Starting phenix.real_space_refine on Wed Mar 4 18:12:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k3r_22656/03_2026/7k3r_22656.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k3r_22656/03_2026/7k3r_22656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k3r_22656/03_2026/7k3r_22656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k3r_22656/03_2026/7k3r_22656.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k3r_22656/03_2026/7k3r_22656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k3r_22656/03_2026/7k3r_22656.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 10332 2.51 5 N 2730 2.21 5 O 3024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16170 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U Time building chain proxies: 1.35, per 1000 atoms: 0.08 Number of scatterers: 16170 At special positions: 0 Unit cell: (107.58, 107.58, 126.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3024 8.00 N 2730 7.00 C 10332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 709.6 milliseconds 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3822 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 0 sheets defined 88.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN A 17 " --> pdb=" O GLY A 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 18 " --> pdb=" O LEU A 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 14 through 18' Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 58 through 73 Processing helix chain 'A' and resid 75 through 94 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN B 17 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 18 " --> pdb=" O LEU B 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 14 through 18' Processing helix chain 'B' and resid 19 through 29 Processing helix chain 'B' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 58 through 73 Processing helix chain 'B' and resid 75 through 94 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN C 17 " --> pdb=" O GLY C 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 18 " --> pdb=" O LEU C 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 14 through 18' Processing helix chain 'C' and resid 19 through 29 Processing helix chain 'C' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 58 Processing helix chain 'C' and resid 58 through 73 Processing helix chain 'C' and resid 75 through 94 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 14 through 18 removed outlier: 3.515A pdb=" N ASN D 17 " --> pdb=" O GLY D 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 18 " --> pdb=" O LEU D 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 14 through 18' Processing helix chain 'D' and resid 19 through 29 Processing helix chain 'D' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 58 Processing helix chain 'D' and resid 58 through 73 Processing helix chain 'D' and resid 75 through 94 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN E 17 " --> pdb=" O GLY E 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE E 18 " --> pdb=" O LEU E 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 14 through 18' Processing helix chain 'E' and resid 19 through 29 Processing helix chain 'E' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 58 through 73 Processing helix chain 'E' and resid 75 through 94 Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN F 17 " --> pdb=" O GLY F 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE F 18 " --> pdb=" O LEU F 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 14 through 18' Processing helix chain 'F' and resid 19 through 29 Processing helix chain 'F' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU F 41 " --> pdb=" O ALA F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 58 Processing helix chain 'F' and resid 58 through 73 Processing helix chain 'F' and resid 75 through 94 Processing helix chain 'G' and resid 2 through 13 Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.515A pdb=" N ASN G 17 " --> pdb=" O GLY G 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE G 18 " --> pdb=" O LEU G 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 14 through 18' Processing helix chain 'G' and resid 19 through 29 Processing helix chain 'G' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 58 Processing helix chain 'G' and resid 58 through 73 Processing helix chain 'G' and resid 75 through 94 Processing helix chain 'H' and resid 2 through 13 Processing helix chain 'H' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN H 17 " --> pdb=" O GLY H 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE H 18 " --> pdb=" O LEU H 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 14 through 18' Processing helix chain 'H' and resid 19 through 29 Processing helix chain 'H' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 58 Processing helix chain 'H' and resid 58 through 73 Processing helix chain 'H' and resid 75 through 94 Processing helix chain 'I' and resid 2 through 13 Processing helix chain 'I' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN I 17 " --> pdb=" O GLY I 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE I 18 " --> pdb=" O LEU I 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 14 through 18' Processing helix chain 'I' and resid 19 through 29 Processing helix chain 'I' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU I 41 " --> pdb=" O ALA I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 58 Processing helix chain 'I' and resid 58 through 73 Processing helix chain 'I' and resid 75 through 94 Processing helix chain 'J' and resid 2 through 13 Processing helix chain 'J' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN J 17 " --> pdb=" O GLY J 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE J 18 " --> pdb=" O LEU J 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 14 through 18' Processing helix chain 'J' and resid 19 through 29 Processing helix chain 'J' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU J 41 " --> pdb=" O ALA J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 58 Processing helix chain 'J' and resid 58 through 73 Processing helix chain 'J' and resid 75 through 94 Processing helix chain 'K' and resid 2 through 13 Processing helix chain 'K' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN K 17 " --> pdb=" O GLY K 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE K 18 " --> pdb=" O LEU K 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 14 through 18' Processing helix chain 'K' and resid 19 through 29 Processing helix chain 'K' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU K 41 " --> pdb=" O ALA K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 58 Processing helix chain 'K' and resid 58 through 73 Processing helix chain 'K' and resid 75 through 94 Processing helix chain 'L' and resid 2 through 13 Processing helix chain 'L' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN L 17 " --> pdb=" O GLY L 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE L 18 " --> pdb=" O LEU L 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 14 through 18' Processing helix chain 'L' and resid 19 through 29 Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU L 41 " --> pdb=" O ALA L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 58 Processing helix chain 'L' and resid 58 through 73 Processing helix chain 'L' and resid 