Starting phenix.real_space_refine on Fri Aug 7 01:56:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pq8_17821/08_2026/8pq8_17821.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pq8_17821/08_2026/8pq8_17821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pq8_17821/08_2026/8pq8_17821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pq8_17821/08_2026/8pq8_17821.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pq8_17821/08_2026/8pq8_17821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pq8_17821/08_2026/8pq8_17821.map" } resolution = 3.21 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= 0.000 sd= 0.019 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 18 5.16 5 C 12114 2.51 5 N 3096 2.21 5 O 3708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18936 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "G" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "G" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "H" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "I" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "J" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "K" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "K" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "L" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "L" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "M" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "M" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "N" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "N" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "O" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "O" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "P" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "P" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "Q" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "Q" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "R" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 4.08, per 1000 atoms: 0.22 Number of scatterers: 18936 At special positions: 0 Unit cell: (169.342, 170.834, 58.188, 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 18 16.00 O 3708 8.00 N 3096 7.00 C 12114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 708.8 milliseconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4428 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 72 sheets defined 34.4% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 Processing helix chain 'A' and resid 29 through 41 Processing helix chain 'A' and resid 105 through 122 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'B' and resid 5 through 12 Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 105 through 122 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'C' and resid 5 through 12 Processing helix chain 'C' and resid 29 through 41 Processing helix chain 'C' and resid 105 through 122 Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'D' and resid 5 through 12 Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 105 through 122 Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'E' and resid 5 through 12 Processing helix chain 'E' and resid 29 through 41 Processing helix chain 'E' and resid 105 through 122 Processing helix chain 'E' and resid 127 through 131 Processing helix chain 'F' and resid 5 through 12 Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 105 through 122 Processing helix chain 'F' and resid 127 through 131 Processing helix chain 'G' and resid 5 through 12 Processing helix chain 'G' and resid 29 through 41 Processing helix chain 'G' and resid 105 through 122 Processing helix chain 'G' and resid 127 through 131 Processing helix chain 'H' and resid 5 through 12 Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 105 through 122 Processing helix chain 'H' and resid 127 through 131 Processing helix chain 'I' and resid 5 through 12 Processing helix chain 'I' and resid 29 through 41 Processing helix chain 'I' and resid 105 through 122 Processing helix chain 'I' and resid 127 through 131 Processing helix chain 'J' and resid 5 through 12 Processing helix chain 'J' and resid 29 through 41 Processing helix chain 'J' and resid 105 through 122 Processing helix chain 'J' and resid 127 through 131 Processing helix chain 'K' and resid 5 through 12 Processing helix chain 'K' and resid 29 through 41 Processing helix chain 'K' and resid 105 through 122 Processing helix chain 'K' and resid 127 through 131 Processing helix chain 'L' and resid 5 through 12 Processing helix chain 'L' and resid 29 through 41 Processing helix chain 'L' and resid 105 through 122 Processing helix chain 'L' and resid 127 through 131 Processing helix chain 'M' and resid 5 through 12 Processing helix chain 'M' and resid 29 through 41 Processing helix chain 'M' and resid 105 through 122 Processing helix chain 'M' and resid 127 through 131 Processing helix chain 'N' and resid 5 through 12 Processing helix chain 'N' and resid 29 through 41 Processing helix chain 'N' and resid 105 through 122 Processing helix chain 'N' and resid 127 through 131 Processing helix chain 'O' and resid 5 through 12 Processing helix chain 'O' and resid 29 through 41 Processing helix chain 'O' and resid 105 through 122 Processing helix chain 'O' and resid 127 through 131 Processing helix chain 'P' and resid 5 through 12 Processing helix chain 'P' and resid 29 through 41 Processing helix chain 'P' and resid 105 through 122 Processing helix chain 'P' and resid 127 through 131 Processing helix chain 'Q' and resid 5 through 12 Processing helix chain 'Q' and resid 29 through 41 Processing helix chain 'Q' and resid 105 through 122 Processing helix chain 'Q' and resid 127 through 131 Processing helix chain 'R' and resid 5 through 12 Processing helix chain 'R' and resid 29 through 41 Processing helix chain 'R' and resid 105 through 122 Processing helix chain 'R' and resid 127 through 131 Processing sheet with id=1, first strand: chain 'A' and resid 19 through 22 Processing sheet with id=2, first strand: chain 'A' and resid 45 through 48 Processing sheet with id=3, first strand: chain 'A' and resid 45 through 48 Processing sheet with id=4, first strand: chain 'A' and resid 51 through 52 Processing sheet with id=5, first strand: chain 'B' and resid 19 through 22 Processing sheet with id=6, first strand: chain 'B' and resid 45 through 48 Processing sheet with id=7, first strand: chain 'B' and resid 45 through 48 Processing sheet with id=8, first strand: chain 'B' and resid 51 through 52 Processing sheet with id=9, first strand: chain 'C' and resid 19 through 22 Processing sheet with id=10, first strand: chain 'C' and resid 45 through 48 Processing sheet with id=11, first strand: chain 'C' and resid 45 through 48 Processing sheet with id=12, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=13, first strand: chain 'D' and resid 19 through 22 Processing sheet with id=14, first strand: chain 'D' and resid 45 through 48 Processing sheet with id=15, first strand: chain 'D' and resid 45 through 48 Processing sheet with id=16, first strand: chain 'D' and resid 51 through 52 Processing sheet with id=17, first strand: chain 'E' and resid 19 through 22 Processing sheet with id=18, first strand: chain 'E' and resid 45 through 48 Processing sheet with id=19, first strand: chain 'E' and resid 45 through 48 Processing sheet with id=20, first strand: chain 'E' and resid 51 through 52 Processing sheet with id=21, first strand: chain 'F' and resid 19 through 22 Processing sheet with id=22, first strand: chain 'F' and resid 45 through 48 Processing sheet with id=23, first strand: chain 'F' and resid 45 through 48 Processing sheet with id=24, first strand: chain 'F' and resid 51 through 52 Processing sheet with id=25, first strand: chain 'G' and resid 19 through 22 Processing sheet with id=26, first strand: chain 'G' and resid 45 through 48 Processing sheet with id=27, first strand: chain 'G' and resid 45 through 48 Processing sheet with id=28, first strand: chain 'G' and resid 51 through 52 Processing