Starting phenix.real_space_refine on Sun Aug 24 09:19:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pq8_17821/08_2025/8pq8_17821.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pq8_17821/08_2025/8pq8_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8pq8_17821/08_2025/8pq8_17821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pq8_17821/08_2025/8pq8_17821.map" model { file = "/net/cci-nas-00/data/ceres_data/8pq8_17821/08_2025/8pq8_17821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pq8_17821/08_2025/8pq8_17821.cif" } 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-2.0-5787/lib/python3.9/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: 4.73, per 1000 atoms: 0.25 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: 1.66 Conformation dependent library (CDL) restraints added in 856.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.11 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: 3.94 Time building geometry restraints manager: 2.19 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: 0.07 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: 6.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.480 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.070 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 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 aren 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 covalent geometry : bond 0.01129 (19296) covalent geometry : angle 1.48625 (26262) hydrogen bonds : bond 0.25955 ( 918) hydrogen bonds : angle 7.19379 ( 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 : 0.752 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: 0.1792 time to fit residues: 109.6477 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 : 0.741 ------------------------------------------------------------------------------- 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: 0.0270 chunk 194 optimal weight: 0.0980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 0.0070 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 77 optimal weight: 0.0870 overall best weight: 0.0834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4108 r_free = 0.4108 target = 0.188863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.126096 restraints weight = 20956.263| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.48 r_work: 0.3265 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.275 19296 Z= 0.475 Angle : 1.527 37.488 26262 Z= 0.823 Chirality : 0.066 0.641 2880 Planarity : 0.017 0.192 3348 Dihedral : 6.098 28.777 2466 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.50 % Favored : 98.19 % Rotamer: Outliers : 3.29 % Allowed : 11.88 % Favored : 84.83 % Cbeta Deviations : 0.05 % 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 aren not related in a simple way. whole: -1.43 (0.15), residues: 2268 helix: -0.79 (0.16), residues: 666 sheet: -0.05 (0.23), residues: 396 loop : -1.33 (0.15), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.096 0.011 ARG P 95 TYR 0.202 0.013 TYR B 32 PHE 0.117 0.008 PHE L 62 TRP 0.141 0.014 TRP H 30 HIS 0.065 0.006 HIS O 18 Details of bonding type rmsd covalent geometry : bond 0.01079 (19296) covalent geometry : angle 1.52686 (26262) hydrogen bonds : bond 0.11334 ( 918) hydrogen bonds : angle 5.91001 ( 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 384 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 316 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 SER cc_start: 0.8683 (m) cc_final: 0.8211 (t) REVERT: B 42 PRO cc_start: 0.9232 (Cg_endo) cc_final: 0.9004 (Cg_endo) REVERT: B 56 ILE cc_start: 0.8072 (mm) cc_final: 0.7820 (mt) REVERT: B 103 SER cc_start: 0.8698 (m) cc_final: 0.8215 (t) REVERT: C 103 SER cc_start: 0.8659 (m) cc_final: 0.8202 (t) REVERT: