Starting phenix.real_space_refine on Tue May 5 06:10:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u8k_63955/05_2026/9u8k_63955_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u8k_63955/05_2026/9u8k_63955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u8k_63955/05_2026/9u8k_63955_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u8k_63955/05_2026/9u8k_63955_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u8k_63955/05_2026/9u8k_63955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u8k_63955/05_2026/9u8k_63955.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 170 5.16 5 C 17387 2.51 5 N 4644 2.21 5 O 5376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27577 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 715 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "B" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 714 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain breaks: 1 Chain: "C" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 706 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "D" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "E" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 705 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "G" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 705 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "H" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "I" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 706 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "J" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 715 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "K" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 706 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "L" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 706 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "M" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "N" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 714 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "O" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "P" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "Q" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "R" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 723 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "S" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "T" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 705 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "U" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 715 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "V" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "W" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "X" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 705 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "Y" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 705 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "Z" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 706 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "a1" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 706 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "b1" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 715 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "c1" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 723 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "d1" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 715 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "e1" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "f1" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 705 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "g1" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 714 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "h1" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 723 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "i1" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 691 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "j1" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 706 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "k1" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 723 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "l1" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 723 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "m1" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 715 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Time building chain proxies: 6.32, per 1000 atoms: 0.23 Number of scatterers: 27577 At special positions: 0 Unit cell: (94.12, 95.68, 201.76, 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 170 16.00 O 5376 8.00 N 4644 7.00 C 17387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.0 seconds 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6410 Finding SS restraints... Secondary structure from input PDB file: 235 helices and 0 sheets defined 86.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 15 through 29 Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 47 through 60 Processing helix chain 'A' and resid 61 through 76 Processing helix chain 'A' and resid 77 through 90 Processing helix chain 'B' and resid 2 through 14 removed outlier: 4.008A pdb=" N ASP B 6 " --> pdb=" O GLY B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 28 removed outlier: 3.666A pdb=" N LEU B 28 " --> pdb=" O LYS B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 48 through 61 Processing helix chain 'B' and resid 61 through 77 Processing helix chain 'B' and resid 78 through 79 No H-bonds generated for 'chain 'B' and resid 78 through 79' Processing helix chain 'B' and resid 80 through 80 No H-bonds generated for 'chain 'B' and resid 80 through 80' Processing helix chain 'B' and resid 81 through 90 Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 15 through 29 removed outlier: 3.513A pdb=" N THR C 28 " --> pdb=" O MET C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 45 removed outlier: 4.062A pdb=" N GLN C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 60 Processing helix chain 'C' and resid 61 through 76 Processing helix chain 'C' and resid 77 through 89 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 15 through 29 removed outlier: 3.538A pdb=" N THR D 28 " --> pdb=" O MET D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 47 through 60 Processing helix chain 'D' and resid 61 through 76 Processing helix chain 'D' and resid 77 through 88 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 15 through 27 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 61 through 76 Processing helix chain 'E' and resid 77 through 88 Processing helix chain 'F' and resid 2 through 14 removed outlier: 3.663A pdb=" N ASP F 6 " --> pdb=" O GLY F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 28 removed outlier: 3.597A pdb=" N LEU F 28 " --> pdb=" O LYS F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 48 through 77 removed outlier: 7.702A pdb=" N GLU F 62 " --> pdb=" O SER F 58 " (cutoff:3.500A) removed outlier: 9.651A pdb=" N SER F 63 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR F 64 " --> pdb=" O TYR F 60 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU F 67 " --> pdb=" O SER F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 89 Processing helix chain 'G' and resid 2 through 14 Processing helix chain 'G' and resid 16 through 28 removed outlier: 3.544A pdb=" N LEU G 28 " --> pdb=" O LYS G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 47 removed outlier: 3.873A pdb=" N GLN G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 60 Processing helix chain 'G' and resid 61 through 77 Processing helix chain 'G' and resid 78 through 89 Processing helix chain 'H' and resid 2 through 13 Processing helix chain 'H' and resid 15 through 29 removed outlier: 3.593A pdb=" N LEU H 27 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR H 28 " --> pdb=" O MET H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 46 removed outlier: 3.812A pdb=" N GLN H 45 " --> pdb=" O GLY H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 60 Processing helix chain 'H' and resid 60 through 76 Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'I' and resid 2 through 13 Processing helix chain 'I' and resid 15 through 29 Processing helix chain 'I' and resid 39 through 44 Processing helix chain 'I' and resid 47 through 60 Processing helix chain 'I' and resid 60 through 76 Processing helix chain 'I' and resid 77 through 89 Processing helix chain 'J' and resid 2 through 13 Processing helix chain 'J' and resid 15 through 29 removed outlier: 3.646A pdb=" N LEU J 27 " --> pdb=" O LYS J 23 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR J 28 " --> pdb=" O MET J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 44 Processing helix chain 'J' and resid 47 through 60 Processing helix chain 'J' and resid 61 through 76 Processing helix chain 'J' and resid 77 through 90 Processing helix chain 'K' and resid 2 through 13 Processing helix chain 'K' and resid 15 through 29 removed outlier: 3.543A pdb=" N THR K 28 " --> pdb=" O MET K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 44 Processing helix chain 'K' and resid 47 through 60 Processing helix chain 'K' and resid 60 through 76 Processing helix chain 'K' and resid 77 through 89 Processing helix chain 'L' and resid 2 through 13 removed outlier: 3.831A pdb=" N ASN L 13 " --> pdb=" O ASP L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 29 removed outlier: 3.517A pdb=" N LEU L 27 " --> pdb=" O LYS L 23 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR L 28 " --> pdb=" O MET L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 45 removed outlier: 4.138A pdb=" N GLN L 45 " --> pdb=" O GLY L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 60 Processing helix chain 'L' and resid 60 through 76 Processing helix chain 'L' and resid 77 through 89 Processing helix chain 'M' and resid 2 through 13 removed outlier: 3.859A pdb=" N ASN M 13 " --> pdb=" O ASP M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 29 Processing helix chain 'M' and resid 39 through 46 removed outlier: 4.065A pdb=" N GLN M 45 " --> pdb=" O GLY M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 60 Processing helix chain 'M' and resid 61 through 76 Processing helix chain 'M' and resid 77 through 88 Processing helix chain 'N' and resid 2 through 14 removed outlier: 3.618A pdb=" N ASP N 6 " --> pdb=" O GLY N 2 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 30 Processing helix chain 'N' and resid 40 through 46 removed outlier: 4.133A pdb=" N GLN N 46 " --> pdb=" O GLY N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 61 Processing helix chain 'N' and resid 62 through 77 Processing