sheet with id=29, first strand: chain 'H' and resid 19 through 22 Processing sheet with id=30, first strand: chain 'H' and resid 45 through 48 Processing sheet with id=31, first strand: chain 'H' and resid 45 through 48 Processing sheet with id=32, first strand: chain 'H' and resid 51 through 52 Processing sheet with id=33, first strand: chain 'I' and resid 19 through 22 Processing sheet with id=34, first strand: chain 'I' and resid 45 through 48 Processing sheet with id=35, first strand: chain 'I' and resid 45 through 48 Processing sheet with id=36, first strand: chain 'I' and resid 51 through 52 Processing sheet with id=37, first strand: chain 'J' and resid 19 through 22 Processing sheet with id=38, first strand: chain 'J' and resid 45 through 48 Processing sheet with id=39, first strand: chain 'J' and resid 45 through 48 Processing sheet with id=40, first strand: chain 'J' and resid 51 through 52 Processing sheet with id=41, first strand: chain 'K' and resid 19 through 22 Processing sheet with id=42, first strand: chain 'K' and resid 45 through 48 Processing sheet with id=43, first strand: chain 'K' and resid 45 through 48 Processing sheet with id=44, first strand: chain 'K' and resid 51 through 52 Processing sheet with id=45, first strand: chain 'L' and resid 19 through 22 Processing sheet with id=46, first strand: chain 'L' and resid 45 through 48 Processing sheet with id=47, first strand: chain 'L' and resid 45 through 48 Processing sheet with id=48, first strand: chain 'L' and resid 51 through 52 Processing sheet with id=49, first strand: chain 'M' and resid 19 through 22 Processing sheet with id=50, first strand: chain 'M' and resid 45 through 48 Processing sheet with id=51, first strand: chain 'M' and resid 45 through 48 Processing sheet with id=52, first strand: chain 'M' and resid 51 through 52 Processing sheet with id=53, first strand: chain 'N' and resid 19 through 22 Processing sheet with id=54, first strand: chain 'N' and resid 45 through 48 Processing sheet with id=55, first strand: chain 'N' and resid 45 through 48 Processing sheet with id=56, first strand: chain 'N' and resid 51 through 52 Processing sheet with id=57, first strand: chain 'O' and resid 19 through 22 Processing sheet with id=58, first strand: chain 'O' and resid 45 through 48 Processing sheet with id=59, first strand: chain 'O' and resid 45 through 48 Processing sheet with id=60, first strand: chain 'O' and resid 51 through 52 Processing sheet with id=61, first strand: chain 'P' and resid 19 through 22 Processing sheet with id=62, first strand: chain 'P' and resid 45 through 48 Processing sheet with id=63, first strand: chain 'P' and resid 45 through 48 Processing sheet with id=64, first strand: chain 'P' and resid 51 through 52 Processing sheet with id=65, first strand: chain 'Q' and resid 19 through 22 Processing sheet with id=66, first strand: chain 'Q' and resid 45 through 48 Processing sheet with id=67, first strand: chain 'Q' and resid 45 through 48 Processing sheet with id=68, first strand: chain 'Q' and resid 51 through 52 Processing sheet with id=69, first strand: chain 'R' and resid 19 through 22 Processing sheet with id=70, first strand: chain 'R' and resid 45 through 48 Processing sheet with id=71, first strand: chain 'R' and resid 45 through 48 Processing sheet with id=72, first strand: chain 'R' and resid 51 through 52 990 hydrogen bonds defined for protein. 2484 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.40 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3168 1.32 - 1.44: 5472 1.44 - 1.56: 10638 1.56 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 19296 Sorted by residual: bond pdb=" N ILE M 56 " pdb=" CA ILE M 56 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.19e-02 7.06e+03 1.18e+01 bond pdb=" N ILE L 56 " pdb=" CA ILE L 56 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.19e-02 7.06e+03 1.18e+01 bond pdb=" N ILE G 56 " pdb=" CA ILE G 56 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.19e-02 7.06e+03 1.17e+01 bond pdb=" N ILE E 56 " pdb=" CA ILE E 56 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.19e-02 7.06e+03 1.17e+01 bond pdb=" N ILE R 56 " pdb=" CA ILE R 56 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.19e-02 7.06e+03 1.17e+01 ... (remaining 19291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 19767 1.65 - 3.29: 5588 3.29 - 4.94: 817 4.94 - 6.59: 36 6.59 - 8.23: 54 Bond angle restraints: 26262 Sorted by residual: angle pdb=" N HIS G 124 " pdb=" CA HIS G 124 " pdb=" C HIS G 124 " ideal model delta sigma weight residual 110.53 102.56 7.97 1.29e+00 6.01e-01 3.82e+01 angle pdb=" N HIS I 124 " pdb=" CA HIS I 124 " pdb=" C HIS I 124 " ideal model delta sigma weight residual 110.53 102.57 7.96 1.29e+00 6.01e-01 3.81e+01 angle pdb=" N HIS M 124 " pdb=" CA HIS M 124 " pdb=" C HIS M 124 " ideal model delta sigma weight residual 110.53 102.57 7.96 1.29e+00 6.01e-01 3.81e+01 angle pdb=" N HIS C 124 " pdb=" CA HIS C 124 " pdb=" C HIS C 124 " ideal model delta sigma weight residual 110.53 102.57 7.96 1.29e+00 6.01e-01 3.80e+01 angle pdb=" N HIS B 124 " pdb=" CA HIS B 124 " pdb=" C HIS B 124 " ideal model delta sigma weight residual 110.53 102.57 7.96 1.29e+00 6.01e-01 3.80e+01 ... (remaining 26257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.13: 10242 12.13 - 24.27: 540 24.27 - 36.40: 414 36.40 - 48.53: 36 48.53 - 60.67: 108 Dihedral angle restraints: 11340 sinusoidal: 4482 harmonic: 6858 Sorted by residual: dihedral pdb=" CB LYS F 111 " pdb=" CG LYS F 111 " pdb=" CD LYS F 111 " pdb=" CE LYS F 111 " ideal model delta sinusoidal sigma weight residual 60.00 9.67 50.33 3 1.50e+01 4.44e-03 8.89e+00 dihedral pdb=" CB LYS P 111 " pdb=" CG LYS P 111 " pdb=" CD LYS P 111 " pdb=" CE LYS P 111 " ideal model delta sinusoidal sigma weight residual 60.00 9.67 50.33 3 1.50e+01 4.44e-03 8.89e+00 dihedral pdb=" CB LYS B 111 " pdb=" CG LYS B 111 " pdb=" CD LYS B 111 " pdb=" CE LYS B 111 " ideal model delta sinusoidal sigma weight residual 60.00 9.71 50.29 3 1.50e+01 4.44e-03 8.88e+00 ... (remaining 11337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1219 0.047 - 0.094: 653 0.094 - 0.141: 664 0.141 - 0.188: 264 0.188 - 0.235: 80 Chirality restraints: 2880 Sorted by residual: chirality pdb=" CA TRP D 88 " pdb=" N TRP D 88 " pdb=" C TRP D 88 " pdb=" CB TRP D 88 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA TRP Q 88 " pdb=" N TRP Q 88 " pdb=" C TRP Q 88 " pdb=" CB TRP Q 88 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA TRP K 88 " pdb=" N TRP K 88 " pdb=" C TRP K 88 " pdb=" CB TRP K 88 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 2877 not shown) Planarity restraints: 3348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP P 88 " 0.027 2.00e-02 2.50e+03 2.24e-02 1.25e+01 pdb=" CG TRP P 88 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP P 88 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP P 88 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP P 88 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP P 88 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP P 88 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 88 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 88 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP P 88 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 88 " 0.027 2.00e-02 2.50e+03 2.23e-02 1.25e+01 pdb=" CG TRP K 88 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP K 88 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP K 88 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP K 88 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP K 88 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP K 88 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 88 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 88 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP K 88 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 88 " 0.027 2.00e-02 2.50e+03 2.23e-02 1.25e+01 pdb=" CG TRP E 88 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP E 88 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP E 88 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 88 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 88 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 88 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 88 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 88 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 88 " 0.001 2.00e-02 2.50e+03 ... (remaining 3345 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 7241 2.90 - 3.40: 16951 3.40 - 3.90: 30426 3.90 - 4.40: 32410 4.40 - 4.90: 58225 Nonbonded interactions: 145253 Sorted by model distance: nonbonded pdb=" OD1 ASN Q 110 " pdb=" O HOH Q 201 " model vdw 2.394 3.040 nonbonded pdb=" OD1 ASN L 110 " pdb=" O HOH L 201 " model vdw 2.395 3.040 nonbonded pdb=" OD1 ASN N 110 " pdb=" O HOH N 201 " model vdw 2.395 3.040 nonbonded pdb=" OD1 ASN B 110 " pdb=" O HOH B 201 " model vdw 2.395 3.040 nonbonded pdb=" OD1 ASN K 110 " pdb=" O HOH K 201 " model vdw 2.395 3.040 ... (remaining 145248 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 5.