D 103 SER cc_start: 0.8763 (m) cc_final: 0.8224 (t) REVERT: E 32 TYR cc_start: 0.7091 (t80) cc_final: 0.6845 (t80) REVERT: E 93 ASP cc_start: 0.7365 (m-30) cc_final: 0.7109 (t0) REVERT: E 103 SER cc_start: 0.8762 (m) cc_final: 0.8268 (t) REVERT: F 103 SER cc_start: 0.8631 (m) cc_final: 0.8161 (t) REVERT: G 103 SER cc_start: 0.8557 (m) cc_final: 0.8182 (t) REVERT: H 103 SER cc_start: 0.8752 (m) cc_final: 0.8328 (t) REVERT: I 103 SER cc_start: 0.8624 (m) cc_final: 0.8142 (t) REVERT: J 103 SER cc_start: 0.8701 (m) cc_final: 0.8196 (t) REVERT: K 103 SER cc_start: 0.8790 (m) cc_final: 0.8263 (t) REVERT: L 103 SER cc_start: 0.8626 (m) cc_final: 0.8082 (t) REVERT: M 103 SER cc_start: 0.8852 (m) cc_final: 0.8297 (t) REVERT: N 103 SER cc_start: 0.8835 (m) cc_final: 0.8280 (t) REVERT: O 103 SER cc_start: 0.8613 (m) cc_final: 0.8157 (t) REVERT: P 103 SER cc_start: 0.8753 (m) cc_final: 0.8223 (t) REVERT: Q 103 SER cc_start: 0.8678 (m) cc_final: 0.8152 (t) REVERT: R 42 PRO cc_start: 0.9249 (Cg_endo) cc_final: 0.9040 (Cg_endo) REVERT: R 93 ASP cc_start: 0.7457 (m-30) cc_final: 0.7037 (t0) REVERT: R 95 ARG cc_start: 0.8582 (mtm180) cc_final: 0.7994 (mtm180) REVERT: R 103 SER cc_start: 0.8910 (m) cc_final: 0.8431 (t) outliers start: 68 outliers final: 41 residues processed: 358 average time/residue: 0.1426 time to fit residues: 78.8072 Evaluate side-chains 327 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 286 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain B residue 31 SER 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 45 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain K residue 32 TYR 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 M residue 31 SER Chi-restraints excluded: chain M residue 83 SER Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 32 TYR 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 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 R residue 31 SER Chi-restraints excluded: chain R residue 98 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 185 optimal weight: 0.0030 chunk 21 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 0.1980 chunk 200 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 125 optimal weight: 0.3980 chunk 133 optimal weight: 9.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.190265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125616 restraints weight = 21360.573| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.68 r_work: 0.3205 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19296 Z= 0.106 Angle : 0.516 6.279 26262 Z= 0.282 Chirality : 0.041 0.121 2880 Planarity : 0.005 0.057 3348 Dihedral : 4.439 18.986 2466 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.92 % Allowed : 11.79 % Favored : 87.29 % 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 aren not related in a simple way. whole: 0.52 (0.16), residues: 2268 helix: 1.34 (0.18), residues: 720 sheet: 0.56 (0.24), residues: 396 loop : -0.31 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 115 TYR 0.025 0.002 TYR H 32 PHE 0.012 0.001 PHE H 73 TRP 0.022 0.002 TRP Q 88 HIS 0.004 0.001 HIS P 124 Details of bonding type rmsd covalent geometry : bond 0.00223 (19296) covalent geometry : angle 0.51588 (26262) hydrogen bonds : bond 0.03823 ( 918) hydrogen bonds : angle 4.30833 ( 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 375 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 356 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 SER cc_start: 0.8760 (m) cc_final: 0.8145 (t) REVERT: A 108 ASP cc_start: 0.7912 (m-30) cc_final: 0.7648 (m-30) REVERT: B 103 SER cc_start: 0.8813 (m) cc_final: 0.8084 (t) REVERT: C 95 ARG cc_start: 0.8654 (mtm180) cc_final: 0.8359 (mtm180) REVERT: C 103 SER cc_start: 0.8707 (m) cc_final: 