (p0) REVERT: P 23 LEU cc_start: 0.8830 (tp) cc_final: 0.8422 (tt) REVERT: P 29 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: Q 25 THR cc_start: 0.8647 (m) cc_final: 0.8404 (p) REVERT: Q 40 ASP cc_start: 0.8131 (t0) cc_final: 0.7653 (t70) REVERT: Q 54 TYR cc_start: 0.8524 (t80) cc_final: 0.8010 (t80) REVERT: Q 69 LYS cc_start: 0.8386 (tttm) cc_final: 0.7941 (ttmt) REVERT: R 24 GLN cc_start: 0.8196 (mp10) cc_final: 0.7831 (pm20) REVERT: R 29 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8191 (tm-30) REVERT: R 33 LYS cc_start: 0.9049 (mtmt) cc_final: 0.8738 (mtmt) REVERT: R 50 LYS cc_start: 0.8380 (mmtt) cc_final: 0.8131 (mmmt) REVERT: R 59 ASN cc_start: 0.8434 (m-40) cc_final: 0.7390 (m110) REVERT: R 69 LYS cc_start: 0.8182 (tttm) cc_final: 0.7256 (ttmt) REVERT: S 17 ASP cc_start: 0.7760 (m-30) cc_final: 0.7307 (m-30) REVERT: S 33 LYS cc_start: 0.8889 (mttp) cc_final: 0.8389 (mtmt) REVERT: S 39 SER cc_start: 0.9327 (m) cc_final: 0.8571 (p) REVERT: S 58 ARG cc_start: 0.9013 (mmt180) cc_final: 0.8784 (mmt90) REVERT: S 59 ASN cc_start: 0.8948 (m-40) cc_final: 0.7842 (m110) REVERT: T 17 ASP cc_start: 0.8013 (m-30) cc_final: 0.7790 (m-30) REVERT: T 22 ASN cc_start: 0.8818 (p0) cc_final: 0.8439 (p0) REVERT: T 25 THR cc_start: 0.8573 (p) cc_final: 0.8129 (t) REVERT: T 48 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8549 (tm-30) REVERT: T 50 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8606 (mmmt) REVERT: T 69 LYS cc_start: 0.7067 (tttm) cc_final: 0.6512 (tttt) outliers start: 29 outliers final: 27 residues processed: 567 average time/residue: 0.2239 time to fit residues: 180.0587 Evaluate side-chains 578 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 550 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain U residue 62 SER Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 40 ASP Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 33 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 GLN D 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.096335 restraints weight = 17629.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.099527 restraints weight = 9398.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.101621 restraints weight = 6106.080| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11837 Z= 0.214 Angle : 0.554 9.368 16112 Z= 0.286 Chirality : 0.039 0.192 1843 Planarity : 0.003 0.018 2109 Dihedral : 3.619 25.776 1596 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.47 % Allowed : 27.35 % Favored : 70.18 % 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: 2.62 (0.22), residues: 1444 helix: 2.29 (0.14), residues: 1273 sheet: None (None), residues: 0 loop : -2.83 (0.43), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 5 PHE 0.008 0.001 PHE E 79 TYR 0.024 0.002 TYR E 47 ARG 0.002 0.000 ARG U 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3164.57 seconds wall clock time: 57 minutes 40.18 seconds (3460.18 seconds total)