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.690 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 : 0.011 0.042 19296 Z= 0.856 Angle : 1.486 8.232 26262 Z= 1.132 Chirality : 0.090 0.235 2880 Planarity : 0.005 0.022 3348 Dihedral : 12.409 60.666 6912 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.16), residues: 2268 helix: 0.75 (0.21), residues: 648 sheet: -0.03 (0.23), residues: 378 loop : -0.66 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 95 TYR 0.023 0.003 TYR M 32 PHE 0.009 0.001 PHE F 7 TRP 0.061 0.008 TRP P 88 HIS 0.004 0.002 HIS G 53 Details of bonding type rmsd/Z covalent geometry : bond 0.01129 / 0.86 (19296) covalent geometry : angle 1.48625 / 1.13 (26262) hydrogen bonds : bond 0.25955 / 17.65 ( 918) hydrogen bonds : angle 7.19379 / 5.09 ( 2484) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 SER cc_start: 0.8768 (m) cc_final: 0.8339 (t) REVERT: B 103 SER cc_start: 0.8827 (m) cc_final: 0.8392 (t) REVERT: C 103 SER cc_start: 0.8741 (m) cc_final: 0.8311 (t) REVERT: D 103 SER cc_start: 0.8811 (m) cc_final: 0.8386 (t) REVERT: E 103 SER cc_start: 0.8860 (m) cc_final: 0.8403 (t) REVERT: F 103 SER cc_start: 0.8781 (m) cc_final: 0.8370 (t) REVERT: G 103 SER cc_start: 0.8760 (m) cc_final: 0.8308 (t) REVERT: G 108 ASP cc_start: 0.8002 (m-30) cc_final: 0.7672 (m-30) REVERT: H 103 SER cc_start: 0.8786 (m) cc_final: 0.8385 (t) REVERT: I 103 SER cc_start: 0.8755 (m) cc_final: 0.8357 (t) REVERT: J 103 SER cc_start: 0.8769 (m) cc_final: 0.8340 (t) REVERT: K 103 SER cc_start: 0.8799 (m) cc_final: 0.8377 (t) REVERT: L 103 SER cc_start: 0.8725 (m) cc_final: 0.8312 (t) REVERT: M 103 SER cc_start: 0.8818 (m) cc_final: 0.8400 (t) REVERT: N 103 SER cc_start: 0.8839 (m) cc_final: 0.8383 (t) REVERT: O 103 SER cc_start: 0.8809 (m) cc_final: 0.8382 (t) REVERT: P 103 SER cc_start: 0.8766 (m) cc_final: 0.8323 (t) REVERT: P 108 ASP cc_start: 0.8009 (m-30) cc_final: 0.7700 (m-30) REVERT: Q 103 SER cc_start: 0.8814 (m) cc_final: 0.8393 (t) REVERT: R 103 SER cc_start: 0.8752 (m) cc_final: 0.8357 (t) outliers start: 0 outliers final: 0 residues processed: 426 average time/residue: 0.1562 time to fit residues: 96.9852 Evaluate side-chains 322 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN A 34 HIS B 4 GLN B 34 HIS C 4 GLN C 34 HIS D 4 GLN D 34 HIS E 4 GLN E 34 HIS F 4 GLN F 34 HIS G 4 GLN G 34 HIS H 4 GLN H 34 HIS I 4 GLN I 34 HIS J 4 GLN J 34 HIS K 4 GLN K 34 HIS L 4 GLN L 34 HIS M 4 GLN M 34 HIS N 4 GLN N 34 HIS O 4 GLN O 34 HIS P 4 GLN P 34 HIS Q 4 GLN Q 34 HIS R 4 GLN R 34 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.189855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.126321 restraints weight = 21038.253| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.53 r_work: 0.3272 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 19296 Z= 0.109 Angle : 0.521 4.403 26262 Z= 0.287 Chirality : 0.041 0.115 2880 Planarity : 0.004 0.033 3348 Dihedral : 4.278 16.401 2466 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 0.82 % Allowed : 10.34 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.16), residues: 2268 helix: 1.68 (0.18), residues: 720 sheet: 0.22 (0.22), residues: 396 loop : -0.18 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 115 TYR 0.022 0.002 TYR H 32 PHE 0.011 0.001 PHE N 73 TRP 0.020 0.003 TRP Q 88 HIS 0.001 0.000 HIS H 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (19296) covalent geometry : angle 0.52126 / 0.29 (26262) hydrogen bonds : bond 0.04060 / 2.69 ( 918) hydrogen bonds : angle 4.39377 / 3.13 ( 2484) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 383 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 SER cc_start: 0.8782 (m) cc_final: 0.8184 (t) REVERT: A 108 ASP cc_start: 0.8024 (m-30) cc_final: 0.7779 (m-30) REVERT: B 103 SER cc_start: 0.8783 (m) cc_final: 0.8082 (t) REVERT: C 95 ARG cc_start: 0.8741 (mtm180) cc_final: 0.8425 (mtm180) REVERT: C 103 SER cc_start: 0.8712 (m) cc_final: 0.8069 (t) REVERT: D 103 SER cc_start: 0.8829 (m) cc_final: 0.8160 (t) REVERT: E 93 ASP cc_start: 0.7406 (m-30) cc_final: 0.6996 (t0) REVERT: E 95 ARG cc_start: 0.8696 (mtm180) cc_final: 0.8306 (mtm180) REVERT: E 103 SER cc_start: 0.8797 (m) cc_final: 0.8079 (t) REVERT: E 108 ASP cc_start: 0.7988 (m-30) cc_final: 0.7788 (m-30) REVERT: F 103 SER cc_start: 0.8711 (m) cc_final: 0.8069 (t) REVERT: G 103 SER cc_start: 0.8762 (m) cc_final: 0.8103 (t) REVERT: H 103 SER cc_start: 0.8754 (m) cc_final: 0.8097 (t) REVERT: H 119 LYS cc_start: 0.6984 (mttm) cc_final: 0.6769 (ttmt) REVERT: I 103 SER cc_start: 0.8709 (m) cc_final: 0.8091 (t) REVERT: J 103 SER cc_start: 0.8778 (m) cc_final: 0.8182 (t) REVERT: J 108 ASP cc_start: 0.8019 (m-30) cc_final: 0.7775 (m-30) REVERT: K 103 SER cc_start: 0.8804 (m) cc_final: 0.8106 (t) REVERT: L 95 ARG cc_start: 0.8736 (mtm180) cc_final: 0.8407 (mtm180) REVERT: L 103 SER cc_start: 0.8686 (m) cc_final: 0.8054 (t) REVERT: L 108 ASP cc_start: 0.7915 (m-30) cc_final: 0.7664 (m-30) REVERT: M 103 SER cc_start: 0.8830 (m) cc_final: 0.8164 (t) REVERT: N 93 ASP cc_start: 0.7401 (m-30) cc_final: 0.6989 (t0) REVERT: N 95 ARG cc_start: 0.8650 (mtm180) cc_final: 0.8265 (mtm180) REVERT: N 103 SER cc_start: 0.8780 (m) cc_final: 0.8064 (t) REVERT: O 103 SER cc_start: 0.8712 (m) cc_final: 0.8061 (t) REVERT: P 103 SER cc_start: 0.8758 (m) cc_final: 0.8098 (t) REVERT: Q 41 ASP cc_start: 0.8409 (t0) cc_final: 0.8147 (t0) REVERT: Q 103 SER cc_start: 0.8760 (m) cc_final: 0.8092 (t) REVERT: Q 119 LYS cc_start: 0.6936 (mttm) cc_final: 0.6727 (ttmt) REVERT: R 103 SER cc_start: 0.8728 (m) cc_final: 0.8116 (t) outliers start: 17 outliers final: 15 residues processed: 400 average time/residue: 0.1420 time to fit residues: 88.1197 Evaluate side-chains 318 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 303 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 35 GLN Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain L residue 35 GLN Chi-restraints excluded: chain N residue 35 GLN Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain P residue 35 GLN Chi-restraints excluded: chain Q residue 35 GLN Chi-restraints excluded: chain R residue 31 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 185 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 125 optimal weight: 0.6980 chunk 133 optimal weight: 20.