0.8043 (t) REVERT: D 103 SER cc_start: 0.8767 (m) cc_final: 0.8063 (t) REVERT: E 93 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.7084 (t0) REVERT: E 95 ARG cc_start: 0.8611 (mtm180) cc_final: 0.8216 (mtm180) REVERT: E 103 SER cc_start: 0.8736 (m) cc_final: 0.8050 (t) REVERT: F 32 TYR cc_start: 0.7007 (t80) cc_final: 0.6768 (t80) REVERT: F 103 SER cc_start: 0.8648 (m) cc_final: 0.8015 (t) REVERT: G 82 ASP cc_start: 0.7886 (m-30) cc_final: 0.7507 (t70) REVERT: G 103 SER cc_start: 0.8772 (m) cc_final: 0.8107 (t) REVERT: H 103 SER cc_start: 0.8741 (m) cc_final: 0.7961 (t) REVERT: H 119 LYS cc_start: 0.6957 (mttm) cc_final: 0.6742 (ttmt) REVERT: I 32 TYR cc_start: 0.7033 (t80) cc_final: 0.6589 (t80) REVERT: I 103 SER cc_start: 0.8819 (m) cc_final: 0.8154 (t) REVERT: J 103 SER cc_start: 0.8770 (m) cc_final: 0.8133 (t) REVERT: K 103 SER cc_start: 0.8818 (m) cc_final: 0.8062 (t) REVERT: L 103 SER cc_start: 0.8680 (m) cc_final: 0.7978 (t) REVERT: L 108 ASP cc_start: 0.7898 (m-30) cc_final: 0.7663 (m-30) REVERT: M 103 SER cc_start: 0.8786 (m) cc_final: 0.8019 (t) REVERT: N 103 SER cc_start: 0.8784 (m) cc_final: 0.8046 (t) REVERT: O 103 SER cc_start: 0.8709 (m) cc_final: 0.8046 (t) REVERT: P 103 SER cc_start: 0.8812 (m) cc_final: 0.8109 (t) REVERT: Q 93 ASP cc_start: 0.7071 (m-30) cc_final: 0.6844 (t0) REVERT: Q 103 SER cc_start: 0.8773 (m) cc_final: 0.8031 (t) REVERT: R 103 SER cc_start: 0.8863 (m) cc_final: 0.8335 (t) outliers start: 19 outliers final: 14 residues processed: 374 average time/residue: 0.1580 time to fit residues: 88.2460 Evaluate side-chains 298 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 283 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain L residue 35 GLN Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain N residue 35 GLN Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain P residue 35 GLN 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: 3.9990 chunk 123 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 154 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.182680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.115481 restraints weight = 21153.068| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.69 r_work: 0.3164 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19296 Z= 0.165 Angle : 0.546 6.774 26262 Z= 0.296 Chirality : 0.044 0.150 2880 Planarity : 0.005 0.044 3348 Dihedral : 4.516 18.880 2466 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.95 % Allowed : 12.56 % Favored : 84.49 % 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 aren not related in a simple way. whole: 0.83 (0.17), residues: 2268 helix: 1.96 (0.18), residues: 720 sheet: 0.55 (0.24), residues: 378 loop : -0.32 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 115 TYR 0.025 0.002 TYR M 32 PHE 0.015 0.002 PHE J 73 TRP 0.021 0.002 TRP Q 88 HIS 0.005 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00419 (19296) covalent geometry : angle 0.54644 (26262) hydrogen bonds : bond 0.04909 ( 918) hydrogen bonds : angle 4.01956 ( 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 320 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 259 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 SER cc_start: 0.8975 (m) cc_final: 0.8381 (t) REVERT: A 108 ASP cc_start: 0.8074 (m-30) cc_final: 0.7775 (m-30) REVERT: B 103 SER cc_start: 0.9051 (m) cc_final: 0.8346 (t) REVERT: C 103 SER cc_start: 0.8883 (m) cc_final: 0.8254 (t) REVERT: C 108 ASP cc_start: 0.8018 (m-30) cc_final: 0.7750 (m-30) REVERT: D 103 SER cc_start: 0.9042 (m) cc_final: 0.8351 (t) REVERT: D 119 LYS cc_start: 0.7099 (mttm) cc_final: 0.6893 (ttmt) REVERT: E 93 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7173 (t0) REVERT: E 95 ARG cc_start: 0.8707 (mtm180) cc_final: 0.8361 (mtm180) REVERT: E 103 SER cc_start: 0.8948 (m) cc_final: 0.8288 (t) REVERT: F 32 TYR cc_start: 0.7271 (t80) cc_final: 0.7019 (t80) REVERT: F 103 SER cc_start: 0.8960 (m) cc_final: 0.8324 (t) REVERT: G 36 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7457 (mm-30) REVERT: G 82 ASP cc_start: 0.7871 (m-30) cc_final: 0.7424 (t70) REVERT: G 103 SER cc_start: 0.8969 (m) cc_final: 0.8314 (t) REVERT: G 108 ASP cc_start: 0.8049 (m-30) cc_final: 0.7815 (m-30) REVERT: H 82 ASP cc_start: 0.7899 (m-30) cc_final: 0.7570 (t0) REVERT: H 103 SER cc_start: 0.8945 (m) cc_final: 0.8233 (t) REVERT: I 103 SER cc_start: 0.8996 (m) cc_final: 0.8334 (t) REVERT: J 93 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6672 (t0) REVERT: J 103 SER cc_start: 0.9018 (m) cc_final: 0.8409 (t) REVERT: J 108 ASP cc_start: 0.8022 (m-30) cc_final: 0.7752 (m-30) REVERT: K 103 SER cc_start: 0.9047 (m) cc_final: 0.8387 (t) REVERT: L 103 SER cc_start: 0.8870 (m) cc_final: 0.8215 (t) REVERT: L 108 ASP cc_start: 0.8121 (m-30) cc_final: 0.7794 (m-30) REVERT: M 103 SER cc_start: 0.9052 (m) cc_final: 0.8362 (t) REVERT: M 108 ASP cc_start: 0.7964 (m-30) cc_final: 0.7699 (m-30) REVERT: N 82 ASP cc_start: 0.7932 (m-30) cc_final: 0.7677 (t0) REVERT: N 103 SER cc_start: 0.8986 (m) cc_final: 0.8297 (t) REVERT: O 82 ASP cc_start: 0.8180 (m-30) cc_final: 0.7667 (t0) REVERT: O 103 SER cc_start: 0.8986 (m) cc_final: 0.8361 (t) REVERT: P 103 SER cc_start: 0.8995 (m) cc_final: 0.8322 (t) REVERT: P 108 ASP cc_start: 0.8019 (m-30) cc_final: 0.7806 (m-30) REVERT: Q 93 ASP cc_start: 0.7230 (m-30) cc_final: 0.6948 (t0) REVERT: Q 103 SER cc_start: 0.8960 (m) cc_final: 0.8264 (t) REVERT: R 103 SER cc_start: 0.9064 (m) cc_final: 0.8542 (t) outliers start: 61 outliers final: 52 residues processed: 318 average time/residue: 0.1620 time to fit residues: 76.9943 Evaluate side-chains 300 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 246 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 26 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain F 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 40 ILE Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain L residue 26 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 L residue 121 SER Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 40 ILE 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 N residue 81 LYS Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 40 ILE 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 84 THR Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 35 GLN Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 121 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 155 optimal weight: 1.9990 chunk 194 optimal weight: 0.1980 chunk 161 optimal weight: 2.9990 chunk 101 optimal weight: 0.1980 chunk 181 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.186768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.122853 restraints weight = 21259.659| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.62 r_work: 0.3217 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19296 Z= 0.111 Angle : 0.470 5.623 26262 Z= 0.253 Chirality : 0.042 0.121 2880 Planarity : 0.004 0.040 3348 Dihedral : 4.109 16.131 2466 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.13 % Allowed : 14.25 % Favored : 83.62 % 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 aren not related in a simple way. whole: 1.12 (0.17), residues: 2268 helix: 2.13 (0.19), residues: 720 sheet: 0.80 (0.24), residues: 378 loop : -0.12 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 95 TYR 0.022 0.001 TYR M 32 PHE 0.010 0.001 PHE J 73 TRP 0.014 0.002 TRP H 88 HIS 0.003 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00264 (19296) covalent geometry : angle 0.47002 (26262) hydrogen