helix chain 'N' and resid 78 through 90 Processing helix chain 'O' and resid 2 through 13 Processing helix chain 'O' and resid 15 through 27 removed outlier: 3.679A pdb=" N LEU O 27 " --> pdb=" O LYS O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 39 through 45 removed outlier: 4.175A pdb=" N GLN O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 60 Processing helix chain 'O' and resid 60 through 76 Processing helix chain 'O' and resid 77 through 88 Processing helix chain 'P' and resid 2 through 13 Processing helix chain 'P' and resid 15 through 29 removed outlier: 3.544A pdb=" N THR P 28 " --> pdb=" O MET P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 45 removed outlier: 4.074A pdb=" N GLN P 45 " --> pdb=" O GLY P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 60 Processing helix chain 'P' and resid 60 through 76 Processing helix chain 'P' and resid 77 through 88 Processing helix chain 'Q' and resid 2 through 13 Processing helix chain 'Q' and resid 15 through 29 removed outlier: 3.533A pdb=" N THR Q 28 " --> pdb=" O MET Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 44 Processing helix chain 'Q' and resid 47 through 60 Processing helix chain 'Q' and resid 61 through 76 Processing helix chain 'Q' and resid 77 through 88 Processing helix chain 'R' and resid 2 through 14 Processing helix chain 'R' and resid 16 through 28 Processing helix chain 'R' and resid 40 through 46 removed outlier: 3.977A pdb=" N GLN R 46 " --> pdb=" O GLY R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 61 Processing helix chain 'R' and resid 62 through 77 Processing helix chain 'R' and resid 78 through 91 Processing helix chain 'S' and resid 2 through 13 Processing helix chain 'S' and resid 15 through 29 Processing helix chain 'S' and resid 39 through 44 Processing helix chain 'S' and resid 47 through 60 Processing helix chain 'S' and resid 60 through 76 Processing helix chain 'S' and resid 77 through 88 removed outlier: 3.568A pdb=" N THR S 87 " --> pdb=" O GLN S 83 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS S 88 " --> pdb=" O LEU S 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 14 Processing helix chain 'T' and resid 16 through 28 removed outlier: 3.559A pdb=" N LEU T 28 " --> pdb=" O LYS T 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 47 removed outlier: 3.836A pdb=" N GLN T 46 " --> pdb=" O GLY T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 60 Processing helix chain 'T' and resid 61 through 77 Processing helix chain 'T' and resid 78 through 89 Processing helix chain 'U' and resid 2 through 13 Processing helix chain 'U' and resid 15 through 29 removed outlier: 3.614A pdb=" N LEU U 27 " --> pdb=" O LYS U 23 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR U 28 " --> pdb=" O MET U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 39 through 46 removed outlier: 4.103A pdb=" N GLN U 45 " --> pdb=" O GLY U 41 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET U 46 " --> pdb=" O ALA U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 60 Processing helix chain 'U' and resid 60 through 76 Processing helix chain 'U' and resid 77 through 90 removed outlier: 3.760A pdb=" N GLU U 90 " --> pdb=" O THR U 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 13 Processing helix chain 'V' and resid 15 through 29 removed outlier: 3.508A pdb=" N THR V 28 " --> pdb=" O MET V 24 " (cutoff:3.500A) Processing helix chain 'V' and resid 39 through 44 Processing helix chain 'V' and resid 47 through 60 Processing helix chain 'V' and resid 60 through 76 Processing helix chain 'V' and resid 77 through 88 Processing helix chain 'W' and resid 2 through 13 Processing helix chain 'W' and resid 15 through 29 removed outlier: 3.645A pdb=" N LEU W 27 " --> pdb=" O LYS W 23 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR W 28 " --> pdb=" O MET W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 45 removed outlier: 3.999A pdb=" N GLN W 45 " --> pdb=" O GLY W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 60 Processing helix chain 'W' and resid 61 through 76 Processing helix chain 'W' and resid 77 through 88 Processing helix chain 'X' and resid 2 through 14 removed outlier: 3.921A pdb=" N ASP X 6 " --> pdb=" O GLY X 2 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 30 removed outlier: 3.525A pdb=" N THR X 29 " --> pdb=" O MET X 25 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 45 Processing helix chain 'X' and resid 48 through 61 Processing helix chain 'X' and resid 62 through 77 Processing helix chain 'X' and resid 78 through 89 Processing helix chain 'Y' and resid 2 through 14 removed outlier: 3.780A pdb=" N ASN Y 14 " --> pdb=" O ASP Y 10 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 30 removed outlier: 3.543A pdb=" N THR Y 29 " --> pdb=" O MET Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 46 removed outlier: 4.079A pdb=" N GLN Y 46 " --> pdb=" O GLY Y 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 61 Processing helix chain 'Y' and resid 62 through 77 Processing helix chain 'Y' and resid 78 through 89 Processing helix chain 'Z' and resid 2 through 13 removed outlier: 3.803A pdb=" N ASN Z 13 " --> pdb=" O ASP Z 9 " (cutoff:3.500A) Processing helix chain 'Z' and resid 15 through 29 Processing helix chain 'Z' and resid 39 through 46 removed outlier: 3.978A pdb=" N GLN Z 45 " --> pdb=" O GLY Z 41 " (cutoff:3.500A) Processing helix chain 'Z' and resid 47 through 60 Processing helix chain 'Z' and resid 61 through 76 Processing helix chain 'Z' and resid 77 through 87 Processing helix chain 'a1' and resid 2 through 13 Processing helix chain 'a1' and resid 15 through 29 Processing helix chain 'a1' and resid 39 through 45 removed outlier: 4.168A pdb=" N GLNa1 45 " --> pdb=" O GLYa1 41 " (cutoff:3.500A) Processing helix chain 'a1' and resid 47 through 60 Processing helix chain 'a1' and resid 61 through 76 Processing helix chain 'a1' and resid 77 through 89 Processing helix chain 'b1' and resid 2 through 13 Processing helix chain 'b1' and resid 15 through 27 removed outlier: 3.681A pdb=" N LEUb1 27 " --> pdb=" O LYSb1 23 " (cutoff:3.500A) Processing helix chain 'b1' and resid 39 through 45 removed outlier: 4.227A pdb=" N GLNb1 45 " --> pdb=" O GLYb1 41 " (cutoff:3.500A) Processing helix chain 'b1' and resid 47 through 60 Processing helix chain 'b1' and resid 60 through 76 Processing helix chain 'b1' and resid 77 through 90 Processing helix chain 'c1' and resid 2 through 14 removed outlier: 3.744A pdb=" N ASPc1 6 " --> pdb=" O GLYc1 2 " (cutoff:3.500A) Processing helix chain 'c1' and resid 16 through 30 removed outlier: 3.554A pdb=" N THRc1 29 " --> pdb=" O METc1 25 " (cutoff:3.500A) Processing helix chain 'c1' and resid 40 through 46 removed outlier: 4.044A pdb=" N GLNc1 46 " --> pdb=" O GLYc1 42 " (cutoff:3.500A) Processing helix chain 'c1' and resid 48 through 61 Processing helix chain 'c1' and resid 62 through 77 Processing helix chain 'c1' and resid 78 through 91 Processing helix chain 'd1' and resid 2 through 13 Processing helix chain 'd1' and resid 15 through 29 removed outlier: 3.553A pdb=" N THRd1 28 " --> pdb=" O METd1 24 " (cutoff:3.500A) Processing helix chain 'd1' and resid 39 through 44 Processing helix chain 'd1' and resid 47 through 60 Processing helix chain 'd1' and resid 61 through 76 Processing helix chain 'd1' and resid 77 through 90 Processing helix chain 'e1' and resid 2 through 13 Processing helix chain 'e1' and resid 15 through 27 Processing helix chain 'e1' and resid 39 through 45 removed outlier: 4.029A pdb=" N GLNe1 45 " --> pdb=" O GLYe1 41 " (cutoff:3.500A) Processing helix chain 'e1' and resid 47 through 60 Processing helix chain 'e1' and resid 60 through 76 Processing helix chain 'e1' and resid 77 through 87 Processing helix chain 'f1' and resid 3 through 14 Processing helix chain 'f1' and resid 16 through 30 Processing helix chain 'f1' and resid 40 through 45 Processing helix chain 'f1' and resid 48 through 61 Processing helix chain 'f1' and resid 61 through 77 Processing helix chain 'f1' and resid 78 through 89 Processing helix chain 'g1' and resid 2 through 14 removed outlier: 4.262A pdb=" N ASPg1 6 " --> pdb=" O GLYg1 2 " (cutoff:3.500A) Processing helix chain 'g1' and resid 16 through 28 removed outlier: 3.538A pdb=" N LEUg1 28 " --> pdb=" O LYSg1 24 " (cutoff:3.500A) Processing helix chain 'g1' and resid 40 through 47 removed outlier: 3.828A pdb=" N GLNg1 46 " --> pdb=" O GLYg1 42 " (cutoff:3.500A) Processing helix chain 'g1' and resid 48 through 60 Processing helix chain 'g1' and resid 61 through 77 Processing helix chain 'g1' and resid 78 through 90 Processing helix chain 'h1' and resid 2 through 14 Processing helix chain 'h1' and resid 16 through 30 removed outlier: 3.620A pdb=" N LEUh1 28 " --> pdb=" O LYSh1 24 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THRh1 29 " --> pdb=" O METh1 25 " (cutoff:3.500A) Processing helix chain 'h1' and resid 40 through 47 removed outlier: 3.835A pdb=" N GLNh1 46 " --> pdb=" O GLYh1 42 " (cutoff:3.500A) Processing helix chain 'h1' and resid 48 through 61 Processing helix chain 'h1' and resid 61 through 77 Processing helix chain 'h1' and resid 78 through 91 removed outlier: 3.833A pdb=" N GLUh1 91 " --> pdb=" O THRh1 87 " (cutoff:3.500A) Processing helix chain 'i1' and resid 5 through 14 Processing helix chain 'i1' and resid 16 through 30 Processing helix chain 'i1' and resid 40 through 45 Processing helix chain 'i1' and resid 48 through 61 Processing helix chain 'i1' and resid 61 through 77 Processing helix chain 'i1' and resid 78 through 90 Processing helix chain 'j1' and resid 2 through 13 Processing helix chain 'j1' and resid 15 through 29 removed outlier: 3.652A pdb=" N LEUj1 27 " --> pdb=" O LYSj1 23 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THRj1 28 " --> pdb=" O METj1 24 " (cutoff:3.500A) Processing helix chain 'j1' and resid 39 through 46 removed outlier: 3.837A pdb=" N GLNj1 45 " --> pdb=" O GLYj1 41 " (cutoff:3.500A) Processing helix chain 'j1' and resid 47 through 60 Processing helix chain 'j1' and resid 60 through 76 Processing helix chain 'j1' and resid 77 through 89 Processing helix chain 'k1' and resid 3 through 14 Processing helix chain 'k1' and resid 16 through 30 removed outlier: 3.557A pdb=" N THRk1 29 " --> pdb=" O METk1 25 " (cutoff:3.500A) Processing helix chain 'k1' and resid 40 through 45 Processing helix chain 'k1' and resid 48 through 61 Processing helix chain 'k1' and resid 61 through 77 Processing helix chain 'k1' and resid 78 through 91 Processing helix chain 'l1' and resid 2 through 14 removed outlier: 3.830A pdb=" N ASPl1 6 " --> pdb=" O GLYl1 2 " (cutoff:3.500A) Processing helix chain 'l1' and resid 16 through 30 removed outlier: 3.562A pdb=" N THRl1 29 " --> pdb=" O METl1 25 " (cutoff:3.500A) Processing helix chain 'l1' and resid 40 through 46 removed outlier: 4.009A pdb=" N GLNl1 46 " --> pdb=" O GLYl1 42 " (cutoff:3.500A) Processing helix chain 'l1' and resid 48 through 61 Processing helix chain 'l1' and resid 61 through 77 Processing helix chain 'l1' and resid 78 through 91 Processing helix chain 'm1' and resid 2 through 13 removed outlier: 3.859A pdb=" N ASNm1 13 " --> pdb=" O ASPm1 9 " (cutoff:3.500A) Processing helix chain 'm1' and resid 15 through 29 Processing helix chain 'm1' and resid 39 through 45 removed outlier: 4.156A pdb=" N GLNm1 45 " --> pdb=" O GLYm1 41 " (cutoff:3.500A) Processing helix chain 'm1' and resid 47 through 60 Processing helix chain 'm1' and resid 61 through 76 Processing helix chain 'm1' and resid 77 through 90 1981 hydrogen bonds defined for protein. 