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.187786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121123 restraints weight = 21392.196| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.70 r_work: 0.3190 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19296 Z= 0.125 Angle : 0.505 6.458 26262 Z= 0.273 Chirality : 0.042 0.148 2880 Planarity : 0.004 0.035 3348 Dihedral : 4.166 16.806 2466 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.13 % Allowed : 12.75 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.17), residues: 2268 helix: 2.23 (0.18), residues: 720 sheet: 0.48 (0.24), residues: 378 loop : -0.13 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 95 TYR 0.021 0.002 TYR F 32 PHE 0.011 0.001 PHE H 73 TRP 0.019 0.003 TRP N 88 HIS 0.003 0.001 HIS Q 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (19296) covalent geometry : angle 0.50537 / 0.27 (26262) hydrogen bonds : bond 0.04304 / 2.85 ( 918) hydrogen bonds : angle 4.08947 / 2.91 ( 2484) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 278 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 SER cc_start: 0.8874 (m) cc_final: 0.8252 (t) REVERT: A 108 ASP cc_start: 0.8105 (m-30) cc_final: 0.7834 (m-30) REVERT: B 93 ASP cc_start: 0.7372 (m-30) cc_final: 0.7130 (t0) REVERT: B 103 SER cc_start: 0.8899 (m) cc_final: 0.8193 (t) REVERT: C 103 SER cc_start: 0.8884 (m) cc_final: 0.8214 (t) REVERT: C 108 ASP cc_start: 0.8023 (m-30) cc_final: 0.7742 (m-30) REVERT: D 103 SER cc_start: 0.8861 (m) cc_final: 0.8122 (t) REVERT: D 108 ASP cc_start: 0.8046 (m-30) cc_final: 0.7796 (m-30) REVERT: E 93 ASP cc_start: 0.7372 (m-30) cc_final: 0.7144 (t0) REVERT: E 95 ARG cc_start: 0.8691 (mtm180) cc_final: 0.8354 (mtm180) REVERT: E 103 SER cc_start: 0.8932 (m) cc_final: 0.8201 (t) REVERT: E 108 ASP cc_start: 0.8111 (m-30) cc_final: 0.7881 (m-30) REVERT: F 103 SER cc_start: 0.8849 (m) cc_final: 0.8168 (t) REVERT: G 103 SER cc_start: 0.8883 (m) cc_final: 0.8198 (t) REVERT: G 108 ASP cc_start: 0.8059 (m-30) cc_final: 0.7677 (m-30) REVERT: H 103 SER cc_start: 0.8916 (m) cc_final: 0.8229 (t) REVERT: I 103 SER cc_start: 0.8937 (m) cc_final: 0.8280 (t) REVERT: J 103 SER cc_start: 0.8884 (m) cc_final: 0.8265 (t) REVERT: J 108 ASP cc_start: 0.8102 (m-30) cc_final: 0.7831 (m-30) REVERT: K 93 ASP cc_start: 0.7365 (m-30) cc_final: 0.7136 (t0) REVERT: K 103 SER cc_start: 0.8955 (m) cc_final: 0.8232 (t) REVERT: L 103 SER cc_start: 0.8873 (m) cc_final: 0.8215 (t) REVERT: L 108 ASP cc_start: 0.8067 (m-30) cc_final: 0.7684 (m-30) REVERT: M 103 SER cc_start: 0.8866 (m) cc_final: 0.8139 (t) REVERT: M 108 ASP cc_start: 0.8058 (m-30) cc_final: 0.7813 (m-30) REVERT: N 103 SER cc_start: 0.8945 (m) cc_final: 0.8220 (t) REVERT: O 103 SER cc_start: 0.8876 (m) cc_final: 0.8199 (t) REVERT: P 103 SER cc_start: 0.8887 (m) cc_final: 0.8203 (t) REVERT: P 108 ASP cc_start: 0.8070 (m-30) cc_final: 0.7683 (m-30) REVERT: Q 41 ASP cc_start: 0.8352 (t0) cc_final: 0.8078 (t0) REVERT: Q 103 SER cc_start: 0.8941 (m) cc_final: 0.8255 (t) REVERT: R 103 SER cc_start: 0.8943 (m) cc_final: 0.8290 (t) outliers start: 44 outliers final: 37 residues processed: 322 average time/residue: 0.1269 time to fit residues: 63.6317 Evaluate side-chains 293 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 256 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 35 GLN Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 35 GLN Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 35 GLN Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 35 GLN Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 35 GLN Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain P residue 35 GLN Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 35 GLN Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain R residue 31 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 122 optimal weight: 0.4980 chunk 123 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 0.0170 chunk 154 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 overall best weight: 1.5024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.184289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.118065 restraints weight = 21355.210| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.69 r_work: 0.3154 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19296 Z= 0.157 Angle : 0.503 4.808 26262 Z= 0.274 Chirality : 0.043 0.132 2880 Planarity : 0.005 0.034 3348 Dihedral : 4.235 17.644 2466 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.66 % Allowed : 14.15 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.17), residues: 2268 helix: 2.19 (0.18), residues: 720 sheet: 0.33 (0.24), residues: 378 loop : -0.18 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 95 TYR 0.016 0.002 TYR J 32 PHE 0.011 0.001 PHE F 73 TRP 0.012 0.002 TRP I 88 HIS 0.004 0.001 HIS Q 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 (19296) covalent geometry : angle 0.50254 / 0.27 (26262) hydrogen bonds : bond 0.04556 / 3.00 ( 918) hydrogen bonds : angle 3.96169 / 2.82 ( 2484) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 249 time to evaluate : 0.551 Fit side-chains REVERT: A 82 ASP cc_start: 0.7913 (m-30) cc_final: 0.7452 (t0) REVERT: A 103 SER cc_start: 0.9092 (m) cc_final: 0.8507 (t) REVERT: A 108 ASP cc_start: 0.8151 (m-30) cc_final: 0.7878 (m-30) REVERT: B 82 ASP cc_start: 0.8021 (m-30) cc_final: 0.7581 (t70) REVERT: B 103 SER cc_start: 0.9045 (m) cc_final: 0.8417 (t) REVERT: C 32 TYR cc_start: 0.7329 (t80) cc_final: 0.7087 (t80) REVERT: C 103 SER cc_start: 0.8984 (m) cc_final: 0.8381 (t) REVERT: C 108 ASP cc_start: 0.8109 (m-30) cc_final: 0.7840 (m-30) REVERT: D 82 ASP cc_start: 0.7842 (m-30) cc_final: 0.7379 (t0) REVERT: D 103 SER cc_start: 0.9039 (m) cc_final: 0.8397 (t) REVERT: D 108 ASP cc_start: 0.8123 (m-30) cc_final: 0.7884 (m-30) REVERT: E 95 ARG cc_start: 0.8733 (mtm180) cc_final: 0.8399 (mtm180) REVERT: E 103 SER cc_start: 0.9066 (m) cc_final: 0.8414 (t) REVERT: E 108 ASP cc_start: 0.8140 (m-30) cc_final: 0.7907 (m-30) REVERT: F 82 ASP cc_start: 0.7907 (m-30) cc_final: 0.7475 (t0) REVERT: F 103 SER cc_start: 0.9019 (m) cc_final: 0.8385 (t) REVERT: G 82 ASP cc_start: 0.7798 (m-30) cc_final: 0.7381 (t70) REVERT: G 103 SER cc_start: 0.9031 (m) cc_final: 0.8415 (t) REVERT: G 108 ASP cc_start: 0.8074 (m-30) cc_final: 0.7639 (m-30) REVERT: H 82 ASP cc_start: 0.7807 (m-30) cc_final: 0.7466 (t0) REVERT: H 103 SER cc_start: 0.9078 (m) cc_final: 0.8451 (t) REVERT: H 108 ASP cc_start: 0.8063 (m-30) cc_final: 0.7858 (m-30) REVERT: H 119 LYS cc_start: 0.7064 (mttm) cc_final: 0.6860 (ttmt) REVERT: I 82 ASP cc_start: 0.7949 (m-30) cc_final: 0.7491 (t0) REVERT: I 103 SER cc_start: 0.9053 (m) cc_final: 0.8428 (t) REVERT: J 82 ASP cc_start: 0.7914 (m-30) cc_final: 0.7447 (t0) REVERT: J 103 SER cc_start: 0.9087 (m) cc_final: 0.8499 (t) REVERT: J 108 ASP cc_start: 0.8148 (m-30) cc_final: 0.7874 (m-30) REVERT: K 82 ASP cc_start: 0.8028 (m-30) cc_final: 0.7597 (t70) REVERT: K 103 SER cc_start: 0.9042 (m) cc_final: 0.8420 (t) REVERT: L 103 SER cc_start: 0.8967 (m) cc_final: 0.8340 (t) REVERT: L 108 ASP cc_start: 0.8122 (m-30) cc_final: 0.7759 (m-30) REVERT: M 82 ASP cc_start: 0.7789 (m-30) cc_final: 0.7319 (t0) REVERT: M 103 SER cc_start: 0.9037 (m) cc_final: 0.8401 (t) REVERT: M 108 ASP cc_start: 0.8113 (m-30) cc_final: 0.7873 (m-30) REVERT: N 103 SER cc_start: 0.9044 (m) cc_final: 0.8389 (t) REVERT: O 82 ASP cc_start: 0.7892 (m-30) cc_final: 0.7468 (t0) REVERT: O 103 SER cc_start: 0.9024 (m) cc_final: 0.8388 (t) REVERT: P 82 ASP cc_start: 0.7782 (m-30) cc_final: 0.7371 (t70) REVERT: P 95 ARG cc_start: 0.8774 (mtm180) cc_final: 0.8563 (mtp180) REVERT: P 103 SER cc_start: 0.9073 (m) cc_final: 0.8423 (t) REVERT: P 108 ASP cc_start: 0.8081 (m-30) cc_final: 0.7638 (m-30) REVERT: Q 82 ASP cc_start: 0.7808 (m-30) cc_final: 0.7474 (t0) REVERT: Q 103 SER cc_start: 0.9101 (m) cc_final: 0.8481 (t) REVERT: Q 108 ASP cc_start: 0.8068 (m-30) cc_final: 0.7863 (m-30) REVERT: R 36 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7355 (mm-30) REVERT: R 82 ASP cc_start: 0.7970 (m-30) cc_final: 0.7501 (t0) REVERT: R 103 SER cc_start: 0.9058 (m) cc_final: 0.8429 (t) outliers start: 55 outliers final: 45 residues processed: 302 average time/residue: 0.1308 time to fit residues: 60.6306 Evaluate side-chains 278 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 35 GLN Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 35 GLN Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 35 GLN Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 35 GLN Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain N residue 35 GLN Chi-restraints excluded: chain N residue 