bonds : bond 0.03715 ( 918) hydrogen bonds : angle 3.86315 ( 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 302 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 258 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.7914 (m-30) cc_final: 0.7461 (t0) REVERT: A 103 SER cc_start: 0.9073 (m) cc_final: 0.8482 (t) REVERT: A 108 ASP cc_start: 0.8104 (m-30) cc_final: 0.7822 (m-30) REVERT: B 82 ASP cc_start: 0.8041 (m-30) cc_final: 0.7635 (t0) REVERT: B 103 SER cc_start: 0.9049 (m) cc_final: 0.8355 (t) REVERT: C 103 SER cc_start: 0.8966 (m) cc_final: 0.8327 (t) REVERT: C 108 ASP cc_start: 0.8061 (m-30) cc_final: 0.7753 (m-30) REVERT: D 82 ASP cc_start: 0.7942 (m-30) cc_final: 0.7553 (t70) REVERT: D 103 SER cc_start: 0.9017 (m) cc_final: 0.8332 (t) REVERT: D 119 LYS cc_start: 0.7031 (mttm) cc_final: 0.6827 (ttmt) REVERT: E 103 SER cc_start: 0.9014 (m) cc_final: 0.8362 (t) REVERT: F 82 ASP cc_start: 0.7950 (m-30) cc_final: 0.7482 (t0) REVERT: F 103 SER cc_start: 0.9056 (m) cc_final: 0.8426 (t) REVERT: G 36 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7346 (mm-30) REVERT: G 82 ASP cc_start: 0.7861 (m-30) cc_final: 0.7409 (t70) REVERT: G 103 SER cc_start: 0.8995 (m) cc_final: 0.8332 (t) REVERT: H 82 ASP cc_start: 0.7827 (m-30) cc_final: 0.7522 (t70) REVERT: H 103 SER cc_start: 0.9027 (m) cc_final: 0.8316 (t) REVERT: I 32 TYR cc_start: 0.7054 (t80) cc_final: 0.6694 (t80) REVERT: I 82 ASP cc_start: 0.7950 (m-30) cc_final: 0.7581 (t0) REVERT: I 103 SER cc_start: 0.9021 (m) cc_final: 0.8330 (t) REVERT: J 93 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6872 (t0) REVERT: J 103 SER cc_start: 0.9044 (m) cc_final: 0.8521 (t) REVERT: J 108 ASP cc_start: 0.8045 (m-30) cc_final: 0.7740 (m-30) REVERT: K 103 SER cc_start: 0.9065 (m) cc_final: 0.8468 (t) REVERT: L 103 SER cc_start: 0.8930 (m) cc_final: 0.8277 (t) REVERT: L 108 ASP cc_start: 0.8117 (m-30) cc_final: 0.7732 (m-30) REVERT: M 82 ASP cc_start: 0.7970 (m-30) cc_final: 0.7611 (t0) REVERT: M 103 SER cc_start: 0.9074 (m) cc_final: 0.8400 (t) REVERT: M 108 ASP cc_start: 0.7874 (m-30) cc_final: 0.7587 (m-30) REVERT: N 82 ASP cc_start: 0.7952 (m-30) cc_final: 0.7694 (t0) REVERT: N 95 ARG cc_start: 0.8754 (mtm180) cc_final: 0.8299 (mtm-85) REVERT: N 103 SER cc_start: 0.9033 (m) cc_final: 0.8367 (t) REVERT: O 82 ASP cc_start: 0.8185 (m-30) cc_final: 0.7658 (t0) REVERT: O 103 SER cc_start: 0.9044 (m) cc_final: 0.8421 (t) REVERT: P 32 TYR cc_start: 0.6970 (t80) cc_final: 0.6749 (t80) REVERT: P 82 ASP cc_start: 0.7871 (m-30) cc_final: 0.7513 (t70) REVERT: P 103 SER cc_start: 0.9062 (m) cc_final: 0.8382 (t) REVERT: P 108 ASP cc_start: 0.7992 (m-30) cc_final: 0.7779 (m-30) REVERT: Q 82 ASP cc_start: 0.7848 (m-30) cc_final: 0.7491 (t70) REVERT: Q 103 SER cc_start: 0.9017 (m) cc_final: 0.8322 (t) REVERT: R 82 ASP cc_start: 0.7885 (m-30) cc_final: 0.7501 (t70) REVERT: R 103 SER cc_start: 0.8997 (m) cc_final: 0.8468 (t) outliers start: 44 outliers final: 35 residues processed: 301 average time/residue: 0.1793 time to fit residues: 78.3198 Evaluate side-chains 279 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain F 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 40 ILE Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain L residue 26 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 40 ILE Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 40 ILE 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 Q residue 31 SER Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 35 GLN Chi-restraints excluded: chain R residue 40 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 30 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 210 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.188243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.124501 