5943 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: 4.79 Time building geometry restraints manager: 2.99 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: 9045 1.34 - 1.46: 2947 1.46 - 1.58: 15439 1.58 - 1.70: 0 1.70 - 1.82: 340 Bond restraints: 27771 Sorted by residual: bond pdb=" N LEU Y 61 " pdb=" CA LEU Y 61 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.96e+00 bond pdb=" N LEU A 60 " pdb=" CA LEU A 60 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.81e+00 bond pdb=" N LEU X 61 " pdb=" CA LEU X 61 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.66e+00 bond pdb=" N LEUa1 60 " pdb=" CA LEUa1 60 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.53e+00 bond pdb=" N LEU N 61 " pdb=" CA LEU N 61 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.44e+00 ... (remaining 27766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 36384 1.74 - 3.48: 694 3.48 - 5.21: 102 5.21 - 6.95: 27 6.95 - 8.69: 6 Bond angle restraints: 37213 Sorted by residual: angle pdb=" CA VALd1 29 " pdb=" C VALd1 29 " pdb=" O VALd1 29 " ideal model delta sigma weight residual 121.97 118.08 3.89 9.80e-01 1.04e+00 1.58e+01 angle pdb=" CA VAL Q 29 " pdb=" C VAL Q 29 " pdb=" O VAL Q 29 " ideal model delta sigma weight residual 121.97 118.26 3.71 9.80e-01 1.04e+00 1.43e+01 angle pdb=" CA VALd1 29 " pdb=" C VALd1 29 " pdb=" N GLNd1 30 " ideal model delta sigma weight residual 115.28 118.81 -3.53 1.14e+00 7.69e-01 9.61e+00 angle pdb=" CG MET M 69 " pdb=" SD MET M 69 " pdb=" CE MET M 69 " ideal model delta sigma weight residual 100.90 94.13 6.77 2.20e+00 2.07e-01 9.48e+00 angle pdb=" CA VAL Q 29 " pdb=" C VAL Q 29 " pdb=" N GLN Q 30 " ideal model delta sigma weight residual 115.28 118.59 -3.31 1.14e+00 7.69e-01 8.45e+00 ... (remaining 37208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 14844 17.93 - 35.86: 1664 35.86 - 53.79: 699 53.79 - 71.72: 121 71.72 - 89.65: 26 Dihedral angle restraints: 17354 sinusoidal: 7351 harmonic: 10003 Sorted by residual: dihedral pdb=" CA LEU G 61 " pdb=" C LEU G 61 " pdb=" N GLU G 62 " pdb=" CA GLU G 62 " ideal model delta harmonic sigma weight residual 180.00 -158.96 -21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA LEU T 61 " pdb=" C LEU T 61 " pdb=" N GLU T 62 " pdb=" CA GLU T 62 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CG ARG U 73 " pdb=" CD ARG U 73 " pdb=" NE ARG U 73 " pdb=" CZ ARG U 73 " ideal model delta sinusoidal sigma weight residual -90.00 -39.89 -50.11 2 1.50e+01 4.44e-03 1.26e+01 ... (remaining 17351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2904 0.033 - 0.066: 1159 0.066 - 0.099: 263 0.099 - 0.133: 40 0.133 - 0.166: 9 Chirality restraints: 4375 Sorted by residual: chirality pdb=" CB VAL Q 29 " pdb=" CA VAL Q 29 " pdb=" CG1 VAL Q 29 " pdb=" CG2 VAL Q 29 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CB VALd1 29 " pdb=" CA VALd1 29 " pdb=" CG1 VALd1 29 " pdb=" CG2 VALd1 29 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CG LEU H 8 " pdb=" CB LEU H 8 " pdb=" CD1 LEU H 8 " pdb=" CD2 LEU H 8 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 4372 not shown) Planarity restraints: 4717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASPl1 18 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" CG ASPl1 18 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASPl1 18 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASPl1 18 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP L 17 " 0.007 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" CG ASP L 17 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASP L 17 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP L 17 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALd1 29 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C VALd1 29 " 0.025 2.00e-02 2.50e+03 pdb=" O VALd1 29 " -0.009 2.00e-02 2.50e+03 pdb=" N GLNd1 30 " -0.009 2.00e-02 2.50e+03 ... (remaining 4714 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 3263 2.74 - 3.28: 25749 3.28 - 3.82: 46469 3.82 - 4.36: 54874 4.36 - 4.90: 95545 Nonbonded interactions: 225900 Sorted by model distance: nonbonded pdb=" O VALd1 29 " pdb=" NH2 ARGd1 37 " model vdw 2.206 3.120 nonbonded pdb=" O VAL Q 29 " pdb=" NH2 ARG Q 37 " model vdw 2.220 3.120 nonbonded pdb=" OD2 ASP S 50 " pdb=" NZ LYS Y 21 " model vdw 2.229 3.120 nonbonded pdb=" O VAL L 29 " pdb=" NH2 ARG L 37 " model vdw 2.237 3.120 nonbonded pdb=" NH2 ARG N 74 " pdb=" OE1 GLN N 86 " model vdw 2.247 3.120 ... (remaining 225895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'B' and resid 4 through 88) selection = (chain 'C' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'D' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'E' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'F' and (resid 4 through 79 or resid 81 through 89)) selection = (chain 'G' and (resid 4 through 79 or resid 81 through 89)) selection = (chain 'H' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'I' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'J' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'K' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'L' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'M' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'N' and (resid 4 through 79 or resid 81 through 89)) selection = (chain 'O' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'P' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'Q' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'R' and (resid 4 through 79 or resid 81 through 89)) selection = (chain 'S' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'T' and (resid 4 through 79 or resid 81 through 89)) selection = (chain 'U' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'V' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'W' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'X' and (resid 4 through 79 or resid 81 through 89)) selection = (chain 'Y' and (resid 4 through 79 or resid 81 through 89)) selection = (chain 'Z' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'a1' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'b1' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'c1' and (resid 4 through 79 or resid 81 through 89)) selection = (chain 'd1' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'e1' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'f1' and (resid 4 through 79 or resid 81 through 89)) selection = (chain 'g1' and (resid 4 through 79 or resid 81 through 89)) selection = (chain 'h1' and (resid 4 through 79 or resid 81 through 89)) selection = (chain 'i1' and (resid 4 through 79 or resid 81 through 89)) selection = (chain 'j1' and (resid 3 through 78 or resid 80 through 88)) selection = (chain 'k1' and (resid 4 through 79 or resid 81 through 89)) selection = (chain 'l1' and (resid 4 through 79 or resid 81 through 89)) selection = (chain 'm1' and (resid 3 through 78 or resid 80 through 88)) } 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: 9.200 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: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 23.790 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 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 : 0.005 0.043 27771 Z= 0.216 Angle : 0.615 8.688 37213 Z= 0.324 Chirality : 0.036 0.166 4375 Planarity : 0.003 0.043 4717 Dihedral : 17.893 89.654 10944 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.27 % Favored : 97.67 % Rotamer: Outliers : 1.92 % Allowed : 22.25 % Favored : 75.83 % 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: 1.54 (0.14), residues: 3397 helix: 1.32 (0.10), residues: 2861 sheet: None (None), residues: 0 loop : -0.26 (0.23), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 73 TYR 0.015 0.002 TYR P 63 PHE 0.009 0.001 PHE M 22 Details of bonding type rmsd covalent geometry : bond 0.00509 (27771) covalent geometry : angle 0.61501 (37213) hydrogen bonds : bond 0.08185 ( 1981) hydrogen bonds : angle 5.72181 ( 5943) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 691 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6715 (tp30) REVERT: K 47 ASP cc_start: 0.7239 (p0) cc_final: 0.6935 (p0) REVERT: M 20 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6785 (ttpt) REVERT: P 24 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7281 (ttp) REVERT: T 1 MET cc_start: 0.3881 (tmm) cc_final: 0.3555 (ttp) REVERT: c1 1 MET cc_start: 0.4051 (tmm) cc_final: 0.3566 (tmm) REVERT: c1 25 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7192 (ttp) REVERT: m1 30 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6341 (tm-30) outliers start: 57 outliers final: 30 residues processed: 712 average time/residue: 0.8300 time to fit residues: 665.9789 Evaluate side-chains 717 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 682 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain M residue 20 LYS Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain O residue 30 GLN Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain P residue 24 MET Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain b1 residue 30 GLN Chi-restraints excluded: chain b1 residue 57 SER Chi-restraints excluded: chain b1 residue 84 LEU Chi-restraints excluded: chain c1 residue 25 MET Chi-restraints excluded: chain e1 residue 79 GLU Chi-restraints excluded: chain f1 residue 1 MET Chi-restraints excluded: chain g1 residue 29 THR Chi-restraints excluded: chain h1 residue 58 SER Chi-restraints excluded: chain h1 residue 71 THR Chi-restraints excluded: chain i1 residue 29 THR Chi-restraints excluded: chain k1 residue 16 SER Chi-restraints excluded: chain m1 residue 30 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.0070 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN D 13 ASN D 78 GLN I 78 GLN I 85 GLN K 85 GLN M 45 GLN N 14 ASN O 13 ASN Q 78 GLN V 78 GLN X 31 GLN X 84 GLN Y 84 GLN d1 78 GLN h1 84 GLN i1 79 GLN l1 84 GLN m1 83 