81 LYS Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain P residue 35 GLN Chi-restraints excluded: chain P residue 84 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 35 GLN Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain R residue 31 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 155 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 161 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 90 optimal weight: 0.1980 chunk 165 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.184442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.117982 restraints weight = 21465.981| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.74 r_work: 0.3144 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19296 Z= 0.150 Angle : 0.485 4.522 26262 Z= 0.268 Chirality : 0.043 0.129 2880 Planarity : 0.005 0.034 3348 Dihedral : 4.187 17.445 2466 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.80 % Allowed : 14.40 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.17), residues: 2268 helix: 2.15 (0.19), residues: 720 sheet: 0.47 (0.24), residues: 378 loop : -0.16 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 95 TYR 0.017 0.002 TYR D 32 PHE 0.011 0.001 PHE E 73 TRP 0.012 0.002 TRP Q 88 HIS 0.004 0.001 HIS M 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 (19296) covalent geometry : angle 0.48468 / 0.27 (26262) hydrogen bonds : bond 0.04341 / 2.86 ( 918) hydrogen bonds : angle 3.87295 / 2.76 ( 2484) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 260 time to evaluate : 0.431 Fit side-chains REVERT: A 82 ASP cc_start: 0.7862 (m-30) cc_final: 0.7365 (t0) REVERT: A 93 ASP cc_start: 0.7579 (t0) cc_final: 0.7311 (t0) REVERT: A 103 SER cc_start: 0.9117 (m) cc_final: 0.8555 (t) REVERT: A 108 ASP cc_start: 0.8145 (m-30) cc_final: 0.7832 (m-30) REVERT: B 82 ASP cc_start: 0.7920 (m-30) cc_final: 0.7487 (t70) REVERT: B 103 SER cc_start: 0.9075 (m) cc_final: 0.8444 (t) REVERT: C 82 ASP cc_start: 0.7792 (m-30) cc_final: 0.7330 (t70) REVERT: C 103 SER cc_start: 0.9002 (m) cc_final: 0.8388 (t) REVERT: C 108 ASP cc_start: 0.8118 (m-30) cc_final: 0.7815 (m-30) REVERT: D 82 ASP cc_start: 0.7827 (m-30) cc_final: 0.7334 (t0) REVERT: D 103 SER cc_start: 0.9038 (m) cc_final: 0.8412 (t) REVERT: D 108 ASP cc_start: 0.8118 (m-30) cc_final: 0.7882 (m-30) REVERT: E 82 ASP cc_start: 0.7272 (t0) cc_final: 0.7072 (t70) REVERT: E 103 SER cc_start: 0.9088 (m) cc_final: 0.8443 (t) REVERT: E 108 ASP cc_start: 0.8125 (m-30) cc_final: 0.7895 (m-30) REVERT: F 82 ASP cc_start: 0.7798 (m-30) cc_final: 0.7308 (t0) REVERT: F 103 SER cc_start: 0.9016 (m) cc_final: 0.8409 (t) REVERT: G 32 TYR cc_start: 0.7302 (t80) cc_final: 0.7027 (t80) REVERT: G 82 ASP cc_start: 0.7771 (m-30) cc_final: 0.7343 (t70) REVERT: G 103 SER cc_start: 0.9065 (m) cc_final: 0.8436 (t) REVERT: G 108 ASP cc_start: 0.8046 (m-30) cc_final: 0.7587 (m-30) REVERT: H 82 ASP cc_start: 0.7796 (m-30) cc_final: 0.7444 (t0) REVERT: H 93 ASP cc_start: 0.7698 (t0) cc_final: 0.7491 (t0) REVERT: H 103 SER cc_start: 0.9115 (m) cc_final: 0.8506 (t) REVERT: I 82 ASP cc_start: 0.7838 (m-30) cc_final: 0.7383 (t0) REVERT: I 103 SER cc_start: 0.9081 (m) cc_final: 0.8475 (t) REVERT: I 115 ARG cc_start: 0.7671 (mtm180) cc_final: 0.7452 (mtm180) REVERT: J 82 ASP cc_start: 0.7858 (m-30) cc_final: 0.7361 (t0) REVERT: J 93 ASP cc_start: 0.7578 (t0) cc_final: 0.7311 (t0) REVERT: J 103 SER cc_start: 0.9120 (m) cc_final: 0.8564 (t) REVERT: J 108 ASP cc_start: 0.8138 (m-30) cc_final: 0.7823 (m-30) REVERT: K 103 SER cc_start: 0.9089 (m) cc_final: 0.8466 (t) REVERT: L 82 ASP cc_start: 0.7807 (m-30) cc_final: 0.7341 (t70) REVERT: L 103 SER cc_start: 0.9002 (m) cc_final: 0.8391 (t) REVERT: L 108 ASP cc_start: 0.8115 (m-30) cc_final: 0.7749 (m-30) REVERT: M 82 ASP cc_start: 0.7830 (m-30) cc_final: 0.7335 (t0) REVERT: M 103 SER cc_start: 0.9037 (m) cc_final: 0.8411 (t) REVERT: M 108 ASP cc_start: 0.8099 (m-30) cc_final: 0.7849 (m-30) REVERT: N 82 ASP cc_start: 0.7275 (t0) cc_final: 0.7073 (t70) REVERT: N 103 SER cc_start: 0.9109 (m) cc_final: 0.8473 (t) REVERT: O 82 ASP cc_start: 0.7814 (m-30) cc_final: 0.7326 (t0) REVERT: O 103 SER cc_start: 0.9027 (m) cc_final: 0.8408 (t) REVERT: P 82 ASP cc_start: 0.7770 (m-30) cc_final: 0.7323 (t70) REVERT: P 103 SER cc_start: 0.9075 (m) cc_final: 0.8454 (t) REVERT: P 108 ASP cc_start: 0.8048 (m-30) cc_final: 0.7592 (m-30) REVERT: Q 82 ASP cc_start: 0.7787 (m-30) cc_final: 0.7440 (t0) REVERT: Q 93 ASP cc_start: 0.7683 (t0) cc_final: 0.7471 (t0) REVERT: Q 103 SER cc_start: 0.9115 (m) cc_final: 0.8512 (t) REVERT: R 82 ASP cc_start: 0.7885 (m-30) cc_final: 0.7410 (t0) REVERT: R 103 SER cc_start: 0.9100 (m) cc_final: 0.8488 (t) outliers start: 58 outliers final: 47 residues processed: 318 average time/residue: 0.1319 time to fit residues: 63.4575 Evaluate side-chains 282 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 235 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 35 GLN Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 35 GLN Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 35 GLN Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 35 GLN Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain N residue 35 GLN Chi-restraints excluded: chain N residue 81 LYS Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain P residue 35 GLN Chi-restraints excluded: chain P residue 84 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 35 GLN Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain R residue 31 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 30 optimal weight: 0.1980 chunk 161 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 210 optimal weight: 0.0670 chunk 70 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.189837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.124428 restraints weight = 20840.320| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.60 r_work: 0.3207 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 19296 Z= 0.092 Angle : 0.432 3.690 26262 Z= 0.236 Chirality : 0.041 0.121 2880 Planarity : 0.004 0.035 3348 Dihedral : 3.844 14.550 2466 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.88 % Allowed : 16.81 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.36 (0.17), residues: 2268 helix: 2.28 (0.20), residues: 720 sheet: 0.94 (0.25), residues: 378 loop : 0.07 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 95 TYR 0.013 0.001 TYR L 32 PHE 0.007 0.001 PHE C 73 TRP 0.012 0.001 TRP H 88 HIS 0.002 0.001 HIS P 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (19296) covalent geometry : angle 0.43207 / 0.24 (26262) hydrogen bonds : bond 0.03300 / 2.18 ( 918) hydrogen bonds : angle 3.77888 / 2.69 ( 2484) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 283 time to evaluate : 0.677 Fit side-chains REVERT: A 82 ASP cc_start: 0.7802 (m-30) cc_final: 0.7355 (t0) REVERT: A 103 SER cc_start: 0.9089 (m) cc_final: 0.8519 (t) REVERT: A 108 ASP cc_start: 0.8167 (m-30) cc_final: 0.7872 (m-30) REVERT: B 103 SER cc_start: 0.9041 (m) cc_final: 0.8426 (t) REVERT: C 82 ASP cc_start: 0.7838 (m-30) cc_final: 0.7439 (t70) REVERT: C 103 SER cc_start: 0.9048 (m) cc_final: 0.8421 (t) REVERT: C 108 ASP cc_start: 0.8172 (m-30) cc_final: 0.7836 (m-30) REVERT: D 70 GLU cc_start: 0.8271 (mp0) cc_final: 0.7923 (mp0) REVERT: D 82 ASP cc_start: 0.7880 (m-30) cc_final: 0.7372 (t0) REVERT: D 103 SER cc_start: 0.9068 (m) cc_final: 0.8391 (t) REVERT: D 108 ASP cc_start: 0.8117 (m-30) cc_final: 0.7842 (m-30) REVERT: E 82 ASP cc_start: 0.7235 (t0) cc_final: 0.7017 (t70) REVERT: E 103 SER cc_start: 0.9138 (m) cc_final: 0.8480 (t) REVERT: E 108 ASP cc_start: 0.8102 (m-30) cc_final: 0.7855 (m-30) REVERT: F 82 ASP cc_start: 0.7848 (m-30) cc_final: 0.7371 (t0) REVERT: F 103 SER cc_start: 0.9074 (m) cc_final: 0.8476 (t) REVERT: F 108 ASP cc_start: 0.8163 (m-30) cc_final: 0.7773 (m-30) REVERT: G 82 ASP cc_start: 0.7797 (m-30) cc_final: 0.7392 (t70) REVERT: G 103 SER cc_start: 0.9062 (m) cc_final: 0.8442 (t) REVERT: G 108 ASP cc_start: 0.8064 (m-30) cc_final: 0.7650 (m-30) REVERT: H 82 ASP cc_start: 0.7844 (m-30) cc_final: 0.7454 (t0) REVERT: H 103 SER cc_start: 0.9118 (m) cc_final: 0.8466 (t) REVERT: I 70 GLU cc_start: 0.8264 (mp0) cc_final: 0.7918 (mp0) REVERT: I 82 ASP cc_start: 0.7882 (m-30) cc_final: 0.7409 (t0) REVERT: I 103 SER cc_start: 0.9074 (m) cc_final: 0.8450 (t) REVERT: I 115 ARG cc_start: 0.7758 (mtm180) cc_final: 0.7538 (mtm180) REVERT: J 82 ASP cc_start: 0.7813 (m-30) cc_final: 0.7358 (t0) REVERT: J 103 SER cc_start: 0.9095 (m) cc_final: 0.8527 (t) REVERT: J 108 ASP cc_start: 0.8162 (m-30) cc_final: 0.7867 (m-30) REVERT: K 103 SER cc_start: 0.9043 (m) cc_final: 0.8429 (t) REVERT: L 32 TYR cc_start: 0.7280 (t80) cc_final: 0.7037 (t80) REVERT: L 82 ASP cc_start: 0.7843 (m-30) cc_final: 0.7450 (t70) REVERT: L 103 SER cc_start: 0.9071 (m) cc_final: 0.8445 (t) REVERT: L 108 ASP cc_start: 0.8141 (m-30) cc_final: 0.7797 (m-30) REVERT: M 82 ASP cc_start: 0.7863 (m-30) cc_final: 0.7373 (t0) REVERT: M 103 SER cc_start: 0.9072 (m) cc_final: 0.8395 (t) REVERT: M 108 ASP cc_start: 0.8116 (m-30) cc_final: 0.7818 (m-30) REVERT: N 82 ASP cc_start: 0.7255 (t0) cc_final: 0.7040 (t70) REVERT: N 103 SER cc_start: 0.9103 (m) cc_final: 0.8460 (t) REVERT: O 82 ASP cc_start: 0.7823 (m-30) cc_final: 0.7358 (t0) REVERT: O 103 SER cc_start: 0.9035 (m) cc_final: 0.8471 (t) REVERT: O 108 ASP cc_start: 0.8160 (m-30) cc_final: 0.7757 (m-30) REVERT: P 82 ASP cc_start: 0.7791 (m-30) cc_final: 0.7392 (t70) REVERT: P 103 SER cc_start: 0.9053 (m) cc_final: 0.8434 (t) REVERT: P 108 ASP cc_start: 0.8082 (m-30) cc_final: 0.7674 (m-30) REVERT: Q 82 ASP cc_start: 0.7794 (m-30) cc_final: 0.7434 (t0) REVERT: Q 103 SER cc_start: 0.9121 (m) cc_final: 0.8490 (t) REVERT: R 70 GLU cc_start: 0.8225 (mp0) cc_final: 0.7903 (mp0) REVERT: R 82 ASP cc_start: 0.7876 (m-30) cc_final: 0.7442 (t0) REVERT: R 103 SER cc_start: 0.9076 (m) cc_final: 0.8450 (t) outliers start: 39 outliers final: 31 residues processed: 318 average time/residue: 0.1313 time to fit residues: 62.3161 Evaluate side-chains 279 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 35 GLN Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 35 GLN Chi-restraints excluded: chain L residue 11 ASN Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 35 GLN Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain N residue 81 LYS Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain P residue 35 GLN Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 35 GLN Chi-restraints excluded: chain R residue 31 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 208 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 212 optimal weight: 0.6980 chunk 205 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 chunk 131 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.183225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.115041 restraints weight = 20963.978| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.70 r_work: 0.3136 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19296 Z= 0.143 Angle : 0.466 4.218 26262 Z= 0.255 Chirality : 0.042 0.121 2880 Planarity : 0.004 0.034 3348 Dihedral : 4.055 15.934 2466 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.84 % Allowed : 17.54 % Favored : 80.63 % 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 (0.17), residues: 2268 helix: 2.60 (0.19), residues: 720 sheet: 0.92 (0.25), residues: 378 loop : -0.00 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 115 TYR 0.022 0.002 TYR I 32 PHE 0.010 0.001 PHE I 73 TRP 0.009 0.001 TRP I 88 HIS 0.004 0.001 HIS M 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.14 (19296) covalent geometry : angle 0.46588 / 0.26 (26262) hydrogen bonds : bond 0.04035 / 2.66 ( 918) hydrogen bonds : angle 3.69895 / 2.64 ( 2484) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 273 time to evaluate : 0.697 Fit side-chains REVERT: A 82 ASP cc_start: 0.7823 (m-30) cc_final: 0.7335 (t0) REVERT: A 103 SER cc_start: 0.9116 (m) cc_final: 0.8567 (t) REVERT: A 108 ASP cc_start: 0.8156 (m-30) cc_final: 0.7845 (m-30) REVERT: B 32 TYR cc_start: 0.7476 (t80) cc_final: 0.7259 (t80) REVERT: B 103 SER cc_start: 0.9051 (m) cc_final: 0.8448 (t) REVERT: C 82 ASP cc_start: 0.7982 (m-30) cc_final: 0.7505 (t70) REVERT: C 103 SER cc_start: 0.9022 (m) cc_final: 0.8411 (t) REVERT: C 108 ASP cc_start: 0.8167 (m-30) cc_final: 0.7856 (m-30) REVERT: D 82 ASP cc_start: 0.7775 (m-30) cc_final: 0.7282 (t0) REVERT: D 103 SER cc_start: 0.9071 (m) cc_final: 0.8454 (t) REVERT: D 108 ASP cc_start: 0.8140 (m-30) cc_final: 0.7885 (m-30) REVERT: E 82 ASP cc_start: 0.7251 (t0) cc_final: 0.7036 (t70) REVERT: E 95 ARG cc_start: 0.8568 (mtm180) cc_final: 0.7731 (mtt-85) REVERT: E 103 SER cc_start: 0.9134 (m) cc_final: 0.8496 (t) REVERT: E 108 ASP cc_start: 0.8103 (m-30) cc_final: 0.7872 (m-30) REVERT: F 82 ASP cc_start: 0.7824 (m-30) cc_final: 0.7335 (t0) REVERT: F 103 SER cc_start: 0.9047 (m) cc_final: 0.8441 (t) REVERT: F 108 ASP cc_start: 0.8124 (m-30) cc_final: 0.7696 (m-30) REVERT: G 82 ASP cc_start: 0.7773 (m-30) cc_final: 0.7340 (t70) REVERT: G 103 SER cc_start: 0.9086 (m) cc_final: 0.8480 (t) REVERT: G 108 ASP cc_start: 0.8015 (m-30) cc_final: 0.7549 (m-30) REVERT: H 82 ASP cc_start: 0.7881 (m-30) cc_final: 0.7456 (t0) REVERT: H 103 SER cc_start: 0.9122 (m) cc_final: 0.8505 (t) REVERT: I 82 ASP cc_start: 0.7881 (m-30) cc_final: 0.7386 (t70) REVERT: I 103 SER cc_start: 0.9084 (m) cc_final: 0.8482 (t) REVERT: J 82 ASP cc_start: 0.7831 (m-30) cc_final: 0.7340 (t0) REVERT: J 103 SER cc_start: 0.9119 (m) cc_final: 0.8564 (t) REVERT: J 108 ASP cc_start: 0.8153 (m-30) cc_final: 0.7841 (m-30) REVERT: K 32 TYR cc_start: 0.7482 (t80) cc_final: 0.7268 (t80) REVERT: K 103 SER cc_start: 0.9077 (m) cc_final: 0.8476 (t) REVERT: L 32 TYR cc_start: 0.7293 (t80) cc_final: 0.7070 (t80) REVERT: L 82 ASP cc_start: 0.7785 (m-30) cc_final: 0.7294 (t70) REVERT: L 103 SER cc_start: 0.9016 (m) cc_final: 0.8407 (t) REVERT: L 108 ASP cc_start: 0.8149 (m-30) cc_final: 0.7819 (m-30) REVERT: M 82 ASP cc_start: 0.7775 (m-30) cc_final: 0.7287 (t0) REVERT: M 103 SER cc_start: 0.9062 (m) cc_final: 0.8438 (t) REVERT: M 108 ASP cc_start: 0.8127 (m-30) cc_final: 0.7865 (m-30) REVERT: N 82 ASP cc_start: 0.7267 (t0) cc_final: 0.7057 (t70) REVERT: N 103 SER cc_start: 0.9105 (m) cc_final: 0.8489 (t) REVERT: O 82 ASP cc_start: 0.7788 (m-30) cc_final: 0.7290 (t0) REVERT: O 103 SER cc_start: 0.9071 (m) cc_final: 0.8485 (t) REVERT: O 108 ASP cc_start: 0.8121 (m-30) cc_final: 0.7694 (m-30) REVERT: P 82 ASP cc_start: 0.7933 (m-30) cc_final: 0.7504 (t70) REVERT: P 103 SER cc_start: 0.9050 (m) cc_final: 0.8471 (t) REVERT: P 108 ASP cc_start: 0.8030 (m-30) cc_final: 0.7564 (m-30) REVERT: Q 82 ASP cc_start: 0.7871 (m-30) cc_final: 0.7464 (t0) REVERT: Q 103 SER cc_start: 0.9121 (m) cc_final: 0.8508 (t) REVERT: R 82 ASP cc_start: 0.7861 (m-30) cc_final: 0.7388 (t70) REVERT: R 103 SER cc_start: 0.9092 (m) cc_final: 0.8491 (t) outliers start: 38 outliers final: 36 residues processed: 310 average time/residue: 0.1401 time to fit residues: 65.6788 Evaluate side-chains 303 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 267 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 35 GLN Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 35 GLN Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 35 GLN Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain N residue 81 LYS Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain P residue 35 GLN Chi-restraints excluded: chain P residue 84 THR Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 35 GLN Chi-restraints excluded: chain R residue 31 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 176 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 150 optimal weight: 0.0020 chunk 88 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.178442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116840 restraints weight = 20064.040| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.26 r_work: 0.3129 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19296 