restraints weight = 20851.252| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.61 r_work: 0.3227 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19296 Z= 0.101 Angle : 0.450 4.873 26262 Z= 0.244 Chirality : 0.041 0.121 2880 Planarity : 0.004 0.037 3348 Dihedral : 3.930 15.425 2466 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.93 % Allowed : 14.78 % Favored : 83.29 % 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 aren not related in a simple way. whole: 1.37 (0.17), residues: 2268 helix: 2.26 (0.19), residues: 720 sheet: 1.14 (0.25), residues: 378 loop : 0.02 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 95 TYR 0.021 0.001 TYR M 32 PHE 0.012 0.001 PHE E 94 TRP 0.012 0.001 TRP E 88 HIS 0.002 0.001 HIS L 18 Details of bonding type rmsd covalent geometry : bond 0.00235 (19296) covalent geometry : angle 0.45008 (26262) hydrogen bonds : bond 0.03566 ( 918) hydrogen bonds : angle 3.76046 ( 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 295 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8347 (t0) cc_final: 0.8134 (t0) REVERT: A 82 ASP cc_start: 0.7855 (m-30) cc_final: 0.7388 (t0) REVERT: A 103 SER cc_start: 0.9076 (m) cc_final: 0.8493 (t) REVERT: A 108 ASP cc_start: 0.8087 (m-30) cc_final: 0.7808 (m-30) REVERT: B 82 ASP cc_start: 0.8051 (m-30) cc_final: 0.7642 (t70) REVERT: B 103 SER cc_start: 0.9017 (m) cc_final: 0.8330 (t) REVERT: C 103 SER cc_start: 0.8963 (m) cc_final: 0.8332 (t) REVERT: C 108 ASP cc_start: 0.8087 (m-30) cc_final: 0.7742 (m-30) REVERT: D 82 ASP cc_start: 0.7812 (m-30) cc_final: 0.7417 (t70) REVERT: D 103 SER cc_start: 0.8976 (m) cc_final: 0.8306 (t) REVERT: E 95 ARG cc_start: 0.8696 (mtm180) cc_final: 0.8272 (mtm-85) REVERT: E 103 SER cc_start: 0.9022 (m) cc_final: 0.8371 (t) REVERT: F 82 ASP cc_start: 0.7901 (m-30) cc_final: 0.7439 (t0) REVERT: F 103 SER cc_start: 0.9072 (m) cc_final: 0.8451 (t) REVERT: F 108 ASP cc_start: 0.8117 (m-30) cc_final: 0.7719 (m-30) REVERT: G 82 ASP cc_start: 0.7854 (m-30) cc_final: 0.7410 (t70) REVERT: G 103 SER cc_start: 0.8960 (m) cc_final: 0.8314 (t) REVERT: G 108 ASP cc_start: 0.8072 (m-30) cc_final: 0.7817 (m-30) REVERT: H 82 ASP cc_start: 0.7806 (m-30) cc_final: 0.7490 (t0) REVERT: H 103 SER cc_start: 0.9018 (m) cc_final: 0.8290 (t) REVERT: I 32 TYR cc_start: 0.7085 (t80) cc_final: 0.6843 (t80) REVERT: I 82 ASP cc_start: 0.7891 (m-30) cc_final: 0.7523 (t0) REVERT: I 103 SER cc_start: 0.8998 (m) cc_final: 0.8302 (t) REVERT: J 41 ASP cc_start: 0.8262 (t0) cc_final: 0.8038 (t0) REVERT: J 93 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.6956 (t0) REVERT: J 103 SER cc_start: 0.9048 (m) cc_final: 0.8478 (t) REVERT: J 108 ASP cc_start: 0.8060 (m-30) cc_final: 0.7779 (m-30) REVERT: K 103 SER cc_start: 0.9095 (m) cc_final: 0.8439 (t) REVERT: L 103 SER cc_start: 0.8925 (m) cc_final: 0.8277 (t) REVERT: L 108 ASP cc_start: 0.8104 (m-30) cc_final: 0.7748 (m-30) REVERT: M 82 ASP cc_start: 0.7997 (m-30) cc_final: 0.7627 (t0) REVERT: M 103 SER cc_start: 0.9073 (m) cc_final: 0.8398 (t) REVERT: M 108 ASP cc_start: 0.7875 (m-30) cc_final: 0.7577 (m-30) REVERT: N 32 TYR cc_start: 0.7060 (t80) cc_final: 0.6802 (t80) REVERT: N 82 ASP cc_start: 0.7816 (m-30) cc_final: 0.7564 (t0) REVERT: N 103 SER cc_start: 0.9001 (m) cc_final: 0.8341 (t) REVERT: O 82 ASP cc_start: 0.8185 (m-30) cc_final: 0.7654 (t0) REVERT: O 103 SER cc_start: 0.9032 (m) cc_final: 0.8408 (t) REVERT: O 108 ASP cc_start: 0.8127 (m-30) cc_final: 0.7732 (m-30) REVERT: P 82 ASP cc_start: 0.7854 (m-30) cc_final: 0.7504 (t0) REVERT: P 103 SER cc_start: 0.9034 (m) cc_final: 0.8352 (t) REVERT: P 108 ASP cc_start: 0.7948 (m-30) cc_final: 0.7726 (m-30) REVERT: Q 82 ASP cc_start: 0.7865 (m-30) cc_final: 0.7493 (t70) REVERT: Q 93 ASP