75 through 94 Processing helix chain 'M' and resid 2 through 13 Processing helix chain 'M' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN M 17 " --> pdb=" O GLY M 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE M 18 " --> pdb=" O LEU M 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 14 through 18' Processing helix chain 'M' and resid 19 through 29 Processing helix chain 'M' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU M 41 " --> pdb=" O ALA M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 58 Processing helix chain 'M' and resid 58 through 73 Processing helix chain 'M' and resid 75 through 94 Processing helix chain 'N' and resid 2 through 13 Processing helix chain 'N' and resid 14 through 18 removed outlier: 3.515A pdb=" N ASN N 17 " --> pdb=" O GLY N 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE N 18 " --> pdb=" O LEU N 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 14 through 18' Processing helix chain 'N' and resid 19 through 29 Processing helix chain 'N' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU N 41 " --> pdb=" O ALA N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 58 Processing helix chain 'N' and resid 58 through 73 Processing helix chain 'N' and resid 75 through 94 Processing helix chain 'O' and resid 2 through 13 Processing helix chain 'O' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN O 17 " --> pdb=" O GLY O 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE O 18 " --> pdb=" O LEU O 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 14 through 18' Processing helix chain 'O' and resid 19 through 29 Processing helix chain 'O' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU O 41 " --> pdb=" O ALA O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 58 Processing helix chain 'O' and resid 58 through 73 Processing helix chain 'O' and resid 75 through 94 Processing helix chain 'P' and resid 2 through 13 Processing helix chain 'P' and resid 14 through 18 removed outlier: 3.517A pdb=" N ASN P 17 " --> pdb=" O GLY P 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE P 18 " --> pdb=" O LEU P 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 14 through 18' Processing helix chain 'P' and resid 19 through 29 Processing helix chain 'P' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU P 41 " --> pdb=" O ALA P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 58 Processing helix chain 'P' and resid 58 through 73 Processing helix chain 'P' and resid 75 through 94 Processing helix chain 'Q' and resid 2 through 13 Processing helix chain 'Q' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN Q 17 " --> pdb=" O GLY Q 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE Q 18 " --> pdb=" O LEU Q 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 14 through 18' Processing helix chain 'Q' and resid 19 through 29 Processing helix chain 'Q' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU Q 41 " --> pdb=" O ALA Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 58 Processing helix chain 'Q' and resid 58 through 73 Processing helix chain 'Q' and resid 75 through 94 Processing helix chain 'R' and resid 2 through 13 Processing helix chain 'R' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN R 17 " --> pdb=" O GLY R 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE R 18 " --> pdb=" O LEU R 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 14 through 18' Processing helix chain 'R' and resid 19 through 29 Processing helix chain 'R' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU R 41 " --> pdb=" O ALA R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 58 Processing helix chain 'R' and resid 58 through 73 Processing helix chain 'R' and resid 75 through 94 Processing helix chain 'S' and resid 2 through 13 Processing helix chain 'S' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN S 17 " --> pdb=" O GLY S 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE S 18 " --> pdb=" O LEU S 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 14 through 18' Processing helix chain 'S' and resid 19 through 29 Processing helix chain 'S' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 58 Processing helix chain 'S' and resid 58 through 73 Processing helix chain 'S' and resid 75 through 94 Processing helix chain 'T' and resid 2 through 13 Processing helix chain 'T' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN T 17 " --> pdb=" O GLY T 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE T 18 " --> pdb=" O LEU T 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 14 through 18' Processing helix chain 'T' and resid 19 through 29 Processing helix chain 'T' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU T 41 " --> pdb=" O ALA T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 58 Processing helix chain 'T' and resid 58 through 73 Processing helix chain 'T' and resid 75 through 94 Processing helix chain 'U' and resid 2 through 13 Processing helix chain 'U' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN U 17 " --> pdb=" O GLY U 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE U 18 " --> pdb=" O LEU U 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 14 through 18' Processing helix chain 'U' and resid 19 through 29 Processing helix chain 'U' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU U 41 " --> pdb=" O ALA U 37 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 58 Processing helix chain 'U' and resid 58 through 73 Processing helix chain 'U' and resid 75 through 94 1135 hydrogen bonds defined for protein. 3405 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: 2.25 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5229 1.34 - 1.46: 2430 1.46 - 1.57: 8511 1.57 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 16338 Sorted by residual: bond pdb=" SD MET U 53 " pdb=" CE MET U 53 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.55e+00 bond pdb=" SD MET N 53 " pdb=" CE MET N 53 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.55e+00 bond pdb=" SD MET B 53 " pdb=" CE MET B 53 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.53e+00 bond pdb=" SD MET D 53 " pdb=" CE MET D 53 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.52e+00 bond pdb=" SD MET Q 53 " pdb=" CE MET Q 53 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.52e+00 ... (remaining 16333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 18470 0.97 - 1.93: 2555 1.93 - 2.90: 569 2.90 - 3.86: 141 3.86 - 4.83: 84 Bond angle restraints: 21819 Sorted by residual: angle pdb=" C LEU R 73 " pdb=" N ASN R 74 " pdb=" CA ASN R 74 " ideal model delta sigma weight residual 122.19 125.92 -3.73 1.41e+00 5.03e-01 6.98e+00 angle pdb=" C LEU O 73 " pdb=" N ASN O 74 " pdb=" CA ASN O 74 " ideal model delta sigma weight residual 122.19 125.91 -3.72 1.41e+00 5.03e-01 6.96e+00 angle pdb=" C LEU N 73 " pdb=" N ASN N 74 " pdb=" CA ASN N 74 " ideal model delta sigma weight residual 122.19 125.91 -3.72 1.41e+00 5.03e-01 6.96e+00 angle pdb=" C LEU H 73 " pdb=" N ASN H 74 " pdb=" CA ASN H 74 " ideal model delta sigma weight residual 122.19 125.91 -3.72 1.41e+00 5.03e-01 6.96e+00 angle pdb=" C LEU M 73 " pdb=" N ASN M 74 " pdb=" CA ASN M 74 " ideal model delta sigma weight residual 122.19 125.91 -3.72 1.41e+00 5.03e-01 6.95e+00 ... (remaining 21814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.68: 8795 