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.146531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.116088 restraints weight = 29431.574| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.92 r_work: 0.3289 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 27771 Z= 0.149 Angle : 0.495 6.688 37213 Z= 0.251 Chirality : 0.033 0.157 4375 Planarity : 0.003 0.029 4717 Dihedral : 5.728 125.440 3892 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.59 % Favored : 97.38 % Rotamer: Outliers : 3.60 % Allowed : 20.20 % Favored : 76.20 % 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: 1.75 (0.14), residues: 3397 helix: 1.47 (0.10), residues: 2862 sheet: None (None), residues: 0 loop : -0.28 (0.23), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 73 TYR 0.010 0.001 TYR Z 58 PHE 0.006 0.001 PHE M 22 Details of bonding type rmsd covalent geometry : bond 0.00357 (27771) covalent geometry : angle 0.49545 (37213) hydrogen bonds : bond 0.04278 ( 1981) hydrogen bonds : angle 4.84080 ( 5943) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 682 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7364 (ttp) REVERT: C 9 ASP cc_start: 0.7567 (m-30) cc_final: 0.7270 (m-30) REVERT: C 66 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7525 (tp30) REVERT: E 66 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7510 (tp30) REVERT: H 20 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7959 (ttpt) REVERT: J 82 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7407 (mm-30) REVERT: M 30 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.6577 (tm-30) REVERT: P 66 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7611 (tp30) REVERT: P 83 GLN cc_start: 0.7388 (tm-30) cc_final: 0.6843 (mt0) REVERT: R 1 MET cc_start: 0.4773 (OUTLIER) cc_final: 0.4308 (ptp) REVERT: R 13 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7623 (mt-10) REVERT: U 13 ASN cc_start: 0.8779 (m-40) cc_final: 0.8536 (m-40) REVERT: W 82 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: a1 21 LYS cc_start: 0.7619 (mtpp) cc_final: 0.7226 (ttmt) REVERT: c1 1 MET cc_start: 0.5343 (tmm) cc_final: 0.5059 (tmm) REVERT: d1 24 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8039 (ttp) REVERT: f1 1 MET cc_start: 0.4943 (OUTLIER) cc_final: 0.4726 (tmm) REVERT: g1 25 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.5972 (ttt) REVERT: j1 82 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: m1 50 ASP cc_start: 0.7691 (m-30) cc_final: 0.7393 (m-30) outliers start: 107 outliers final: 26 residues processed: 716 average time/residue: 0.8193 time to fit residues: 662.9802 Evaluate side-chains 705 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 667 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain M residue 30 GLN Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain V residue 24 MET Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Z residue 45 GLN Chi-restraints excluded: chain Z residue 55 LEU Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain a1 residue 30 GLN Chi-restraints excluded: chain c1 residue 29 THR Chi-restraints excluded: chain c1 residue 67 GLU Chi-restraints excluded: chain d1 residue 24 MET Chi-restraints excluded: chain f1 residue 1 MET Chi-restraints excluded: chain g1 residue 25 MET Chi-restraints excluded: chain i1 residue 63 SER Chi-restraints excluded: chain j1 residue 82 GLU Chi-restraints excluded: chain k1 residue 71 THR Chi-restraints excluded: chain k1 residue 87 THR Chi-restraints excluded: chain m1 residue 45 GLN Chi-restraints excluded: chain m1 residue 57 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 121 optimal weight: 8.9990 chunk 203 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 188 optimal weight: 0.6980 chunk 210 optimal weight: 4.9990 chunk 229 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 217 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 85 GLN K 85 GLN M 45 GLN X 31 GLN Y 84 GLN Z 45 GLN h1 84 GLN m1 83 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.145873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114384 restraints weight = 29823.470| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.16 r_work: 0.3274 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 27771 Z= 0.152 Angle : 0.485 7.313 37213 Z= 0.246 Chirality : 0.033 0.135 4375 Planarity : 0.003 0.029 4717 Dihedral : 3.772 37.292 3829 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.87 % Allowed : 20.90 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.80 (0.14), residues: 3397 helix: 1.52 (0.10), residues: 2862 sheet: None (None), residues: 0 loop : -0.30 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 73 TYR 0.013 0.001 TYRb1 63 PHE 0.006 0.001 PHE F 23 Details of bonding type rmsd covalent geometry : bond 0.00366 (27771) covalent geometry : angle 0.48516 (37213) hydrogen bonds : bond 0.04270 ( 1981) hydrogen bonds : angle 4.71416 ( 5943) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 691 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7471 (ttp) REVERT: C 9 ASP cc_start: 0.7693 (m-30) cc_final: 0.7328 (m-30) REVERT: C 66 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7751 (tp30) REVERT: D 82 GLU cc_start: 0.7752 (mp0) cc_final: 0.7505 (mm-30) REVERT: E 66 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7610 (tp30) REVERT: H 24 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7584 (ttp) REVERT: J 82 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7611 (mm-30) REVERT: M 30 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.6704 (tm-30) REVERT: N 13 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7347 (mm-30) REVERT: N 19 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7541 (mt-10) REVERT: P 24 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7736 (ttp) REVERT: P 66 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7843 (tp30) REVERT: P 83 GLN cc_start: 0.7550 (tm-30) cc_final: 0.7075 (mt0) REVERT: R 13 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7652 (mt-10) REVERT: R 61 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8454 (mm) REVERT: R 67 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7328 (tp30) REVERT: T 41 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6707 (ttm170) REVERT: W 82 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: Z 30 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.6745 (tm-30) REVERT: a1 12 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7470 (mm-30) REVERT: a1 21 LYS cc_start: 0.7844 (mtpp) cc_final: 0.7463 (ttpt) REVERT: d1 24 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8172 (ttp) REVERT: g1 25 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.6072 (ttt) REVERT: g1 41 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6635 (ttm110) REVERT: h1 1 MET cc_start: 0.3982 (OUTLIER) cc_final: 0.3712 (mpm) REVERT: h1 19 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7209 (mt-10) REVERT: h1 46 GLN cc_start: 0.7760 (mt0) cc_final: 0.7455 (mm-40) REVERT: h1 51 ASP cc_start: 0.8385 (m-30) cc_final: 0.8086 (m-30) REVERT: i1 55 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8080 (ttpt) REVERT: j1 82 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: l1 34 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: m1 30 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.6717 (tm-30) REVERT: m1 45 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7062 (mm-40) REVERT: m1 50 ASP cc_start: 0.7859 (m-30) cc_final: 0.7564 (m-30) REVERT: m1 70 THR cc_start: 0.7173 (OUTLIER) cc_final: 0.6729 (p) outliers start: 115 outliers final: 40 residues processed: 729 average time/residue: 0.8248 time to fit residues: 680.3430 Evaluate side-chains 741 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 676 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain M residue 30 GLN Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain P residue 24 MET Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 67 GLU Chi-restraints excluded: chain R residue 80 GLU Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 41 ARG Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain V residue 24 MET Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain Z residue 55 LEU Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a1 residue 30 GLN Chi-restraints excluded: chain c1 residue 29 THR Chi-restraints excluded: chain c1 residue 67 GLU Chi-restraints excluded: chain c1 residue 84 GLN Chi-restraints excluded: chain d1 residue 24 MET Chi-restraints excluded: chain d1 residue 79 GLU Chi-restraints excluded: chain g1 residue 25 MET Chi-restraints excluded: chain g1 residue 41 ARG Chi-restraints excluded: chain h1 residue 1 MET Chi-restraints excluded: chain h1 residue 19 GLU Chi-restraints excluded: chain i1 residue 25 MET Chi-restraints excluded: chain i1 residue 55 LYS Chi-restraints excluded: chain i1 residue 63 SER Chi-restraints excluded: chain j1 residue 82 GLU Chi-restraints excluded: chain k1 residue 16 SER Chi-restraints excluded: chain k1 residue 29 THR Chi-restraints excluded: chain k1 residue 71 THR Chi-restraints excluded: chain k1 residue 87 THR Chi-restraints excluded: chain l1 residue 34 GLU Chi-restraints excluded: chain m1 residue 30 GLN Chi-restraints excluded: chain m1 residue 45 GLN Chi-restraints excluded: chain m1 residue 46 MET Chi-restraints excluded: chain m1 residue 57 SER Chi-restraints excluded: chain m1 residue 70 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 175 optimal weight: 5.9990 chunk 255 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 277 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 264 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 85 GLN K 85 GLN M 45 GLN M 83 GLN X 31 GLN Y 84 GLN Z 83 GLN h1 84 GLN m1 83 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.119527 restraints weight = 30121.421| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.06 r_work: 0.3306 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 27771 Z= 0.126 Angle : 0.455 7.069 37213 Z= 0.233 Chirality : 0.032 0.139 4375 Planarity : 0.002 0.030 4717 Dihedral : 3.649 18.765 3826 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.37 % Allowed : 22.18 % Favored : 74.45 % 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: 1.94 (0.15), residues: 3397 helix: 1.61 (0.10), residues: 2868 sheet: None (None), residues: 0 loop : -0.27 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 73 TYR 0.013 0.001 TYRb1 63 PHE 0.006 0.001 PHE F 23 Details of bonding type rmsd covalent geometry : bond 0.00298 (27771) covalent geometry : angle 0.45465 (37213) hydrogen bonds : bond 0.03880 ( 1981) hydrogen bonds : angle 4.61617 ( 5943) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 681 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 ASP cc_start: 0.7622 (m-30) cc_final: 