cc_start: 0.7245 (m-30) cc_final: 0.7036 (t0) REVERT: Q 103 SER cc_start: 0.9013 (m) cc_final: 0.8326 (t) REVERT: R 82 ASP cc_start: 0.7859 (m-30) cc_final: 0.7468 (t70) REVERT: R 103 SER cc_start: 0.8991 (m) cc_final: 0.8447 (t) outliers start: 40 outliers final: 36 residues processed: 294 average time/residue: 0.1752 time to fit residues: 75.0752 Evaluate side-chains 282 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 245 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain G residue 35 GLN Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 35 GLN Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O 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 84 THR Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 35 GLN Chi-restraints excluded: chain R residue 40 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 208 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 212 optimal weight: 0.9990 chunk 205 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 214 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.187144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.119080 restraints weight = 20995.632| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.71 r_work: 0.3188 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19296 Z= 0.110 Angle : 0.448 4.968 26262 Z= 0.243 Chirality : 0.041 0.121 2880 Planarity : 0.004 0.035 3348 Dihedral : 3.902 15.238 2466 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.27 % Allowed : 15.36 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.17), residues: 2268 helix: 2.32 (0.19), residues: 720 sheet: 1.26 (0.25), residues: 378 loop : 0.07 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 115 TYR 0.022 0.001 TYR M 32 PHE 0.009 0.001 PHE J 73 TRP 0.011 0.001 TRP E 88 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00263 (19296) covalent geometry : angle 0.44842 (26262) hydrogen bonds : bond 0.03657 ( 918) hydrogen bonds : angle 3.70306 ( 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 314 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 267 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.8725 (ttmt) cc_final: 0.8525 (ttmt) REVERT: A 82 ASP cc_start: 0.7828 (m-30) cc_final: 0.7362 (t0) REVERT: A 103 SER cc_start: 0.9089 (m) cc_final: 0.8509 (t) REVERT: A 108 ASP cc_start: 0.8161 (m-30) cc_final: 0.7892 (m-30) REVERT: B 82 ASP cc_start: 0.7998 (m-30) cc_final: 0.7544 (t70) REVERT: B 103 SER cc_start: 0.9044 (m) cc_final: 0.8380 (t) REVERT: C 82 ASP cc_start: 0.8030 (m-30) cc_final: 0.7700 (t70) REVERT: C 103 SER cc_start: 0.8979 (m) cc_final: 0.8351 (t) REVERT: C 108 ASP cc_start: 0.8121 (m-30) cc_final: 0.7798 (m-30) REVERT: D 82 ASP cc_start: 0.7798 (m-30) cc_final: 0.7409 (t70) REVERT: D 103 SER cc_start: 0.9008 (m) cc_final: 0.8357 (t) REVERT: E 95 ARG cc_start: 0.8647 (mtm180) cc_final: 0.8179 (mtm-85) REVERT: E 103 SER cc_start: 0.9080 (m) cc_final: 0.8448 (t) REVERT: F 82 ASP cc_start: 0.7912 (m-30) cc_final: 0.7432 (t0) REVERT: F 103 SER cc_start: 0.9076 (m) cc_final: 0.8480 (t) REVERT: F 108 ASP cc_start: 0.8110 (m-30) cc_final: 0.7712 (m-30) REVERT: G 82 ASP cc_start: 0.7841 (m-30) cc_final: 0.7406 (t70) REVERT: G 103 SER cc_start: 0.8976 (m) cc_final: 0.8338 (t) REVERT: G 108 ASP cc_start: 0.8063 (m-30) cc_final: 0.7778 (m-30) REVERT: H 82 ASP cc_start: 0.7820 (m-30) cc_final: 0.7468 (t0) REVERT: H 103 SER cc_start: 0.9049 (m) cc_final: 0.8331 (t) REVERT: I 32 TYR cc_start: 0.7057 (t80) cc_final: 0.6801 (t80) REVERT: I 82 ASP cc_start: 0.7918 (m-30) cc_final: 0.7521 (t0) REVERT: I 103 SER cc_start: 0.9008 (m) cc_final: 0.8310 (t) REVERT: J 41 ASP cc_start: 0.8276 (t0) cc_final: 0.8066 (t0) REVERT: J 82 ASP cc_start: 0.7866 (m-30) cc_final: 0.7453 (t0) REVERT: J 93 