9.68 - 19.35: 1180 19.35 - 29.02: 63 29.02 - 38.70: 84 38.70 - 48.37: 42 Dihedral angle restraints: 10164 sinusoidal: 4305 harmonic: 5859 Sorted by residual: dihedral pdb=" CB MET M 76 " pdb=" CG MET M 76 " pdb=" SD MET M 76 " pdb=" CE MET M 76 " ideal model delta sinusoidal sigma weight residual 60.00 108.37 -48.37 3 1.50e+01 4.44e-03 8.63e+00 dihedral pdb=" CB MET T 76 " pdb=" CG MET T 76 " pdb=" SD MET T 76 " pdb=" CE MET T 76 " ideal model delta sinusoidal sigma weight residual 60.00 108.37 -48.37 3 1.50e+01 4.44e-03 8.63e+00 dihedral pdb=" CB MET B 76 " pdb=" CG MET B 76 " pdb=" SD MET B 76 " pdb=" CE MET B 76 " ideal model delta sinusoidal sigma weight residual 60.00 108.36 -48.36 3 1.50e+01 4.44e-03 8.63e+00 ... (remaining 10161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1066 0.024 - 0.048: 669 0.048 - 0.072: 436 0.072 - 0.096: 262 0.096 - 0.120: 87 Chirality restraints: 2520 Sorted by residual: chirality pdb=" CA ASN P 74 " pdb=" N ASN P 74 " pdb=" C ASN P 74 " pdb=" CB ASN P 74 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA ASN D 74 " pdb=" N ASN D 74 " pdb=" C ASN D 74 " pdb=" CB ASN D 74 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA ASN E 74 " pdb=" N ASN E 74 " pdb=" C ASN E 74 " pdb=" CB ASN E 74 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.46e-01 ... (remaining 2517 not shown) Planarity restraints: 2730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 34 " 0.004 2.00e-02 2.50e+03 9.09e-03 1.45e+00 pdb=" CG PHE C 34 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE C 34 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE C 34 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 34 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 34 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 34 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 34 " 0.004 2.00e-02 2.50e+03 9.07e-03 1.44e+00 pdb=" CG PHE G 34 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE G 34 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE G 34 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE G 34 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE G 34 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE G 34 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 34 " 0.004 2.00e-02 2.50e+03 9.05e-03 1.43e+00 pdb=" CG PHE A 34 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 34 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 34 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 34 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 34 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 34 " -0.004 2.00e-02 2.50e+03 ... (remaining 2727 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3220 2.76 - 3.30: 15216 3.30 - 3.83: 25692 3.83 - 4.37: 32587 4.37 - 4.90: 56178 Nonbonded interactions: 132893 Sorted by model distance: nonbonded pdb=" O ALA P 62 " pdb=" OG1 THR P 66 " model vdw 2.229 3.040 nonbonded pdb=" O ALA H 62 " pdb=" OG1 THR H 66 " model vdw 2.229 3.040 nonbonded pdb=" O ALA K 62 " pdb=" OG1 THR K 66 " model vdw 2.229 3.040 nonbonded pdb=" O ALA Q 62 " pdb=" OG1 THR Q 66 " model vdw 2.229 3.040 nonbonded pdb=" O ALA B 62 " pdb=" OG1 THR B 66 " model vdw 2.229 3.040 ... (remaining 132888 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.020 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 16338 Z= 0.261 Angle : 0.781 4.825 21819 Z= 0.466 Chirality : 0.046 0.120 2520 Planarity : 0.003 0.011 2730 Dihedral : 9.105 48.374 6342 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.15), residues: 1953 helix: -2.60 (0.08), residues: 1449 sheet: None (None), residues: 0 loop : 0.55 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 25 TYR 0.010 0.002 TYR U 75 PHE 0.016 0.003 PHE T 34 HIS 0.003 0.002 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00613 (16338) covalent geometry : angle 0.78080 (21819) hydrogen bonds : bond 0.06802 ( 1135) hydrogen bonds : angle 9.89409 ( 3405) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1008 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 63 VAL cc_start: 0.9299 (t) cc_final: 0.9085 (t) REVERT: R 63 VAL cc_start: 0.9275 (t) cc_final: 0.9050 (t) REVERT: S 63 VAL cc_start: 0.9307 (t) cc_final: 0.9090 (t) outliers start: 0 outliers final: 0 residues processed: 1008 average time/residue: 0.1646 time to fit residues: 225.6606 Evaluate side-chains 787 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 787 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.0470 chunk 149 optimal weight: 10.0000 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN B 55 GLN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 GLN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN H 55 GLN ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 GLN ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN ** M 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 ASN O 56 ASN ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 GLN ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 71 GLN S 48 GLN ** T 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 71 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.086437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.074411 restraints weight = 33291.788| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.43 r_work: 0.2915 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16338 Z= 0.174 Angle : 0.571 5.942 21819 Z= 0.329 Chirality : 0.042 0.173 2520 Planarity : 0.004 0.024 2730 Dihedral : 4.646 13.400 2121 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.47 % Allowed : 11.17 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.18), residues: 1953 helix: 0.52 (0.12), residues: 1470 sheet: None (None), residues: 0 loop : 1.21 (0.33), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 81 TYR 0.008 0.001 TYR B 6 PHE 0.009 0.001 PHE K 70 HIS 0.001 0.000 HIS R 42 Details of bonding type rmsd covalent geometry : bond 0.00379 (16338) covalent geometry : angle 0.57101 (21819) hydrogen bonds : bond 0.03328 ( 1135) hydrogen bonds : angle 5.92642 ( 3405) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 859 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 GLN cc_start: 0.9123 (mt0) cc_final: 0.8722 (mt0) REVERT: D 33 GLU cc_start: 0.8176 (tp30) cc_final: 0.7963 (tp30) REVERT: E 8 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8337 (mt-10) REVERT: E 16 ASP cc_start: 0.8865 (t0) cc_final: 0.8463 (m-30) REVERT: F 16 ASP cc_start: 0.8873 (t0) cc_final: 0.8545 (m-30) REVERT: G 8 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8360 (mt-10) REVERT: H 33 GLU cc_start: 0.7997 (tp30) cc_final: 0.7785 (tp30) REVERT: I 16 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8245 (m-30) REVERT: I 33 GLU cc_start: 0.8077 (tp30) cc_final: 0.7496 (tp30) REVERT: I 68 ARG cc_start: 0.8914 (ttp-110) cc_final: 0.8450 (ttm-80) REVERT: J 33 GLU cc_start: 0.8167 (tp30) cc_final: 0.7944 (tp30) REVERT: J 92 GLN cc_start: 0.8508 (tp40) cc_final: 0.8251 (tp40) REVERT: K 16 ASP cc_start: 0.8966 (t0) cc_final: 0.8464 (m-30) REVERT: K 92 GLN cc_start: 0.8553 (tp40) cc_final: 0.8269 (tp40) REVERT: M 16 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8115 (m-30) REVERT: M 68 ARG cc_start: 0.8815 (ttp-110) cc_final: 0.8586 (ttp-110) REVERT: N 48 GLN cc_start: 0.9039 (mt0) cc_final: 0.8723 (mt0) REVERT: O 33 GLU cc_start: 0.8256 (tp30) cc_final: 0.7838 (tp30) REVERT: O 68 ARG cc_start: 0.8788 (ttp-110) cc_final: 0.8478 (ttm-80) REVERT: Q 8 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8274 (mt-10) REVERT: Q 16 ASP cc_start: 0.8849 (t0) cc_final: 0.8433 (m-30) REVERT: Q 33 GLU cc_start: 0.8121 (tp30) cc_final: 0.7918 (tp30) REVERT: Q 86 LYS cc_start: 0.9279 (ttpp) cc_final: 0.8967 (ttpp) REVERT: Q 92 GLN cc_start: 0.8501 (tp40) cc_final: 0.8216 (tp40) REVERT: R 16 ASP cc_start: 0.8808 (t0) cc_final: 0.8512 (m-30) REVERT: R 91 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8468 (mtmt) REVERT: R 92 GLN cc_start: 0.8262 (tp40) cc_final: 0.8062 (tp40) REVERT: R 93 TYR cc_start: 0.8643 (m-10) cc_final: 0.8415 (m-10) REVERT: S 33 GLU cc_start: 0.8199 (tp30) cc_final: 0.7972 (tp30) REVERT: S 68 ARG cc_start: 0.8852 (ttp-110) cc_final: 0.8612 (ttm-80) outliers start: 26 outliers final: 8 residues processed: 871 average time/residue: 0.1644 time to fit residues: 195.3090 Evaluate side-chains 819 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 809 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain M residue 16 ASP Chi-restraints excluded: chain O residue 16 ASP Chi-restraints excluded: chain Q residue 61 SER Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain T residue 16 ASP Chi-restraints excluded: chain T residue 31 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 63 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 chunk 160 optimal weight: 0.9980 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 71 GLN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN G 56 ASN H 56 ASN ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 71 GLN P 56 ASN P 71 GLN ** Q 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 56 ASN ** T 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 71 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.082509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.070219 restraints weight = 34185.983| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.43 r_work: 0.2837 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16338 Z= 0.260 Angle : 0.627 5.391 21819 Z= 0.351 Chirality : 0.045 0.184 2520 Planarity : 0.004 0.031 2730 Dihedral : 4.655 16.662 2121 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.17 % Allowed : 15.02 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.19), residues: 1953 helix: 1.41 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : 1.47 (0.35), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 81 TYR 0.010 0.001 TYR G 93 PHE 0.012 0.002 PHE L 29 HIS 0.001 0.000 HIS K 42 Details of bonding type rmsd covalent geometry : bond 0.00585 (16338) covalent geometry : angle 0.62732 (21819) hydrogen bonds : bond 0.03469 ( 1135) hydrogen bonds : angle 5.40682 ( 3405) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 835 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 64 MET cc_start: 0.8889 (mmm) cc_final: 0.8672 (mmm) REVERT: D 8 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8489 (mt-10) REVERT: E 8 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8513 (mt-10) REVERT: E 48 GLN cc_start: 0.9234 (mt0) cc_final: 0.8743 (mt0) REVERT: F 21 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8275 (tp30) REVERT: G 8 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8356 (mt-10) REVERT: H 8 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8504 (mt-10) REVERT: H 83 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8627 (mm-40) REVERT: I 16 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8171 (m-30) REVERT: J 48 GLN cc_start: 0.9189 (mt0) cc_final: 0.8740 (mt0) REVERT: J 92 GLN cc_start: 0.8555 (tp40) cc_final: 0.8288 (tp40) REVERT: L 86 LYS cc_start: 0.9365 (ttpp) cc_final: 0.9161 (ttpp) REVERT: O 68 ARG cc_start: 0.8870 (ttp-110) cc_final: 0.8605 (ttm-80) REVERT: Q 8 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8347 (mt-10) REVERT: Q 64 MET cc_start: 0.8762 (mmm) cc_final: 0.8513 (mmm) REVERT: Q 92 GLN cc_start: 0.8572 (tp40) cc_final: 0.8179 (tp40) REVERT: Q 93 TYR cc_start: 0.8801 (m-10) cc_final: 0.8581 (m-10) REVERT: R 8 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8254 (tt0) REVERT: R 16 ASP cc_start: 0.8878 (t0) cc_final: 0.8513 (m-30) REVERT: R 91 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8481 (mtmt) REVERT: R 92 GLN cc_start: 0.8270 (tp40) cc_final: 0.8031 (tp40) REVERT: S 68 ARG cc_start: 0.8902 (ttp-110) cc_final: 0.8671 (ttm-80) REVERT: T 64 MET cc_start: 0.8865 (mmm) cc_final: 0.8582 (mmm) REVERT: T 86 LYS cc_start: 0.9229 (ttpp) cc_final: 0.8982 (ttpp) REVERT: U 89 VAL cc_start: 0.9169 (t) cc_final: 0.8945 (p) outliers start: 56 outliers final: 23 residues processed: 846 average time/residue: 0.1654 time to fit residues: 190.1350 Evaluate side-chains 832 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 804 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain K residue 4 SER Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain O residue 16 ASP Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain Q residue 61 SER Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain T residue 16 ASP Chi-restraints excluded: chain T residue 38 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 9 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 94 optimal weight: 0.0970 chunk 5 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 39 optimal weight: 0.0670 chunk 99 optimal weight: 0.7980 overall best weight: 2.1920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN B 55 GLN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN C 56 ASN D 55 GLN D 56 ASN E 55 GLN E 56 ASN F 56 ASN G 35 ASN G 55 GLN H 55 GLN H 56 ASN ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 GLN J 56 ASN ** K 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 ASN ** Q 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 56 ASN U 56 ASN U 71 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.086047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.074211 restraints weight = 33667.425| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.42 r_work: 0.2943 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16338 Z= 0.131 Angle : 0.524 7.005 21819 Z= 0.300 Chirality : 0.041 0.174 2520 Planarity : 0.003 0.022 2730 Dihedral : 4.409 17.471 2121 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.21 % Allowed : 18.14 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.20), residues: 1953 helix: 1.83 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : 1.72 (0.37), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 81 TYR 0.011 0.001 TYR B 6 PHE 0.006 0.001 PHE Q 70 HIS 0.001 0.000 HIS C 42 Details of bonding type rmsd covalent geometry : bond 0.00292 (16338) covalent geometry : angle 0.52428 (21819) hydrogen bonds : bond 0.02937 ( 1135) hydrogen bonds : angle 5.21150 ( 3405) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 846 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8411 (mt-10) REVERT: B 48 GLN cc_start: 0.9109 (mt0) cc_final: 0.8625 (mt0) REVERT: C 64 MET cc_start: 0.8930 (mmm) cc_final: 0.8722 (mmm) REVERT: F 81 ARG cc_start: 0.8754 (ttm-80) cc_final: 0.8522 (mtp85) REVERT: G 83 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8772 (mm-40) REVERT: I 33 GLU cc_start: 0.8235 (tp30) cc_final: 0.7806 (tp30) REVERT: I 68 ARG cc_start: 0.8868 (ttp-110) cc_final: 0.8541 (ttm-80) REVERT: J 8 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8463 (mt-10) REVERT: J 9 ILE cc_start: 0.9165 (mm) cc_final: 0.8915 (pt) REVERT: J 92 GLN cc_start: 0.8471 (tp40) cc_final: 0.8136 (tp40) REVERT: M 8 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8340 (mt-10) REVERT: M 91 LYS cc_start: 0.8659 (mtpp) cc_final: 0.8344 (mtmm) REVERT: N 81 ARG cc_start: 0.8707 (ttm-80) cc_final: 0.8477 (mtp85) REVERT: O 8 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8209 (mt-10) REVERT: O 68 ARG cc_start: 0.8832 (ttp-110) cc_final: 0.8600 (ttm-80) REVERT: P 64 MET cc_start: 0.8890 (mmm) cc_final: 0.8653 (mmm) REVERT: Q 9 ILE cc_start: 0.9093 (mm) cc_final: 0.8882 (pt) REVERT: Q 64 MET cc_start: 0.8667 (mmm) cc_final: 0.8368 (mmm) REVERT: Q 72 LYS cc_start: 0.9283 (ttmt) cc_final: 0.8952 (ttpt) REVERT: R 16 ASP cc_start: 0.8839 (t0) cc_final: 0.8491 (m-30) REVERT: R 33 GLU cc_start: 0.8310 (tp30) cc_final: 0.8021 (tp30) REVERT: R 65 LYS cc_start: 0.8789 (mtpt) cc_final: 0.8543 (mtpt) REVERT: R 91 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8417 (mtmt) REVERT: S 33 GLU cc_start: 0.8428 (tp30) cc_final: 0.8150 (tp30) REVERT: S 68 ARG cc_start: 0.8896 (ttp-110) cc_final: 0.8641 (ttm-80) outliers start: 39 outliers final: 21 residues processed: 852 average time/residue: 0.1637 time to fit residues: 190.3007 Evaluate side-chains 834 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 813 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain K residue 4 SER Chi-restraints excluded: chain M residue 16 ASP Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain O residue 16 ASP Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain Q residue 61 SER Chi-restraints excluded: chain R residue 4 SER Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain T residue 16 ASP Chi-restraints excluded: chain U residue 16 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 161 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN B 56 ASN C 55 GLN D 55 GLN D 71 GLN E 55 GLN ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN I 35 ASN I 55 GLN I 56 ASN K 48 GLN K 56 ASN L 48 GLN L 71 GLN Q 35 ASN Q 56 ASN R 56 ASN S 48 GLN S 56 ASN S 92 GLN U 71 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.084524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.072288 restraints weight = 33639.777| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.42 r_work: 0.2865 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16338 Z= 0.184 Angle : 0.581 7.937 21819 Z= 0.326 Chirality : 0.043 0.177 2520 Planarity : 0.003 0.022 2730 Dihedral : 4.459 19.329 2121 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.00 % Allowed : 18.59 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.20), residues: 1953 helix: 1.86 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : 2.08 (0.38), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 81 TYR 0.008 0.001 TYR T 6 PHE 0.009 0.001 PHE L 29 HIS 0.001 0.000 HIS C 42 Details of bonding type rmsd covalent geometry : bond 0.00425 (16338) covalent geometry : angle 0.58075 (21819) hydrogen bonds : bond 0.03114 ( 1135) hydrogen bonds : angle 5.12709 ( 3405) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 839 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 MET cc_start: 0.8926 (mmm) cc_final: 0.8710 (mmm) REVERT: E 91 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8331 (tptp) REVERT: F 81 ARG cc_start: 0.8784 (ttm-80) cc_final: 0.8561 (mtp85) REVERT: G 83 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8767 (mm-40) REVERT: I 68 ARG cc_start: 0.8885 (ttp-110) cc_final: 0.8556 (ttm-80) REVERT: J 9 ILE cc_start: 0.9171 (mm) cc_final: 0.8938 (pt) REVERT: O 8 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8394 (mt-10) REVERT: O 68 ARG cc_start: 0.8843 (ttp-110) cc_final: 0.8620 (ttm-80) REVERT: P 8 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8363 (mt-10) REVERT: P 64 MET cc_start: 0.8868 (mmm) cc_final: 0.8493 (mmm) REVERT: P 72 LYS cc_start: 0.9388 (ttpp) cc_final: 0.9178 (ttmt) REVERT: Q 9 ILE cc_start: 0.9118 (mm) cc_final: 0.8881 (pt) REVERT: Q 64 MET cc_start: 0.8765 (mmm) cc_final: 0.8475 (mmm) REVERT: R 80 LYS cc_start: 0.9215 (ttmt) cc_final: 0.9003 (ttpp) REVERT: R 91 LYS cc_start: 0.8703 (mmtt) cc_final: 0.8426 (mtmt) REVERT: S 68 ARG cc_start: 0.8894 (ttp-110) cc_final: 0.8654 (ttm-80) REVERT: T 48 GLN cc_start: 0.9187 (mt0) cc_final: 0.8878 (mt0) outliers start: 53 outliers final: 32 residues processed: 846 average time/residue: 0.1653 time to fit residues: 190.9225 Evaluate side-chains 845 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 813 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 55 GLN Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain K residue 4 SER Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain M residue 16 ASP Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 21 GLU Chi-restraints excluded: chain O residue 16 ASP Chi-restraints excluded: chain P residue 21 GLU Chi-restraints excluded: chain R residue 4 SER Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain T residue 16 ASP Chi-restraints excluded: chain U residue 16 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 57 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN D 55 GLN E 55 GLN ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 GLN K 92 GLN U 71 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.084644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.072623 restraints weight = 33786.535| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.40 r_work: 0.2888 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16338 Z= 0.170 Angle : 0.588 8.941 21819 Z= 0.331 Chirality : 0.042 0.188 2520 Planarity : 0.003 0.022 2730 Dihedral : 4.432 18.612 2121 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.06 % Allowed : 18.82 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.21), residues: 1953 helix: 1.85 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : 2.26 (0.40), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 81 TYR 0.008 0.001 TYR H 6 PHE 0.008 0.001 PHE F 34 HIS 0.001 0.000 HIS J 42 Details of bonding type rmsd covalent geometry : bond 0.00394 (16338) covalent geometry : angle 0.58822 (21819) hydrogen bonds : bond 0.03070 ( 1135) hydrogen bonds : angle 5.12317 ( 3405) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 835 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 MET cc_start: 0.8968 (mmm) cc_final: 0.8734 (mmm) REVERT: E 91 LYS cc_start: 0.8635 (mtmt) cc_final: 0.8338 (tptp) REVERT: F 81 ARG cc_start: 0.8749 (ttm-80) cc_final: 0.8538 (mtp85) REVERT: G 83 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8749 (mm-40) REVERT: I 5 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8415 (mmtm) REVERT: I 33 GLU cc_start: 0.8256 (tp30) cc_final: 0.7826 (tp30) REVERT: I 68 ARG cc_start: 0.8874 (ttp-110) cc_final: 0.8556 (ttm-80) REVERT: I 93 TYR cc_start: 0.8709 (m-10) cc_final: 0.8508 (m-80) REVERT: K 81 ARG cc_start: 0.8729 (ttm-80) cc_final: 0.8517 (mtp85) REVERT: M 5 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8426 (mmtt) REVERT: M 8 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8498 (mt-10) REVERT: M 93 TYR cc_start: 0.8693 (m-10) cc_final: 0.8247 (m-10) REVERT: N 5 LYS cc_start: 0.8942 (mmmt) cc_final: 0.8479 (mmtt) REVERT: O 5 LYS cc_start: 0.9059 (mmmt) cc_final: 0.8355 (mmtm) REVERT: O 9 ILE cc_start: 0.9208 (mm) cc_final: 