0.7142 (m-30) REVERT: C 66 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7728 (tp30) REVERT: D 82 GLU cc_start: 0.7635 (mp0) cc_final: 0.7382 (mm-30) REVERT: E 66 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7542 (tp30) REVERT: H 24 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7546 (ttp) REVERT: J 82 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7567 (mm-30) REVERT: M 30 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.6693 (tm-30) REVERT: N 13 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7252 (mm-30) REVERT: N 19 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: P 24 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7662 (ttp) REVERT: P 66 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7816 (tp30) REVERT: P 83 GLN cc_start: 0.7542 (tm-30) cc_final: 0.7025 (mt0) REVERT: R 61 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8416 (mm) REVERT: R 67 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7284 (tp30) REVERT: T 1 MET cc_start: 0.5999 (tmm) cc_final: 0.5536 (tmt) REVERT: T 41 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6413 (ttm110) REVERT: U 13 ASN cc_start: 0.8868 (m-40) cc_final: 0.8641 (m-40) REVERT: W 82 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: Z 30 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.6760 (tm-30) REVERT: a1 12 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7426 (mm-30) REVERT: a1 21 LYS cc_start: 0.7846 (mtpp) cc_final: 0.7455 (ttpt) REVERT: c1 25 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.7712 (ttp) REVERT: d1 24 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8104 (ttp) REVERT: e1 66 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7281 (tp30) REVERT: g1 22 LYS cc_start: 0.7624 (ttmm) cc_final: 0.7374 (mtpt) REVERT: g1 25 MET cc_start: 0.6560 (OUTLIER) cc_final: 0.6037 (ttt) REVERT: h1 1 MET cc_start: 0.3931 (OUTLIER) cc_final: 0.3654 (mpm) REVERT: h1 19 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7106 (mt-10) REVERT: h1 46 GLN cc_start: 0.7693 (mt0) cc_final: 0.7415 (mm110) REVERT: h1 51 ASP cc_start: 0.8364 (m-30) cc_final: 0.8048 (m-30) REVERT: i1 55 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7982 (ttpt) REVERT: j1 82 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: k1 1 MET cc_start: 0.4977 (OUTLIER) cc_final: 0.4733 (tmt) REVERT: m1 30 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.6658 (tm-30) REVERT: m1 45 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7045 (mm-40) REVERT: m1 50 ASP cc_start: 0.7849 (m-30) cc_final: 0.7586 (m-30) REVERT: m1 70 THR cc_start: 0.7094 (OUTLIER) cc_final: 0.6678 (p) outliers start: 100 outliers final: 35 residues processed: 710 average time/residue: 0.8196 time to fit residues: 657.8753 Evaluate side-chains 727 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 667 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain M residue 30 GLN Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain P residue 24 MET Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 67 GLU Chi-restraints excluded: chain S residue 66 GLU Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 41 ARG Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain V residue 24 MET Chi-restraints excluded: chain V residue 28 THR Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain a1 residue 30 GLN Chi-restraints excluded: chain c1 residue 25 MET Chi-restraints excluded: chain c1 residue 29 THR Chi-restraints excluded: chain c1 residue 67 GLU Chi-restraints excluded: chain c1 residue 84 GLN Chi-restraints excluded: chain d1 residue 24 MET Chi-restraints excluded: chain e1 residue 66 GLU Chi-restraints excluded: chain e1 residue 79 GLU Chi-restraints excluded: chain g1 residue 25 MET Chi-restraints excluded: chain h1 residue 1 MET Chi-restraints excluded: chain h1 residue 19 GLU Chi-restraints excluded: chain i1 residue 25 MET Chi-restraints excluded: chain i1 residue 55 LYS Chi-restraints excluded: chain i1 residue 63 SER Chi-restraints excluded: chain j1 residue 82 GLU Chi-restraints excluded: chain k1 residue 1 MET Chi-restraints excluded: chain k1 residue 16 SER Chi-restraints excluded: chain k1 residue 29 THR Chi-restraints excluded: chain k1 residue 87 THR Chi-restraints excluded: chain m1 residue 30 GLN Chi-restraints excluded: chain m1 residue 45 GLN Chi-restraints excluded: chain m1 residue 46 MET Chi-restraints excluded: chain m1 residue 57 SER Chi-restraints excluded: chain m1 residue 70 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 26 optimal weight: 4.9990 chunk 307 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 286 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 289 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 239 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 85 GLN K 85 GLN M 45 GLN M 83 GLN X 31 GLN Y 84 GLN Z 45 GLN Z 83 GLN h1 84 GLN m1 83 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.150862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121163 restraints weight = 30137.341| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.06 r_work: 0.3307 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 27771 Z= 0.106 Angle : 0.432 6.388 37213 Z= 0.223 Chirality : 0.031 0.143 4375 Planarity : 0.002 0.035 4717 Dihedral : 3.569 18.562 3826 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.57 % Allowed : 22.28 % Favored : 74.15 % 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: 2.10 (0.15), residues: 3397 helix: 1.73 (0.10), residues: 2860 sheet: None (None), residues: 0 loop : -0.29 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 73 TYR 0.012 0.001 TYRb1 63 PHE 0.006 0.001 PHE F 23 Details of bonding type rmsd covalent geometry : bond 0.00241 (27771) covalent geometry : angle 0.43151 (37213) hydrogen bonds : bond 0.03520 ( 1981) hydrogen bonds : angle 4.53315 ( 5943) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 677 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: A 24 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7397 (ttp) REVERT: C 9 ASP cc_start: 0.7635 (m-30) cc_final: 0.7143 (m-30) REVERT: C 24 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8009 (ttp) REVERT: C 66 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7769 (tp30) REVERT: D 82 GLU cc_start: 0.7647 (mp0) cc_final: 0.7399 (mm-30) REVERT: E 66 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7608 (tp30) REVERT: H 18 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7224 (mt-10) REVERT: H 24 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7626 (ttp) REVERT: J 82 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7569 (mm-30) REVERT: M 30 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.6651 (tm-30) REVERT: M 57 SER cc_start: 0.8367 (m) cc_final: 0.8147 (p) REVERT: N 13 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7267 (mm-30) REVERT: N 19 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7350 (mt-10) REVERT: N 22 LYS cc_start: 0.7849 (mtpp) cc_final: 0.7454 (ttmt) REVERT: P 24 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7660 (ttp) REVERT: P 66 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7886 (tp30) REVERT: P 83 GLN cc_start: 0.7544 (tm-30) cc_final: 0.7039 (mt0) REVERT: R 1 MET cc_start: 0.4949 (OUTLIER) cc_final: 0.4564 (ptp) REVERT: R 67 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7356 (tp30) REVERT: T 41 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6424 (ttm110) REVERT: U 13 ASN cc_start: 0.8876 (m-40) cc_final: 0.8672 (m-40) REVERT: W 82 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: Z 30 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.6817 (tm-30) REVERT: a1 12 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7424 (mm-30) REVERT: a1 21 LYS cc_start: 0.7897 (mtpp) cc_final: 0.7526 (ttpt) REVERT: c1 25 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.7713 (ttp) REVERT: d1 24 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8137 (ttp) REVERT: e1 66 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7287 (tp30) REVERT: f1 1 MET cc_start: 0.5003 (OUTLIER) cc_final: 0.4710 (tmm) REVERT: g1 22 LYS cc_start: 0.7661 (ttmm) cc_final: 0.7451 (mtpt) REVERT: g1 41 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.6503 (ttm110) REVERT: h1 1 MET cc_start: 0.3903 (OUTLIER) cc_final: 0.3642 (mpm) REVERT: h1 19 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7152 (mt-10) REVERT: h1 46 GLN cc_start: 0.7723 (mt0) cc_final: 0.7438 (mm-40) REVERT: h1 51 ASP cc_start: 0.8365 (m-30) cc_final: 0.8060 (m-30) REVERT: j1 24 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8249 (ttp) REVERT: j1 82 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7742 (mm-30) REVERT: k1 66 LEU cc_start: 0.8308 (mt) cc_final: 0.8091 (mt) REVERT: m1 30 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.6667 (tm-30) REVERT: m1 45 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7067 (mm-40) REVERT: m1 50 ASP cc_start: 0.7886 (m-30) cc_final: 0.7672 (m-30) REVERT: m1 57 SER cc_start: 0.8277 (OUTLIER) cc_final: 0.7961 (p) REVERT: m1 70 THR cc_start: 0.7081 (OUTLIER) cc_final: 0.6719 (p) outliers start: 106 outliers final: 33 residues processed: 715 average time/residue: 0.7946 time to fit residues: 643.3867 Evaluate side-chains 719 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 656 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 24 MET Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain M residue 30 GLN Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain P residue 24 MET Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 67 GLU Chi-restraints excluded: chain R residue 80 GLU Chi-restraints excluded: chain S residue 66 GLU Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 41 ARG Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain V residue 24 MET Chi-restraints excluded: chain V residue 28 THR Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain a1 residue 30 GLN Chi-restraints excluded: chain c1 residue 25 MET Chi-restraints excluded: chain c1 residue 29 THR Chi-restraints excluded: chain c1 residue 67 GLU Chi-restraints excluded: chain c1 residue 84 GLN Chi-restraints excluded: chain d1 residue 24 MET Chi-restraints excluded: chain e1 residue 66 GLU Chi-restraints excluded: chain f1 residue 1 MET Chi-restraints excluded: chain f1 residue 5 ARG Chi-restraints excluded: chain g1 residue 41 ARG Chi-restraints excluded: chain h1 residue 1 MET Chi-restraints excluded: chain h1 residue 19 GLU Chi-restraints excluded: chain i1 residue 25 MET Chi-restraints excluded: chain i1 residue 63 SER Chi-restraints excluded: chain j1 residue 24 MET Chi-restraints excluded: chain j1 residue 28 THR Chi-restraints excluded: chain j1 residue 82 GLU Chi-restraints excluded: chain k1 residue 29 THR Chi-restraints