Z= 0.181 Angle : 0.504 4.491 26262 Z= 0.282 Chirality : 0.043 0.130 2880 Planarity : 0.005 0.034 3348 Dihedral : 4.250 17.157 2466 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.03 % Allowed : 18.16 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.17), residues: 2268 helix: 2.58 (0.20), residues: 720 sheet: 0.86 (0.24), residues: 378 loop : -0.12 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 115 TYR 0.024 0.002 TYR R 32 PHE 0.012 0.002 PHE I 73 TRP 0.008 0.001 TRP R 88 HIS 0.005 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.18 (19296) covalent geometry : angle 0.50443 / 0.28 (26262) hydrogen bonds : bond 0.04429 / 2.91 ( 918) hydrogen bonds : angle 3.79601 / 2.70 ( 2484) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 279 time to evaluate : 0.706 Fit side-chains REVERT: A 11 ASN cc_start: 0.6590 (t0) cc_final: 0.6333 (t0) REVERT: A 82 ASP cc_start: 0.7720 (m-30) cc_final: 0.7222 (t0) REVERT: A 103 SER cc_start: 0.9166 (m) cc_final: 0.8594 (t) REVERT: A 108 ASP cc_start: 0.8123 (m-30) cc_final: 0.7818 (m-30) REVERT: B 32 TYR cc_start: 0.7577 (t80) cc_final: 0.7366 (t80) REVERT: B 103 SER cc_start: 0.9092 (m) cc_final: 0.8525 (t) REVERT: C 82 ASP cc_start: 0.7876 (m-30) cc_final: 0.7467 (t0) REVERT: C 103 SER cc_start: 0.9021 (m) cc_final: 0.8436 (t) REVERT: C 108 ASP cc_start: 0.8133 (m-30) cc_final: 0.7864 (m-30) REVERT: D 82 ASP cc_start: 0.7787 (m-30) cc_final: 0.7323 (t70) REVERT: D 103 SER cc_start: 0.9082 (m) cc_final: 0.8489 (t) REVERT: D 108 ASP cc_start: 0.8136 (m-30) cc_final: 0.7894 (m-30) REVERT: E 82 ASP cc_start: 0.7228 (t0) cc_final: 0.7007 (t70) REVERT: E 95 ARG cc_start: 0.8570 (mtm180) cc_final: 0.7739 (mtt-85) REVERT: E 103 SER cc_start: 0.9131 (m) cc_final: 0.8507 (t) REVERT: E 108 ASP cc_start: 0.8079 (m-30) cc_final: 0.7840 (m-30) REVERT: F 82 ASP cc_start: 0.7702 (m-30) cc_final: 0.7222 (t0) REVERT: F 103 SER cc_start: 0.9094 (m) cc_final: 0.8480 (t) REVERT: G 82 ASP cc_start: 0.7719 (m-30) cc_final: 0.7268 (t70) REVERT: G 103 SER cc_start: 0.9146 (m) cc_final: 0.8520 (t) REVERT: G 108 ASP cc_start: 0.7994 (m-30) cc_final: 0.7502 (m-30) REVERT: H 82 ASP cc_start: 0.7846 (m-30) cc_final: 0.7413 (t0) REVERT: H 103 SER cc_start: 0.9151 (m) cc_final: 0.8561 (t) REVERT: I 82 ASP cc_start: 0.7894 (m-30) cc_final: 0.7375 (t70) REVERT: I 103 SER cc_start: 0.9129 (m) cc_final: 0.8517 (t) REVERT: J 11 ASN cc_start: 0.6605 (t0) cc_final: 0.6347 (t0) REVERT: J 82 ASP cc_start: 0.7716 (m-30) cc_final: 0.7219 (t0) REVERT: J 103 SER cc_start: 0.9157 (m) cc_final: 0.8587 (t) REVERT: J 108 ASP cc_start: 0.8123 (m-30) cc_final: 0.7816 (m-30) REVERT: K 32 TYR cc_start: 0.7562 (t80) cc_final: 0.7359 (t80) REVERT: K 103 SER cc_start: 0.9083 (m) cc_final: 0.8520 (t) REVERT: L 82 ASP cc_start: 0.7785 (m-30) cc_final: 0.7348 (t70) REVERT: L 103 SER cc_start: 0.9028 (m) cc_final: 0.8446 (t) REVERT: L 108 ASP cc_start: 0.8128 (m-30) cc_final: 0.7781 (m-30) REVERT: M 82 ASP cc_start: 0.7804 (m-30) cc_final: 0.7340 (t70) REVERT: M 103 SER cc_start: 0.9089 (m) cc_final: 0.8499 (t) REVERT: M 108 ASP cc_start: 0.8122 (m-30) cc_final: 0.7866 (m-30) REVERT: N 82 ASP cc_start: 0.7238 (t0) cc_final: 0.7016 (t70) REVERT: N 103 SER cc_start: 0.9118 (m) cc_final: 0.8538 (t) REVERT: O 82 ASP cc_start: 0.7702 (m-30) cc_final: 0.7214 (t0) REVERT: O 103 SER cc_start: 0.9094 (m) cc_final: 0.8501 (t) REVERT: P 32 TYR cc_start: 0.7403 (t80) cc_final: 0.7058 (t80) REVERT: P 82 ASP cc_start: 0.7933 (m-30) cc_final: 0.7462 (t70) REVERT: P 103 SER cc_start: 0.9077 (m) cc_final: 0.8497 (t) REVERT: P 108 ASP cc_start: 0.8002 (m-30) cc_final: 0.7511 (m-30) REVERT: Q 82 ASP cc_start: 0.7805 (m-30) cc_final: 0.7393 (t0) REVERT: Q 103 SER cc_start: 0.9153 (m) cc_final: 0.8574 (t) REVERT: R 82 ASP cc_start: 0.7856 (m-30) cc_final: 0.7370 (t70) REVERT: R 103 SER cc_start: 0.9134 (m) cc_final: 0.8538 (t) outliers start: 42 outliers final: 40 residues processed: 321 average time/residue: 0.1328 time to fit residues: 65.8686 Evaluate side-chains 312 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 272 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 35 GLN Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 35 GLN Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 35 GLN Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain N residue 81 LYS Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain P residue 35 GLN Chi-restraints excluded: chain P residue 84 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 35 GLN Chi-restraints excluded: chain Q residue 121 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 42 optimal weight: 0.0770 chunk 97 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.182514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.114087 restraints weight = 20799.366| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.76 r_work: 0.3123 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19296 Z= 0.146 Angle : 0.481 4.478 26262 Z= 0.270 Chirality : 0.042 0.122 2880 Planarity : 0.005 0.036 3348 Dihedral : 4.129 16.300 2466 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.74 % Allowed : 19.37 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.40 (0.17), residues: 2268 helix: 2.53 (0.20), residues: 720 sheet: 0.94 (0.24), residues: 378 loop : -0.06 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 115 TYR 0.023 0.002 TYR C 32 PHE 0.015 0.001 PHE E 94 TRP 0.009 0.001 TRP R 88 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (19296) covalent geometry : angle 0.48142 / 0.27 (26262) hydrogen bonds : bond 0.03961 / 2.61 ( 918) hydrogen bonds : angle 3.73308 / 2.66 ( 2484) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 270 time to evaluate : 0.744 Fit side-chains REVERT: A 82 ASP cc_start: 0.7710 (m-30) cc_final: 0.7209 (t0) REVERT: A 95 ARG cc_start: 0.8394 (mtm180) cc_final: 0.7878 (mtm-85) REVERT: A 103 SER cc_start: 0.9134 (m) cc_final: 0.8577 (t) REVERT: A 108 ASP cc_start: 0.8071 (m-30) cc_final: 0.7759 (m-30) REVERT: B 103 SER cc_start: 0.9060 (m) cc_final: 0.8488 (t) REVERT: C 82 ASP cc_start: 0.7857 (m-30) cc_final: 0.7429 (t0) REVERT: C 103 SER cc_start: 0.9023 (m) cc_final: 0.8444 (t) REVERT: C 108 ASP cc_start: 0.8140 (m-30) cc_final: 0.7847 (m-30) REVERT: D 82 ASP cc_start: 0.7900 (m-30) cc_final: 0.7420 (t70) REVERT: D 103 SER cc_start: 0.9087 (m) cc_final: 0.8493 (t) REVERT: D 108 ASP cc_start: 0.8100 (m-30) cc_final: 0.7841 (m-30) REVERT: E 82 ASP cc_start: 0.7228 (t0) cc_final: 0.7021 (t70) REVERT: E 95 ARG cc_start: 0.8598 (mtm180) cc_final: 0.8086 (mtm-85) REVERT: E 103 SER cc_start: 0.9145 (m) cc_final: 0.8533 (t) REVERT: E 108 ASP cc_start: 0.8038 (m-30) cc_final: 0.7792 (m-30) REVERT: F 82 ASP cc_start: 0.7829 (m-30) cc_final: 0.7308 (t0) REVERT: F 103 SER cc_start: 0.9064 (m) cc_final: 0.8454 (t) REVERT: F 108 ASP cc_start: 0.8119 (m-30) cc_final: 0.7684 (m-30) REVERT: G 82 ASP cc_start: 0.7928 (m-30) cc_final: 0.7464 (t70) REVERT: G 103 SER cc_start: 0.9117 (m) cc_final: 0.8515 (t) REVERT: G 108 ASP cc_start: 0.7969 (m-30) cc_final: 0.7498 (m-30) REVERT: H 32 TYR cc_start: 0.7439 (t80) cc_final: 0.7232 (t80) REVERT: H 103 SER cc_start: 0.9132 (m) cc_final: 0.8544 (t) REVERT: I 82 ASP cc_start: 0.7911 (m-30) cc_final: 0.7381 (t70) REVERT: I 95 ARG cc_start: 0.8691 (mtm180) cc_final: 0.8200 (mtm-85) REVERT: I 103 SER cc_start: 0.9123 (m) cc_final: 0.8523 (t) REVERT: I 115 ARG cc_start: 0.7679 (mtm180) cc_final: 0.7446 (mtm180) REVERT: J 82 ASP cc_start: 0.7715 (m-30) cc_final: 0.7207 (t0) REVERT: J 95 ARG cc_start: 0.8398 (mtm180) cc_final: 0.7882 (mtm-85) REVERT: J 103 SER cc_start: 0.9149 (m) cc_final: 0.8590 (t) REVERT: J 108 ASP cc_start: 0.8068 (m-30) cc_final: 0.7753 (m-30) REVERT: K 103 SER cc_start: 0.9065 (m) cc_final: 0.8499 (t) REVERT: L 82 ASP cc_start: 0.7711 (m-30) cc_final: 0.7296 (t70) REVERT: L 93 ASP cc_start: 0.7683 (t0) cc_final: 0.7456 (t0) REVERT: L 103 SER cc_start: 0.9043 (m) cc_final: 0.8471 (t) REVERT: L 108 ASP cc_start: 0.8113 (m-30) cc_final: 0.7750 (m-30) REVERT: M 82 ASP cc_start: 0.7914 (m-30) cc_final: 0.7446 (t70) REVERT: M 103 SER cc_start: 0.9075 (m) cc_final: 0.8487 (t) REVERT: M 108 ASP cc_start: 0.8072 (m-30) cc_final: 0.7805 (m-30) REVERT: N 32 TYR cc_start: 0.7274 (t80) cc_final: 0.6987 (t80) REVERT: N 82 ASP cc_start: 0.7236 (t0) cc_final: 0.7030 (t70) REVERT: N 103 SER cc_start: 0.9113 (m) cc_final: 0.8538 (t) REVERT: O 82 ASP cc_start: 0.7819 (m-30) cc_final: 0.7295 (t0) REVERT: O 103 SER cc_start: 0.9067 (m) cc_final: 0.8492 (t) REVERT: O 108 ASP cc_start: 0.8097 (m-30) cc_final: 0.7661 (m-30) REVERT: P 32 TYR cc_start: 0.7429 (t80) cc_final: 0.7229 (t80) REVERT: P 103 SER cc_start: 0.9068 (m) cc_final: 0.8500 (t) REVERT: P 108 ASP cc_start: 0.7991 (m-30) cc_final: 0.7519 (m-30) REVERT: Q 103 SER cc_start: 0.9145 (m) cc_final: 0.8573 (t) REVERT: R 82 ASP cc_start: 0.7874 (m-30) cc_final: 0.7366 (t70) REVERT: R 95 ARG cc_start: 0.8699 (mtm180) cc_final: 0.8206 (mtm-85) REVERT: R 103 SER cc_start: 0.9121 (m) cc_final: 0.8516 (t) outliers start: 36 outliers final: 36 residues processed: 306 average time/residue: 0.1301 time to fit residues: 60.7475 Evaluate side-chains 297 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 261 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 35 GLN Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 35 GLN Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain L residue 35 GLN Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain N residue 81 LYS Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain P residue 35 GLN Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 35 GLN Chi-restraints excluded: chain Q residue 121 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 105 optimal weight: 3.9990 chunk 201 optimal weight: 0.0070 chunk 124 optimal weight: 0.0050 chunk 162 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 186 optimal weight: 0.5980 chunk 138 optimal weight: 0.2980 chunk 81 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 overall best weight: 0.3212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.188922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.120835 restraints weight = 20947.595| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.82 r_work: 0.3189 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 19296 Z= 0.087 Angle : 0.429 3.704 26262 Z= 0.241 Chirality : 0.040 0.124 2880 Planarity : 0.005 0.037 3348 Dihedral : 3.712 12.502 2466 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.01 % Allowed : 20.05 % Favored : 78.94 % 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: 1.67 (0.18), residues: 2268 helix: 2.55 (0.20), residues: 720 sheet: 1.43 (0.26), residues: 378 loop : 0.12 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 95 TYR 0.017 0.001 TYR E 32 PHE 0.014 0.001 PHE C 94 TRP 0.010 0.001 TRP R 88 HIS 0.002 0.000 HIS Q 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00184 / 0.09 (19296) covalent geometry : angle 0.42853 / 0.24 (26262) hydrogen bonds : bond 0.02955 / 1.95 ( 918) hydrogen bonds : angle 3.58793 / 2.57 ( 2484) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 283 time to evaluate : 0.730 Fit side-chains REVERT: A 11 ASN cc_start: 0.6478 (t0) cc_final: 0.6255 (m-40) REVERT: A 82 ASP cc_start: 0.7942 (m-30) cc_final: 0.7468 (t70) REVERT: A 95 ARG cc_start: 0.8364 (mtm180) cc_final: 0.7844 (mtm-85) REVERT: A 103 SER cc_start: 0.9065 (m) cc_final: 0.8521 (t) REVERT: A 108 ASP cc_start: 0.8004 (m-30) cc_final: 0.7717 (m-30) REVERT: B 103 SER cc_start: 0.8995 (m) cc_final: 0.8391 (t) REVERT: C 70 GLU cc_start: 0.8302 (mp0) cc_final: 0.7922 (mp0) REVERT: C 82 ASP cc_start: 0.8044 (m-30) cc_final: 0.7617 (t70) REVERT: C 103 SER cc_start: 0.9043 (m) cc_final: 0.8424 (t) REVERT: C 108 ASP cc_start: 0.8105 (m-30) cc_final: 0.7745 (m-30) REVERT: D 70 GLU cc_start: 0.8265 (mp0) cc_final: 0.7956 (mp0) REVERT: D 95 ARG cc_start: 0.8466 (mtm180) cc_final: 0.7944 (mtm-85) REVERT: D 103 SER cc_start: 0.9065 (m) cc_final: 0.8430 (t) REVERT: D 108 ASP cc_start: 0.8043 (m-30) cc_final: 0.7758 (m-30) REVERT: E 95 ARG cc_start: 0.8561 (mtm180) cc_final: 0.8075 (mtm-85) REVERT: E 103 SER cc_start: 0.9100 (m) cc_final: 0.8429 (t) REVERT: E 108 ASP cc_start: 0.8016 (m-30) cc_final: 0.7740 (m-30) REVERT: F 82 ASP cc_start: 0.8017 (m-30) cc_final: 0.7504 (t70) REVERT: F 103 SER cc_start: 0.8993 (m) cc_final: 0.8461 (t) REVERT: F 108 ASP cc_start: 0.8014 (m-30) cc_final: 0.7627 (m-30) REVERT: G 103 SER cc_start: 0.9044 (m) cc_final: 0.8439 (t) REVERT: H 70 GLU cc_start: 0.8313 (mp0) cc_final: 0.8107 (mp0) REVERT: H 103 SER cc_start: 0.9100 (m) cc_final: 0.8487 (t) REVERT: I 70 GLU cc_start: 0.8270 (mp0) cc_final: 0.7883 (mp0) REVERT: I 95 ARG cc_start: 0.8618 (mtm180) cc_final: 0.8095 (mtm-85) REVERT: I 103 SER cc_start: 0.9066 (m) cc_final: 0.8458 (t) REVERT: I 115 ARG cc_start: 0.7645 (mtm180) cc_final: 0.7400 (mtm180) REVERT: J 11 ASN cc_start: 0.6465 (t0) cc_final: 0.6244 (m-40) REVERT: J 82 ASP cc_start: 0.7932 (m-30) cc_final: 0.7457 (t70) REVERT: J 95 ARG cc_start: 0.8357 (mtm180) cc_final: 0.7842 (mtm-85) REVERT: J 103 SER cc_start: 0.9078 (m) cc_final: 0.8533 (t) REVERT: J 108 ASP cc_start: 0.7992 (m-30) cc_final: 0.7704 (m-30) REVERT: K 103 SER cc_start: 0.8998 (m) cc_final: 0.8395 (t) REVERT: L 82 ASP cc_start: 0.7732 (m-30) cc_final: 0.7291 (t70) REVERT: L 103 SER cc_start: 0.9049 (m) cc_final: 0.8431 (t) REVERT: L 108 ASP cc_start: 0.8051 (m-30) cc_final: 0.7733 (m-30) REVERT: M 95 ARG cc_start: 0.8442 (mtm180) cc_final: 0.7920 (mtm-85) REVERT: M 103 SER cc_start: 0.9075 (m) cc_final: 0.8443 (t) REVERT: M 108 ASP cc_start: 0.8035 (m-30) cc_final: 0.7737 (m-30) REVERT: N 103 SER cc_start: 0.9048 (m) cc_final: 0.8417 (t) REVERT: O 82 ASP cc_start: 0.8098 (m-30) cc_final: 0.7570 (t70) REVERT: O 103 SER cc_start: 0.9052 (m) cc_final: 0.8444 (t) REVERT: O 108 ASP cc_start: 0.8007 (m-30) cc_final: 0.7619 (m-30) REVERT: P 32 TYR cc_start: 0.7340 (t80) cc_final: 0.6869 (t80) REVERT: P 103 SER cc_start: 0.9036 (m) cc_final: 0.8432 (t) REVERT: Q 70 GLU cc_start: 0.8319 (mp0) cc_final: 0.8117 (mp0) REVERT: Q 103 SER cc_start: 0.9121 (m) cc_final: 0.8527 (t) REVERT: R 70 GLU cc_start: 0.8244 (mp0) cc_final: 0.7864 (mp0) REVERT: R 95 ARG cc_start: 0.8645 (mtm180) cc_final: 0.8113 (mtm-85) REVERT: R 103 SER cc_start: 0.9072 (m) cc_final: 0.8449 (t) outliers start: 21 outliers final: 15 residues processed: 304 average time/residue: 0.1563 time to fit residues: 69.2368 Evaluate side-chains 288 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 273 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 35 GLN Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain P residue 35 GLN Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 35 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 66 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 25 optimal weight: 0.0470 chunk 97 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.184084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.115481 restraints weight = 20961.050| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.79 r_work: 0.3070 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19296 Z= 0.134 Angle : 0.470 5.194 26262 Z= 0.263 Chirality : 0.042 0.122 2880 Planarity : 0.005 0.033 3348 Dihedral : 3.933 14.046 2466 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.97 % Allowed : 20.48 % Favored : 78.55 % 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: 1.61 (0.18), residues: 2268 helix: 2.56 (0.19), residues: 720 sheet: 1.36 (0.25), residues: 378 loop : 0.05 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 115 TYR 0.025 0.001 TYR B 32 PHE 0.016 0.001 PHE N 94 TRP 0.009 0.001 TRP R 88 HIS 0.004 0.001 HIS Q 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.13 (19296) covalent geometry : angle 0.46990 / 0.26 (26262) hydrogen bonds : bond 0.03838 / 2.53 ( 918) hydrogen bonds : angle 3.64365 / 2.60 ( 2484) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4034.33 seconds wall clock time: 70 minutes 7.60 seconds (4207.60 seconds total)