0.8958 (pt) REVERT: O 68 ARG cc_start: 0.8816 (ttp-110) cc_final: 0.8596 (ttm-80) REVERT: P 64 MET cc_start: 0.8889 (mmm) cc_final: 0.8522 (mmm) REVERT: P 72 LYS cc_start: 0.9366 (ttpp) cc_final: 0.9156 (ttmt) REVERT: P 75 TYR cc_start: 0.9071 (m-10) cc_final: 0.8787 (m-10) REVERT: Q 5 LYS cc_start: 0.8960 (mmmt) cc_final: 0.8458 (mmtm) REVERT: Q 64 MET cc_start: 0.8729 (mmm) cc_final: 0.8415 (mmm) REVERT: R 80 LYS cc_start: 0.9217 (ttmt) cc_final: 0.9004 (ttpp) REVERT: R 91 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8395 (mtmt) REVERT: S 68 ARG cc_start: 0.8912 (ttp-110) cc_final: 0.8701 (ttm-80) REVERT: T 48 GLN cc_start: 0.9178 (mt0) cc_final: 0.8854 (mt0) REVERT: T 81 ARG cc_start: 0.8870 (mtp85) cc_final: 0.8665 (ttm-80) REVERT: U 83 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8824 (mm-40) outliers start: 54 outliers final: 41 residues processed: 844 average time/residue: 0.1604 time to fit residues: 185.4551 Evaluate side-chains 852 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 811 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 55 GLN Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain K residue 4 SER Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain M residue 16 ASP Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain O residue 16 ASP Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain R residue 4 SER Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain T residue 16 ASP Chi-restraints excluded: chain U residue 16 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN K 48 GLN K 92 GLN P 35 ASN Q 48 GLN S 48 GLN S 56 ASN U 71 GLN U 74 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.081867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.069358 restraints weight = 33767.500| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.42 r_work: 0.2812 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 16338 Z= 0.291 Angle : 0.690 9.373 21819 Z= 0.383 Chirality : 0.047 0.199 2520 Planarity : 0.004 0.032 2730 Dihedral : 4.646 20.948 2121 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.68 % Allowed : 18.93 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.20), residues: 1953 helix: 1.69 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : 1.98 (0.38), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 81 TYR 0.011 0.002 TYR I 6 PHE 0.016 0.002 PHE R 29 HIS 0.002 0.000 HIS J 42 Details of bonding type rmsd covalent geometry : bond 0.00669 (16338) covalent geometry : angle 0.69016 (21819) hydrogen bonds : bond 0.03508 ( 1135) hydrogen bonds : angle 5.17673 ( 3405) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 824 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 21 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8206 (tp30) REVERT: C 64 MET cc_start: 0.8949 (mmm) cc_final: 0.8717 (mmm) REVERT: E 5 LYS cc_start: 0.9051 (mmmt) cc_final: 0.8527 (mmtm) REVERT: E 81 ARG cc_start: 0.8891 (ttm-80) cc_final: 0.8673 (mtp85) REVERT: E 91 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8361 (tptp) REVERT: F 81 ARG cc_start: 0.8804 (ttm-80) cc_final: 0.8598 (mtp85) REVERT: F 91 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8284 (mtpp) REVERT: F 92 GLN cc_start: 0.8777 (tp40) cc_final: 0.8518 (tp40) REVERT: G 83 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8740 (mm-40) REVERT: I 68 ARG cc_start: 0.8876 (ttp-110) cc_final: 0.8551 (ttm-80) REVERT: N 5 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8534 (mmtt) REVERT: O 8 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8493 (mt-10) REVERT: O 68 ARG cc_start: 0.8857 (ttp-110) cc_final: 0.8642 (ttm-80) REVERT: O 83 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8848 (mm-40) REVERT: P 75 TYR cc_start: 0.9097 (m-10) cc_final: 0.8882 (m-10) REVERT: R 5 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8841 (mmmt) REVERT: R 8 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8230 (mt-10) REVERT: R 91 LYS cc_start: 0.8722 (mmtt) cc_final: 0.8447 (mtmt) REVERT: S 65 LYS cc_start: 0.9070 (mtpt) cc_final: 0.8808 (mtpt) REVERT: S 68 ARG cc_start: 0.8880 (ttp-110) cc_final: 0.8673 (ttm-80) REVERT: T 48 GLN cc_start: 0.9177 (mt0) cc_final: 0.8856 (mt0) REVERT: U 83 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8821 (mm-40) outliers start: 65 outliers final: 44 residues processed: 837 average time/residue: 0.1635 time to fit residues: 187.5651 Evaluate side-chains 852 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 807 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain K residue 4 SER Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain M residue 16 ASP Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 21 GLU Chi-restraints excluded: chain O residue 16 ASP Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 21 GLU Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain Q residue 34 PHE Chi-restraints excluded: chain R residue 4 SER Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain R residue 55 GLN Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain T residue 16 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 18 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN D 55 GLN E 55 GLN G 35 ASN H 56 ASN H 71 GLN I 55 GLN K 92 GLN P 35 ASN T 92 GLN U 74 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.087348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.075604 restraints weight = 33420.263| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.38 r_work: 0.2967 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16338 Z= 0.129 Angle : 0.587 10.398 21819 Z= 0.332 Chirality : 0.041 0.181 2520 Planarity : 0.003 0.028 2730 Dihedral : 4.413 20.768 2121 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.55 % Allowed : 20.98 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.21), residues: 1953 helix: 1.85 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : 2.24 (0.40), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 81 TYR 0.008 0.001 TYR U 93 PHE 0.007 0.001 PHE G 34 HIS 0.001 0.000 HIS J 42 Details of bonding type rmsd covalent geometry : bond 0.00290 (16338) covalent geometry : angle 0.58681 (21819) hydrogen bonds : bond 0.02956 ( 1135) hydrogen bonds : angle 5.20429 ( 3405) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 848 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 5 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8450 (mmtm) REVERT: E 81 ARG cc_start: 0.8830 (ttm-80) cc_final: 0.8586 (mtp85) REVERT: E 91 LYS cc_start: 0.8602 (mtmt) cc_final: 0.8236 (tptp) REVERT: F 5 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8435 (mmtm) REVERT: F 16 ASP cc_start: 0.8726 (t70) cc_final: 0.8386 (t0) REVERT: F 81 ARG cc_start: 0.8736 (ttm-80) cc_final: 0.8512 (mtp85) REVERT: F 91 LYS cc_start: 0.8666 (mtmt) cc_final: 0.8163 (mtpp) REVERT: G 5 LYS cc_start: 0.8903 (mmmt) cc_final: 0.8257 (mmtm) REVERT: G 83 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8739 (mm-40) REVERT: G 93 TYR cc_start: 0.8571 (m-10) cc_final: 0.8187 (m-10) REVERT: H 5 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8437 (mmtm) REVERT: H 8 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7959 (mt-10) REVERT: I 5 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8413 (mmtm) REVERT: I 64 MET cc_start: 0.8765 (mmm) cc_final: 0.8499 (mmt) REVERT: I 68 ARG cc_start: 0.8902 (ttp-110) cc_final: 0.8596 (ttm-80) REVERT: I 