excluded: chain m1 residue 30 GLN Chi-restraints excluded: chain m1 residue 45 GLN Chi-restraints excluded: chain m1 residue 57 SER Chi-restraints excluded: chain m1 residue 70 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 154 optimal weight: 0.9980 chunk 317 optimal weight: 10.0000 chunk 306 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 299 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 309 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 85 GLN K 85 GLN X 31 GLN Y 84 GLN Z 45 GLN Z 83 GLN h1 84 GLN m1 83 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.151579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.122708 restraints weight = 30305.764| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.96 r_work: 0.3336 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 27771 Z= 0.119 Angle : 0.455 6.390 37213 Z= 0.233 Chirality : 0.032 0.144 4375 Planarity : 0.002 0.028 4717 Dihedral : 3.561 17.882 3826 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.43 % Allowed : 22.58 % Favored : 73.98 % 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: 2.07 (0.15), residues: 3397 helix: 1.69 (0.10), residues: 2868 sheet: None (None), residues: 0 loop : -0.18 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 73 TYR 0.013 0.001 TYR B 64 PHE 0.007 0.001 PHE F 23 Details of bonding type rmsd covalent geometry : bond 0.00279 (27771) covalent geometry : angle 0.45504 (37213) hydrogen bonds : bond 0.03715 ( 1981) hydrogen bonds : angle 4.53651 ( 5943) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 670 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7304 (mt-10) REVERT: A 24 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7450 (ttp) REVERT: C 9 ASP cc_start: 0.7592 (m-30) cc_final: 0.7181 (m-30) REVERT: C 18 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: C 24 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8001 (ttp) REVERT: C 66 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7818 (tp30) REVERT: D 82 GLU cc_start: 0.7657 (mp0) cc_final: 0.7408 (mm-30) REVERT: E 66 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7526 (tp30) REVERT: F 5 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.5984 (ttt90) REVERT: H 18 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7197 (mt-10) REVERT: J 82 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7630 (mm-30) REVERT: M 30 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.6714 (tm-30) REVERT: N 1 MET cc_start: 0.6250 (tmm) cc_final: 0.5507 (tmm) REVERT: N 13 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7324 (mm-30) REVERT: N 19 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7304 (mt-10) REVERT: P 24 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7663 (ttp) REVERT: P 66 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7869 (tp30) REVERT: P 83 GLN cc_start: 0.7600 (tm-30) cc_final: 0.7127 (mt0) REVERT: R 67 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7341 (tp30) REVERT: T 3 ARG cc_start: 0.5634 (OUTLIER) cc_final: 0.5143 (tpt170) REVERT: T 41 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6455 (ttm110) REVERT: U 13 ASN cc_start: 0.8887 (m-40) cc_final: 0.8673 (m-40) REVERT: W 54 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8379 (ttmm) REVERT: Z 30 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: a1 12 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7386 (mm-30) REVERT: a1 21 LYS cc_start: 0.7880 (mtpp) cc_final: 0.7525 (ttpt) REVERT: c1 25 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7748 (ttp) REVERT: d1 24 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8154 (ttp) REVERT: e1 66 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7231 (tp30) REVERT: f1 1 MET cc_start: 0.4954 (OUTLIER) cc_final: 0.4669 (tmm) REVERT: g1 22 LYS cc_start: 0.7662 (ttmm) cc_final: 0.7305 (mtpt) REVERT: g1 25 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.6136 (ttt) REVERT: h1 1 MET cc_start: 0.3946 (OUTLIER) cc_final: 0.3689 (mpm) REVERT: h1 19 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7164 (mt-10) REVERT: h1 46 GLN cc_start: 0.7687 (mt0) cc_final: 0.7412 (mm-40) REVERT: h1 51 ASP cc_start: 0.8369 (m-30) cc_final: 0.8065 (m-30) REVERT: j1 24 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8273 (ttp) REVERT: j1 82 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7740 (mm-30) REVERT: m1 30 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.6719 (tm-30) REVERT: m1 45 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7129 (mm-40) REVERT: m1 50 ASP cc_start: 0.7895 (m-30) cc_final: 0.7667 (m-30) REVERT: m1 70 THR cc_start: 0.7113 (OUTLIER) cc_final: 0.6743 (p) outliers start: 102 outliers final: 43 residues processed: 702 average time/residue: 0.8248 time to fit residues: 654.3770 Evaluate side-chains 734 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 661 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 24 MET Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain M residue 30 GLN Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain P residue 24 MET Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 67 GLU Chi-restraints excluded: chain R residue 80 GLU Chi-restraints excluded: chain S residue 66 GLU Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 41 ARG Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain V residue 24 MET Chi-restraints excluded: chain V residue 28 THR Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 54 LYS Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain Z residue 55 LEU Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain a1 residue 30 GLN Chi-restraints excluded: chain b1 residue 84 LEU Chi-restraints excluded: chain c1 residue 25 MET Chi-restraints excluded: chain c1 residue 67 GLU Chi-restraints excluded: chain d1 residue 24 MET Chi-restraints excluded: chain e1 residue 66 GLU Chi-restraints excluded: chain e1 residue 79 GLU Chi-restraints excluded: chain f1 residue 1 MET Chi-restraints excluded: chain f1 residue 5 ARG Chi-restraints excluded: chain g1 residue 25 MET Chi-restraints excluded: chain h1 residue 1 MET Chi-restraints excluded: chain h1 residue 19 GLU Chi-restraints excluded: chain i1 residue 25 MET Chi-restraints excluded: chain i1 residue 63 SER Chi-restraints excluded: chain j1 residue 24 MET Chi-restraints excluded: chain j1 residue 28 THR Chi-restraints excluded: chain j1 residue 82 GLU Chi-restraints excluded: chain k1 residue 29 THR Chi-restraints excluded: chain k1 residue 87 THR Chi-restraints excluded: chain m1 residue 30 GLN Chi-restraints excluded: chain m1 residue 45 GLN Chi-restraints excluded: chain m1 residue 46 MET Chi-restraints excluded: chain m1 residue 55 LEU Chi-restraints excluded: chain m1 residue 57 SER Chi-restraints excluded: chain m1 residue 70 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 286 optimal weight: 4.9990 chunk 285 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 234 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 319 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 85 GLN K 85 GLN Y 84 GLN Z 83 GLN h1 84 GLN k1 86 GLN m1 83 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.149272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120326 restraints weight = 30330.619| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.95 r_work: 0.3298 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 27771 Z= 0.164 Angle : 0.511 6.705 37213 Z= 0.258 Chirality : 0.034 0.152 4375 Planarity : 0.003 0.032 4717 Dihedral : 3.657 23.165 3826 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.70 % Allowed : 22.85 % Favored : 73.44 % 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: 1.87 (0.15), residues: 3397 helix: 1.55 (0.10), residues: 2866 sheet: None (None), residues: 0 loop : -0.20 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 73 TYR 0.015 0.001 TYRm1 58 PHE 0.008 0.001 PHE F 23 Details of bonding type rmsd covalent geometry : bond 0.00397 (27771) covalent geometry : angle 0.51058 (37213) hydrogen bonds : bond 0.04289 ( 1981) hydrogen bonds : angle 4.60656 ( 5943) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 684 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: A 24 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7525 (ttp) REVERT: C 9 ASP cc_start: 0.7633 (m-30) cc_final: 0.7196 (m-30) REVERT: C 18 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: C 24 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8079 (ttp) REVERT: C 66 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7831 (tp30) REVERT: E 66 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7516 (tp30) REVERT: G 41 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6394 (ttm110) REVERT: H 18 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7200 (mt-10) REVERT: J 82 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7687 (mm-30) REVERT: M 30 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.6732 (tm-30) REVERT: N 1 MET cc_start: 0.6271 (tmm) cc_final: 0.5677 (tmm) REVERT: N 13 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7311 (mm-30) REVERT: N 19 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: P 24 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.7699 (ttp) REVERT: P 66 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7884 (tp30) REVERT: P 83 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7173 (mt0) REVERT: R 67 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7361 (tp30) REVERT: T 41 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6743 (ttm170) REVERT: U 13 ASN cc_start: 0.8904 (m-40) cc_final: 0.8664 (m-40) REVERT: W 54 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8389 (ttmm) REVERT: W 82 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: Z 30 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.6856 (tm-30) REVERT: a1 12 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7422 (mm-30) REVERT: a1 21 LYS cc_start: 0.7894 (mtpp) cc_final: 0.7544 (ttpt) REVERT: b1 17 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7731 (m-30) REVERT: c1 25 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.7802 (ttp) REVERT: d1 24 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8183 (ttp) REVERT: d1 28 THR cc_start: 0.8291 (p) cc_final: 0.7767 (t) REVERT: e1 66 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7255 (tp30) REVERT: f1 1 MET cc_start: 0.4956 (OUTLIER) cc_final: 0.4739 (tmm) REVERT: g1 22 LYS cc_start: 0.7684 (ttmm) cc_final: 0.7309 (mtpt) REVERT: g1 25 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.6126 (ttt) REVERT: h1 19 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: h1 46 GLN cc_start: 0.7664 (mt0) cc_final: 0.7386 (mm-40) REVERT: j1 24 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8310 (ttp) REVERT: j1 82 