93 TYR cc_start: 0.8645 (m-80) cc_final: 0.8118 (m-80) REVERT: J 8 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8480 (mm-30) REVERT: J 16 ASP cc_start: 0.8844 (t0) cc_final: 0.8531 (t0) REVERT: K 5 LYS cc_start: 0.8951 (mmmt) cc_final: 0.8418 (mmtt) REVERT: K 81 ARG cc_start: 0.8744 (ttm-80) cc_final: 0.8463 (mtp85) REVERT: K 93 TYR cc_start: 0.8521 (m-10) cc_final: 0.8131 (m-10) REVERT: M 5 LYS cc_start: 0.9016 (mmmt) cc_final: 0.8381 (mmtt) REVERT: M 8 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8131 (mt-10) REVERT: M 33 GLU cc_start: 0.8176 (tp30) cc_final: 0.7945 (tp30) REVERT: M 68 ARG cc_start: 0.8804 (ttp-110) cc_final: 0.8598 (ttp-110) REVERT: M 91 LYS cc_start: 0.8643 (mtpp) cc_final: 0.8316 (mtmm) REVERT: N 6 TYR cc_start: 0.8858 (m-10) cc_final: 0.8643 (m-10) REVERT: O 5 LYS cc_start: 0.9070 (mmmt) cc_final: 0.8428 (mmtm) REVERT: O 68 ARG cc_start: 0.8789 (ttp-110) cc_final: 0.8571 (ttm-80) REVERT: P 9 ILE cc_start: 0.9141 (mm) cc_final: 0.8905 (pt) REVERT: P 64 MET cc_start: 0.8945 (mmm) cc_final: 0.8648 (mmm) REVERT: P 72 LYS cc_start: 0.9342 (ttpp) cc_final: 0.8813 (ttpp) REVERT: P 75 TYR cc_start: 0.9000 (m-10) cc_final: 0.8774 (m-10) REVERT: Q 5 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8420 (mmtm) REVERT: Q 64 MET cc_start: 0.8697 (mmm) cc_final: 0.8444 (mmm) REVERT: Q 76 MET cc_start: 0.9288 (mmt) cc_final: 0.9039 (mmt) REVERT: Q 93 TYR cc_start: 0.8599 (m-10) cc_final: 0.8367 (m-10) REVERT: R 33 GLU cc_start: 0.8387 (tp30) cc_final: 0.8100 (tp30) REVERT: R 91 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8381 (mtmt) REVERT: S 33 GLU cc_start: 0.8281 (tp30) cc_final: 0.8021 (tp30) REVERT: S 65 LYS cc_start: 0.9018 (mtpt) cc_final: 0.8764 (mtpt) REVERT: S 68 ARG cc_start: 0.8870 (ttp-110) cc_final: 0.8665 (ttm-80) REVERT: T 48 GLN cc_start: 0.9121 (mt0) cc_final: 0.8787 (mt0) REVERT: T 75 TYR cc_start: 0.8881 (m-10) cc_final: 0.8665 (m-10) outliers start: 45 outliers final: 31 residues processed: 854 average time/residue: 0.1632 time to fit residues: 190.7713 Evaluate side-chains 854 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 823 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain K residue 4 SER Chi-restraints excluded: chain K residue 16 ASP Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain P residue 35 ASN Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain R residue 4 SER Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain R residue 55 GLN Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain T residue 16 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 1 optimal weight: 6.9990 chunk 10 optimal weight: 0.0270 chunk 63 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN D 55 GLN H 71 GLN I 71 GLN L 71 GLN N 48 GLN P 71 GLN Q 48 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.088137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.076483 restraints weight = 33419.594| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.37 r_work: 0.2984 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16338 Z= 0.136 Angle : 0.618 10.039 21819 Z= 0.349 Chirality : 0.042 0.242 2520 Planarity : 0.003 0.027 2730 Dihedral : 4.409 22.134 2121 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.10 % Allowed : 21.71 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.21), residues: 1953 helix: 1.84 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : 2.32 (0.41), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 81 TYR 0.008 0.001 TYR U 6 PHE 0.011 0.001 PHE P 34 HIS 0.001 0.000 HIS C 42 Details of bonding type rmsd covalent geometry : bond 0.00312 (16338) covalent geometry : angle 0.61820 (21819) hydrogen bonds : bond 0.03027 ( 1135) hydrogen bonds : angle 5.22666 ( 3405) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 834 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: B 8 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8208 (mm-30) REVERT: C 5 LYS cc_start: 0.8975 (mmmt) cc_final: 0.8314 (mmmt) REVERT: C 8 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7886 (mt-10) REVERT: D 5 LYS cc_start: 0.8922 (mmmt) cc_final: 0.8579 (mmtm) REVERT: E 16 ASP cc_start: 0.8900 (t0) cc_final: 0.8511 (t0) REVERT: E 81 ARG cc_start: 0.8809 (ttm-80) cc_final: 0.8588 (mtp85) REVERT: E 91 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8162 (tptp) REVERT: F 5 LYS cc_start: 0.8964 (mmmt) cc_final: 0.8536 (mmtm) REVERT: F 16 ASP cc_start: 0.8749 (t70) cc_final: 0.8152 (t0) REVERT: F 81 ARG cc_start: 0.8735 (ttm-80) cc_final: 0.8525 (mtp85) REVERT: G 5 LYS cc_start: 0.8893 (mmmt) cc_final: 0.8381 (mmtm) REVERT: G 83 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8776 (mm-40) REVERT: H 5 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8665 (mmtm) REVERT: H 80 LYS cc_start: 0.9122 (ttmt) cc_final: 0.8842 (ttpp) REVERT: I 5 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8420 (mmtm) REVERT: I 33 GLU cc_start: 0.8133 (tp30) cc_final: 0.7722 (tp30) REVERT: I 64 MET cc_start: 0.8709 (mmm) cc_final: 0.8428 (mmt) REVERT: I 68 ARG cc_start: 0.8912 (ttp-110) cc_final: 0.8607 (ttm-80) REVERT: I 93 TYR cc_start: 0.8580 (m-80) cc_final: 0.8248 (m-80) REVERT: J 16 ASP cc_start: 0.8855 (t0) cc_final: 0.8588 (t0) REVERT: K 16 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8507 (t0) REVERT: K 81 ARG cc_start: 0.8755 (ttm-80) cc_final: 0.8486 (mtp85) REVERT: K 91 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8163 (tptp) REVERT: L 5 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8235 (mmtm) REVERT: L 93 TYR cc_start: 0.8724 (m-80) cc_final: 0.8344 (m-10) REVERT: M 5 LYS cc_start: 0.9006 (mmmt) cc_final: 0.8414 (mmtt) REVERT: M 8 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8361 (mt-10) REVERT: M 16 ASP cc_start: 0.8530 (t0) cc_final: 0.8305 (t0) REVERT: M 91 LYS cc_start: 0.8653 (mtpp) cc_final: 0.8318 (mtmm) REVERT: N 5 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8373 (mmtt) REVERT: O 5 LYS cc_start: 0.9041 (mmmt) cc_final: 0.8438 (mmtm) REVERT: O 68 ARG cc_start: 0.8762 (ttp-110) cc_final: 0.8530 (ttm-80) REVERT: P 5 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8233 (mmtt) REVERT: P 9 ILE cc_start: 0.9151 (mm) cc_final: 0.8932 (pt) REVERT: P 64 MET cc_start: 0.8896 (mmm) cc_final: 0.8678 (mmm) REVERT: P 75 TYR cc_start: 0.9019 (m-10) cc_final: 0.8784 (m-10) REVERT: Q 5 LYS cc_start: 0.8942 (mmmt) cc_final: 0.8629 (mmtm) REVERT: Q 64 MET cc_start: 0.8652 (mmm) cc_final: 0.8365 (mmm) REVERT: Q 76 MET cc_start: 0.9247 (mmt) cc_final: 0.9032 (mmt) REVERT: Q 93 TYR cc_start: 0.8577 (m-10) cc_final: 0.8303 (m-10) REVERT: R 4 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8298 (t) REVERT: R 33 GLU cc_start: 0.8356 (tp30) cc_final: 0.8129 (tp30) REVERT: R 65 LYS cc_start: 0.8899 (mtpt) cc_final: 0.8665 (mtpt) REVERT: S 33 GLU cc_start: 0.8208 (tp30) cc_final: 0.7984 (tp30) REVERT: S 65 LYS cc_start: 0.9034 (mtpt) cc_final: 0.8761 (mtpt) REVERT: S 68 ARG cc_start: 0.8862 (ttp-110) cc_final: 0.8653 (ttm-80) REVERT: T 48 GLN cc_start: 0.9136 (mt0) cc_final: 0.8807 (mt0) outliers start: 37 outliers final: 26 residues processed: 840 average time/residue: 0.1589 time to fit residues: 183.1978 Evaluate side-chains 850 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 822 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 55 GLN Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain K residue 