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: m1 30 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.6767 (tm-30) REVERT: m1 45 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7124 (mm-40) REVERT: m1 50 ASP cc_start: 0.7896 (m-30) cc_final: 0.7653 (m-30) REVERT: m1 70 THR cc_start: 0.7145 (OUTLIER) cc_final: 0.6728 (p) outliers start: 110 outliers final: 48 residues processed: 724 average time/residue: 0.8016 time to fit residues: 656.0183 Evaluate side-chains 761 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 683 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain M residue 30 GLN Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain P residue 24 MET Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 67 GLU Chi-restraints excluded: chain R residue 80 GLU Chi-restraints excluded: chain S residue 66 GLU Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 41 ARG Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain V residue 24 MET Chi-restraints excluded: chain V residue 28 THR Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 54 LYS Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain Z residue 55 LEU Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain b1 residue 17 ASP Chi-restraints excluded: chain b1 residue 84 LEU Chi-restraints excluded: chain c1 residue 25 MET Chi-restraints excluded: chain c1 residue 67 GLU Chi-restraints excluded: chain d1 residue 24 MET Chi-restraints excluded: chain e1 residue 66 GLU Chi-restraints excluded: chain e1 residue 79 GLU Chi-restraints excluded: chain f1 residue 1 MET Chi-restraints excluded: chain f1 residue 5 ARG Chi-restraints excluded: chain f1 residue 67 GLU Chi-restraints excluded: chain g1 residue 25 MET Chi-restraints excluded: chain h1 residue 19 GLU Chi-restraints excluded: chain i1 residue 25 MET Chi-restraints excluded: chain i1 residue 63 SER Chi-restraints excluded: chain j1 residue 24 MET Chi-restraints excluded: chain j1 residue 82 GLU Chi-restraints excluded: chain k1 residue 16 SER Chi-restraints excluded: chain k1 residue 29 THR Chi-restraints excluded: chain k1 residue 87 THR Chi-restraints excluded: chain m1 residue 30 GLN Chi-restraints excluded: chain m1 residue 45 GLN Chi-restraints excluded: chain m1 residue 46 MET Chi-restraints excluded: chain m1 residue 55 LEU Chi-restraints excluded: chain m1 residue 57 SER Chi-restraints excluded: chain m1 residue 70 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 205 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 227 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 85 GLN K 85 GLN X 31 GLN Y 84 GLN Z 83 GLN h1 84 GLN k1 86 GLN l1 84 GLN m1 83 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.151256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.122406 restraints weight = 30304.307| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.96 r_work: 0.3332 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27771 Z= 0.123 Angle : 0.473 6.893 37213 Z= 0.243 Chirality : 0.032 0.152 4375 Planarity : 0.002 0.032 4717 Dihedral : 3.629 20.884 3826 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.26 % Allowed : 23.49 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.96 (0.15), residues: 3397 helix: 1.61 (0.10), residues: 2866 sheet: None (None), residues: 0 loop : -0.20 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 73 TYR 0.012 0.001 TYR B 64 PHE 0.006 0.001 PHE F 23 Details of bonding type rmsd covalent geometry : bond 0.00288 (27771) covalent geometry : angle 0.47288 (37213) hydrogen bonds : bond 0.03780 ( 1981) hydrogen bonds : angle 4.56138 ( 5943) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 662 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: A 24 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7481 (ttp) REVERT: B 62 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7322 (mm-30) REVERT: C 9 ASP cc_start: 0.7638 (m-30) cc_final: 0.7209 (m-30) REVERT: C 18 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7959 (mt-10) REVERT: C 24 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8043 (ttp) REVERT: C 66 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7833 (tp30) REVERT: D 66 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: E 66 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7495 (tp30) REVERT: H 18 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7184 (mt-10) REVERT: J 82 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7644 (mm-30) REVERT: M 30 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.6728 (tm-30) REVERT: N 1 MET cc_start: 0.6236 (tmm) cc_final: 0.5564 (tmm) REVERT: N 13 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7296 (mm-30) REVERT: N 19 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7319 (mt-10) REVERT: P 24 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7670 (ttp) REVERT: P 66 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7884 (tp30) REVERT: P 83 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7146 (mt0) REVERT: R 67 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7351 (tp30) REVERT: T 41 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6508 (ttm110) REVERT: T 47 MET cc_start: 0.6411 (ttp) cc_final: 0.6156 (ttm) REVERT: U 13 ASN cc_start: 0.8893 (m-40) cc_final: 0.8673 (m-40) REVERT: W 54 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8360 (ttmm) REVERT: W 82 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: Z 30 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.6860 (tm-30) REVERT: a1 12 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7402 (mm-30) REVERT: a1 21 LYS cc_start: 0.7902 (mtpp) cc_final: 0.7577 (ttpt) REVERT: c1 25 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7765 (ttp) REVERT: d1 24 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8167 (ttp) REVERT: d1 28 THR cc_start: 0.8251 (p) cc_final: 0.7755 (t) REVERT: e1 66 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7243 (tp30) REVERT: f1 1 MET cc_start: 0.4867 (OUTLIER) cc_final: 0.4662 (tmm) REVERT: g1 22 LYS cc_start: 0.7685 (ttmm) cc_final: 0.7321 (mtpt) REVERT: g1 25 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6139 (ttt) REVERT: h1 19 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7164 (mt-10) REVERT: h1 46 GLN cc_start: 0.7658 (mt0) cc_final: 0.7389 (mm-40) REVERT: h1 51 ASP cc_start: 0.8380 (m-30) cc_final: 0.8080 (m-30) REVERT: j1 24 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8266 (ttp) REVERT: j1 82 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7785 (mm-30) REVERT: m1 45 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7132 (mm-40) REVERT: m1 50 ASP cc_start: 0.7904 (m-30) cc_final: 0.7687 (m-30) REVERT: m1 70 THR cc_start: 0.7078 (OUTLIER) cc_final: 0.6693 (p) outliers start: 97 outliers final: 41 residues processed: 697 average time/residue: 0.8091 time to fit residues: 637.9171 Evaluate side-chains 728 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 658 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain M residue 30 GLN Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain P residue 24 MET Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 67 GLU Chi-restraints excluded: chain R residue 80 GLU Chi-restraints excluded: chain S residue 66 GLU Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 41 ARG Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain V residue 24 MET Chi-restraints excluded: chain V residue 28 THR Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 54 LYS Chi-restraints excluded: chain W residue 82 GLU Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain Z residue 55 LEU Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain c1 residue 25 MET Chi-restraints excluded: chain c1 residue 67 GLU Chi-restraints excluded: chain d1 residue 24 MET Chi-restraints excluded: chain e1 residue 66 GLU Chi-restraints excluded: chain e1 residue 79 GLU Chi-restraints excluded: chain f1 residue 1 MET Chi-restraints excluded: chain f1 residue 5 ARG Chi-restraints excluded: chain f1 residue 67 GLU Chi-restraints excluded: chain g1 residue 25 MET Chi-restraints excluded: chain h1 residue 19 GLU Chi-restraints excluded: chain h1 residue 71 THR Chi-restraints excluded: chain i1 residue 25 MET Chi-restraints excluded: chain i1 residue 63 SER Chi-restraints excluded: chain j1 residue 24 MET Chi-restraints excluded: chain j1 residue 82 GLU Chi-restraints excluded: chain k1 residue 16 SER Chi-restraints excluded: chain k1 residue 29 THR Chi-restraints excluded: chain m1 residue 45 GLN Chi-restraints excluded: chain m1 residue 46 MET Chi-restraints excluded: chain m1 residue 55 LEU Chi-restraints excluded: chain m1 residue 57 SER Chi-restraints excluded: chain m1 residue 70 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 288 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 85 GLN K 85 GLN Y 84 GLN Z 83 GLN h1 84 GLN k1 86 GLN m1 83 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.146517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.117685 restraints weight = 30613.296| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.95 r_work: 0.3276 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 27771 Z= 0.241 Angle : 0.606 8.112 37213 Z= 0.302 Chirality : 0.037 0.160 4375 Planarity : 0.003 0.039 4717 Dihedral : 3.842 21.426 3826 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.47 % Allowed : 23.33 % Favored : 73.21 % 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: 1.48 (0.14), residues: 3397 helix: 1.27 (0.10), residues: 2860 sheet: None (None), residues: 0 loop : -0.28 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 73 TYR 0.022 0.001 TYR Z 58 PHE 0.009 0.002 PHE F 23 Details of bonding type rmsd covalent geometry : bond 0.00591 (27771) covalent geometry : angle 0.60579 (37213) hydrogen bonds : bond 0.05116 ( 1981) hydrogen bonds : angle 4.74610 ( 5943) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 692 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 ASP cc_start: 0.7660 (m-30) cc_final: 0.7210 (m-30) REVERT: C 18 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: C 66 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7761 (tp30) REVERT: E 66 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7474 (tp30) REVERT: F 51 ASP cc_start: 0.7761 (m-30) cc_final: 0.7469 (m-30) REVERT: G 41 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6417 (ttm110) REVERT: H 45 GLN cc_start: 0.7859 (mt0) cc_final: 0.7506 (mm-40) REVERT: J 82 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7667 (mm-30) REVERT: M 30 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.6780 (tm-30) REVERT: N 1 MET cc_start: 0.6315 (tmm) cc_final: 0.5876 (tmm) REVERT: N 13 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7324 (mm-30) REVERT: N 19 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: P 66 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7871 (tp30) REVERT: P 83 GLN cc_start: 0.7640 (tm-30) cc_final: 0.7127 (mt0) REVERT: R 67 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7323 (tp30) REVERT: T 41 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6773 (ttm170) REVERT: U 45 GLN cc_start: 0.8040 (mt0) cc_final: 0.7593 (mm-40) REVERT: W 54 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8398 (ttmm) REVERT: Y 54 ASP cc_start: 0.8395 (t0) cc_final: 0.8156 (t0) REVERT: Z 30 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.6846 (tm-30) REVERT: a1 12 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7422 (mm-30) REVERT: b1 17 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7683 (m-30) REVERT: b1 45 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7159 (pp30) REVERT: d1 24 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8215 (ttp) REVERT: e1 66 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7241 (tp30) REVERT: f1 1 MET cc_start: 0.5017 (OUTLIER) cc_final: 0.4760 (tmm) REVERT: f1 51 ASP cc_start: 0.7607 (m-30) cc_final: 0.7302 (m-30) REVERT: g1 25 MET cc_start: 0.6625 (OUTLIER) cc_final: 0.6096 (ttt) REVERT: g1 41 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6739 (ptm160) REVERT: h1 46 GLN cc_start: 0.7664 (mt0) cc_final: 0.7384 (mm-40) REVERT: h1 51 ASP cc_start: 0.8351 (m-30) cc_final: 0.8028 (m-30) REVERT: i1 31 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8238 (tm-30) REVERT: j1 24 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8333 (ttp) REVERT: j1 82 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: m1 30 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.6801 (tm-30) REVERT: m1 45 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7140 (mm-40) REVERT: m1 50 ASP cc_start: 0.7905 (m-30) cc_final: 0.7657 (m-30) outliers start: 103 outliers final: 41 residues processed: 729 average time/residue: 0.8189 time to fit residues: 673.9992 Evaluate side-chains 753 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 688 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain M residue 30 GLN Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 67 GLU Chi-restraints excluded: chain R residue 80 GLU Chi-restraints excluded: chain S residue 66 GLU Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 28 LEU Chi-restraints excluded: chain T residue 41 ARG Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 54 LYS Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain Z residue 55 LEU Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain b1 residue 17 ASP Chi-restraints excluded: chain b1 residue 45 GLN Chi-restraints excluded: chain c1 residue 67 GLU Chi-restraints excluded: chain d1 residue 24 MET Chi-restraints excluded: chain d1 residue 79 GLU Chi-restraints excluded: chain e1 residue 66 GLU Chi-restraints excluded: chain e1 residue 79 GLU Chi-restraints excluded: chain f1 residue 1 MET Chi-restraints excluded: chain f1 residue 5 ARG Chi-restraints excluded: chain g1 residue 25 MET Chi-restraints excluded: chain g1 residue 41 ARG Chi-restraints excluded: chain h1 residue 71 THR Chi-restraints excluded: chain i1 residue 31 GLN Chi-restraints excluded: chain i1 residue 63 SER Chi-restraints excluded: chain j1 residue 24 MET Chi-restraints excluded: chain j1 residue 82 GLU Chi-restraints excluded: chain k1 residue 16 SER Chi-restraints excluded: chain k1 residue 29 THR Chi-restraints excluded: chain k1 residue 71 THR Chi-restraints excluded: chain k1 residue 87 THR Chi-restraints excluded: chain m1 residue 30 GLN Chi-restraints excluded: chain m1 residue 45 GLN Chi-restraints excluded: chain m1 residue 46 MET Chi-restraints excluded: chain m1 residue 55 LEU Chi-restraints excluded: chain m1 residue 57 SER Chi-restraints excluded: chain m1 residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 297 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 85 GLN L 83 GLN Y 84 GLN Z 83 GLN h1 84 GLN l1 84 GLN m1 83 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.149551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.120746 restraints weight = 30482.983| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.97 r_work: 0.3311 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 27771 Z= 0.150 Angle : 0.521 7.747 37213 Z= 0.265 Chirality : 0.033 0.158 4375 Planarity : 0.003 0.036 4717 Dihedral : 3.769 22.811 3826 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.46 % Allowed : 24.60 % Favored : 72.94 % 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: 1.66 (0.14), residues: 3397 helix: 1.42 (0.10), residues: 2853 sheet: None (None), residues: 0 loop : -0.36 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 73 TYR 0.012 0.001 TYRb1 63 PHE 0.007 0.001 PHE F 23 Details of bonding type rmsd covalent geometry : bond 0.00358 (27771) covalent geometry : angle 0.52085 (37213) hydrogen bonds : bond 0.04187 ( 1981) hydrogen bonds : angle 4.65967 ( 5943) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 672 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 9 ASP cc_start: 0.7661 (m-30) cc_final: 0.7220 (m-30) REVERT: C 18 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7914 (mt-10) REVERT: C 66 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7766 (tp30) REVERT: E 66 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7466 (tp30) REVERT: G 41 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6371 (ttm110) REVERT: H 45 GLN cc_start: 0.7830 (mt0) cc_final: 0.7462 (mm-40) REVERT: H 50 ASP cc_start: 0.8363 (m-30) cc_final: 0.8025 (m-30) REVERT: J 82 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7655 (mm-30) REVERT: M 30 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.6752 (tm-30) REVERT: N 1 MET cc_start: 0.6218 (tmm) cc_final: 0.5681 (tmm) REVERT: N 13 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7327 (mm-30) REVERT: N 19 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7448 (mt-10) REVERT: P 66 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7863 (tp30) REVERT: P 83 GLN cc_start: 0.7589 (tm-30) cc_final: 0.7109 (mt0) REVERT: R 67 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7334 (tp30) REVERT: T 41 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6755 (ttm170) REVERT: W 54 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8351 (ttmm) REVERT: a1 12 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7383 (mm-30) REVERT: b1 17 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7684 (m-30) REVERT: b1 45 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7153 (pp30) REVERT: d1 24 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8139 (ttp) REVERT: d1 28 THR cc_start: 0.8236 (p) cc_final: 0.7738 (t) REVERT: e1 66 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7232 (tp30) REVERT: f1 1 MET cc_start: 0.4952 (OUTLIER) cc_final: 0.4695 (tmm) REVERT: f1 21 LYS cc_start: 0.7833 (mtpt) cc_final: 0.7526 (tttp) REVERT: g1 25 MET cc_start: 0.6641 (OUTLIER) cc_final: 0.6107 (ttt) REVERT: h1 46 GLN cc_start: 0.7642 (mt0) cc_final: 0.7372 (mm-40) REVERT: h1 51 ASP cc_start: 0.8376 (m-30) cc_final: 0.8074 (m-30) REVERT: j1 24 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8253 (ttp) REVERT: j1 82 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: m1 45 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7122 (mm-40) REVERT: m1 50 ASP cc_start: 0.7891 (m-30) cc_final: 0.7655 (m-30) REVERT: m1 70 THR cc_start: 0.7082 (OUTLIER) cc_final: 0.6661 (p) outliers start: 73 outliers final: 37 residues processed: 697 average time/residue: 0.8331 time to fit residues: 655.2559 Evaluate side-chains 724 residues out of total 2971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 666 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain M residue 30 GLN Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 67 GLU Chi-restraints excluded: chain R residue 80 GLU Chi-restraints excluded: chain S residue 66 GLU Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 41 ARG Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 54 LYS Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain Y residue 45 LEU Chi-restraints excluded: chain Z residue 55 LEU Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain a1 residue 30 GLN Chi-restraints excluded: chain b1 residue 17 ASP Chi-restraints excluded: chain b1 residue 45 GLN Chi-restraints excluded: chain c1 residue 67 GLU Chi-restraints excluded: chain d1 residue 24 MET Chi-restraints excluded: chain e1 residue 66 GLU Chi-restraints excluded: chain e1 residue 79 GLU Chi-restraints excluded: chain f1 residue 1 MET Chi-restraints excluded: chain f1 residue 5 ARG Chi-restraints excluded: chain f1 residue 67 GLU Chi-restraints excluded: chain g1 residue 25 MET Chi-restraints excluded: chain h1 residue 71 THR Chi-restraints excluded: chain i1 residue 63 SER Chi-restraints excluded: chain j1 residue 24 MET Chi-restraints excluded: chain j1 residue 82 GLU Chi-restraints excluded: chain k1 residue 16 SER Chi-restraints excluded: chain k1 residue 29 THR Chi-restraints excluded: chain k1 residue 87 THR Chi-restraints excluded: chain m1 residue 45 GLN Chi-restraints excluded: chain m1 residue 46 MET Chi-restraints excluded: chain m1 residue 55 LEU Chi-restraints excluded: chain m1 residue 57 SER Chi-restraints excluded: chain m1 residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 293 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 143 optimal weight: 0.0670 chunk 10 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 306 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 85 GLN L 83 GLN Y 84 GLN Z 83 GLN h1 84 GLN k1 86 GLN l1 84 GLN m1 83 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.150984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122202 restraints weight = 30261.325| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.96 r_work: 0.3331 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27771 Z= 0.128 Angle : 0.500 12.959 37213 Z= 0.254 Chirality : 0.033 0.156 4375 Planarity : 0.002 0.036 4717 Dihedral : 3.699 22.588 3826 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.39 % Allowed : 24.74 % Favored : 72.87 % 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: 1.82 (0.15), residues: 3397 helix: 1.52 (0.10), residues: 2859 sheet: None (None), residues: 0 loop : -0.29 (0.24), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 73 TYR 0.011 0.001 TYR O 63 PHE 0.007 0.001 PHE F 23 Details of bonding type rmsd covalent geometry : bond 0.00300 (27771) covalent geometry : angle 0.49965 (37213) hydrogen bonds : bond 0.03853 ( 1981) hydrogen bonds : angle 4.58512 ( 5943) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13201.84 seconds wall clock time: 224 minutes 30.71 seconds (13470.71 seconds total)