4 SER Chi-restraints excluded: chain K residue 16 ASP Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain R residue 4 SER Chi-restraints excluded: chain R residue 55 GLN Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain U residue 16 ASP Chi-restraints excluded: chain U residue 55 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 40 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 163 optimal weight: 0.0020 chunk 20 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 GLN E 55 GLN G 55 GLN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN L 71 GLN ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 GLN Q 48 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.088077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.076109 restraints weight = 33606.079| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.41 r_work: 0.2980 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16338 Z= 0.149 Angle : 0.653 11.237 21819 Z= 0.367 Chirality : 0.043 0.200 2520 Planarity : 0.003 0.049 2730 Dihedral : 4.466 21.667 2121 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.93 % Allowed : 22.96 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.21), residues: 1953 helix: 1.74 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : 2.27 (0.41), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG T 81 TYR 0.011 0.001 TYR U 75 PHE 0.010 0.001 PHE G 34 HIS 0.001 0.000 HIS J 42 Details of bonding type rmsd covalent geometry : bond 0.00350 (16338) covalent geometry : angle 0.65313 (21819) hydrogen bonds : bond 0.03123 ( 1135) hydrogen bonds : angle 5.24592 ( 3405) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 833 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: B 8 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8215 (mt-10) REVERT: C 5 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8488 (mmmt) REVERT: D 5 LYS cc_start: 0.8850 (mmmt) cc_final: 0.8455 (mmtt) REVERT: D 93 TYR cc_start: 0.8353 (m-10) cc_final: 0.7975 (m-10) REVERT: E 5 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8392 (mmtm) REVERT: E 16 ASP cc_start: 0.8898 (t0) cc_final: 0.8517 (t0) REVERT: E 81 ARG cc_start: 0.8827 (ttm-80) cc_final: 0.8608 (mtp85) REVERT: E 91 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8169 (tptp) REVERT: F 5 LYS cc_start: 0.8963 (mmmt) cc_final: 0.8556 (mmtm) REVERT: F 16 ASP cc_start: 0.8729 (t70) cc_final: 0.8405 (t0) REVERT: F 81 ARG cc_start: 0.8700 (ttm-80) cc_final: 0.8491 (mtp85) REVERT: F 93 TYR cc_start: 0.8529 (m-10) cc_final: 0.8200 (m-10) REVERT: G 5 LYS cc_start: 0.8914 (mmmt) cc_final: 0.8616 (mmtm) REVERT: G 33 GLU cc_start: 0.8134 (tp30) cc_final: 0.7878 (tp30) REVERT: G 83 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8776 (mm-40) REVERT: G 93 TYR cc_start: 0.8507 (m-10) cc_final: 0.8278 (m-10) REVERT: H 5 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8428 (mmtt) REVERT: H 80 LYS cc_start: 0.9125 (ttmt) cc_final: 0.8849 (ttpp) REVERT: I 5 LYS cc_start: 0.8944 (mmmt) cc_final: 0.8742 (mmtm) REVERT: I 33 GLU cc_start: 0.8083 (tp30) cc_final: 0.7850 (tp30) REVERT: I 64 MET cc_start: 0.8735 (mmm) cc_final: 0.8470 (mmt) REVERT: I 68 ARG cc_start: 0.8877 (ttp-110) cc_final: 0.8668 (ttm-80) REVERT: J 16 ASP cc_start: 0.8853 (t0) cc_final: 0.8600 (t0) REVERT: K 5 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8525 (mmtt) REVERT: K 16 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8495 (t0) REVERT: K 81 ARG cc_start: 0.8771 (ttm-80) cc_final: 0.8497 (mtp85) REVERT: K 91 LYS cc_start: 0.8654 (mtmt) cc_final: 0.8082 (tptp) REVERT: K 93 TYR cc_start: 0.8411 (m-10) cc_final: 0.8019 (m-10) REVERT: L 5 LYS cc_start: 0.8831 (mmmt) cc_final: 0.8209 (mmtm) REVERT: L 93 TYR cc_start: 0.8727 (m-80) cc_final: 0.8339 (m-10) REVERT: M 5 LYS cc_start: 0.9017 (mmmt) cc_final: 0.8451 (mmtm) REVERT: M 16 ASP cc_start: 0.8539 (t0) cc_final: 0.8280 (t0) REVERT: M 91 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8303 (mtmm) REVERT: M 93 TYR cc_start: 0.8491 (m-10) cc_final: 0.8112 (m-10) REVERT: N 5 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8335 (mmtt) REVERT: O 5 LYS cc_start: 0.9017 (mmmt) cc_final: 0.8445 (mmtm) REVERT: O 16 ASP cc_start: 0.8775 (t0) cc_final: 0.8472 (t0) REVERT: O 68 ARG cc_start: 0.8762 (ttp-110) cc_final: 0.8538 (ttm-80) REVERT: P 5 LYS cc_start: 0.8939 (mmmt) cc_final: 0.8370 (mmtt) REVERT: P 6 TYR cc_start: 0.9002 (m-10) cc_final: 0.8760 (m-10) REVERT: P 9 ILE cc_start: 0.9201 (mm) cc_final: 0.8983 (pt) REVERT: P 64 MET cc_start: 0.8923 (mmm) cc_final: 0.8704 (mmm) REVERT: P 75 TYR cc_start: 0.9035 (m-10) cc_final: 0.8775 (m-10) REVERT: Q 5 LYS cc_start: 0.8949 (mmmt) cc_final: 0.8640 (mmtt) REVERT: Q 64 MET cc_start: 0.8678 (mmm) cc_final: 0.8412 (mmm) REVERT: Q 76 MET cc_start: 0.9258 (mmt) cc_final: 0.9043 (mmt) REVERT: R 4 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8289 (t) REVERT: R 65 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8702 (mtpt) REVERT: S 33 GLU cc_start: 0.8188 (tp30) cc_final: 0.7969 (tp30) REVERT: S 65 LYS cc_start: 0.9058 (mtpt) cc_final: 0.8807 (mtpt) REVERT: T 48 GLN cc_start: 0.9136 (mt0) cc_final: 0.8811 (mt0) outliers start: 34 outliers final: 27 residues processed: 840 average time/residue: 0.1584 time to fit residues: 182.8232 Evaluate side-chains 849 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 820 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 55 GLN Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain K residue 4 SER Chi-restraints excluded: chain K residue 16 ASP Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain R residue 4 SER Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain R residue 55 GLN Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain U residue 16 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 3 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 154 optimal weight: 0.5980 chunk 149 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 48 GLN D 55 GLN D 71 GLN E 55 GLN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN L 48 GLN L 71 GLN M 48 GLN N 71 GLN P 35 ASN ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 GLN Q 48 GLN ** S 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 71 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.085695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.073384 restraints weight = 33483.739| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.44 r_work: 0.2897 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16338 Z= 0.204 Angle : 0.694 10.763 21819 Z= 0.388 Chirality : 0.045 0.212 2520 Planarity : 0.003 0.045 2730 Dihedral : 4.509 21.740 2121 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.27 % Allowed : 22.90 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.20), residues: 1953 helix: 1.57 (0.13), residues: 1491 sheet: None (None), residues: 0 loop : 1.73 (0.40), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG T 81 TYR 0.010 0.001 TYR K 75 PHE 0.009 0.001 PHE R 29 HIS 0.002 0.000 HIS J 42 Details of bonding type rmsd covalent geometry : bond 0.00484 (16338) covalent geometry : angle 0.69397 (21819) hydrogen bonds : bond 0.03312 ( 1135) hydrogen bonds : angle 5.26223 ( 3405) =============================================================================== Job complete usr+sys time: 4297.48 seconds wall clock time: 74 minutes 12.68 seconds (4452.68 seconds total)