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6918 (t0) REVERT: J 103 SER cc_start: 0.9096 (m) cc_final: 0.8524 (t) REVERT: J 108 ASP cc_start: 0.8145 (m-30) cc_final: 0.7873 (m-30) REVERT: K 103 SER cc_start: 0.9077 (m) cc_final: 0.8448 (t) REVERT: L 93 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7131 (t0) REVERT: L 103 SER cc_start: 0.8970 (m) cc_final: 0.8343 (t) REVERT: L 108 ASP cc_start: 0.8121 (m-30) cc_final: 0.7791 (m-30) REVERT: M 82 ASP cc_start: 0.7861 (m-30) cc_final: 0.7469 (t0) REVERT: M 103 SER cc_start: 0.9073 (m) cc_final: 0.8425 (t) REVERT: M 108 ASP cc_start: 0.7939 (m-30) cc_final: 0.7634 (m-30) REVERT: N 32 TYR cc_start: 0.7200 (t80) cc_final: 0.6992 (t80) REVERT: N 82 ASP cc_start: 0.7851 (m-30) cc_final: 0.7590 (t0) REVERT: N 103 SER cc_start: 0.9050 (m) cc_final: 0.8418 (t) REVERT: O 82 ASP cc_start: 0.8158 (m-30) cc_final: 0.7607 (t0) REVERT: O 103 SER cc_start: 0.9042 (m) cc_final: 0.8428 (t) REVERT: O 108 ASP cc_start: 0.8119 (m-30) cc_final: 0.7726 (m-30) REVERT: P 82 ASP cc_start: 0.8004 (m-30) cc_final: 0.7608 (t70) REVERT: P 103 SER cc_start: 0.9061 (m) cc_final: 0.8423 (t) REVERT: P 108 ASP cc_start: 0.7928 (m-30) cc_final: 0.7689 (m-30) REVERT: Q 82 ASP cc_start: 0.7876 (m-30) cc_final: 0.7479 (t70) REVERT: Q 103 SER cc_start: 0.9069 (m) cc_final: 0.8401 (t) REVERT: R 82 ASP cc_start: 0.7960 (m-30) cc_final: 0.7449 (t70) REVERT: R 103 SER cc_start: 0.9030 (m) cc_final: 0.8486 (t) outliers start: 47 outliers final: 43 residues processed: 314 average time/residue: 0.1676 time to fit residues: 77.0178 Evaluate side-chains 303 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 258 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 26 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain F residue 35 GLN 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 40 ILE Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain L residue 26 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 L residue 93 ASP Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 40 ILE 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 Q residue 31 SER Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain R residue 35 GLN Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 121 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 176 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 154 optimal weight: 0.9990 chunk 169 optimal weight: 20.0000 chunk 108 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.184585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116493 restraints weight = 20917.840| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.71 r_work: 0.3151 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19296 Z= 0.143 Angle : 0.477 5.483 26262 Z= 0.259 Chirality : 0.042 0.124 2880 Planarity : 0.004 0.033 3348 Dihedral : 4.079 16.536 2466 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.37 % Allowed : 16.28 % Favored : 81.35 % 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 aren not related in a simple way. whole: 1.38 (0.17), residues: 2268 helix: 2.24 (0.19), residues: 720 sheet: 1.22 (0.25), residues: 378 loop : 0.02 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 95 TYR 0.022 0.002 TYR M 32 PHE 0.012 0.001 PHE R 94 TRP 0.011 0.001 TRP E 88 HIS 0.004 0.001 HIS Q 49 Details of bonding type rmsd covalent geometry : bond 0.00360 (19296) covalent geometry : angle 0.47719 (26262) hydrogen bonds : bond 0.04173 ( 918) hydrogen bonds : angle 3.76371 ( 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 312 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 263 time to evaluate : 0.791 Fit side-chains REVERT: A 82 ASP cc_start: 0.7828 (m-30) cc_final: 0.7343 (t0) REVERT: A 103 SER cc_start: 0.9108 (m) cc_final: 0.8555 (t) REVERT: A 108 ASP cc_start: 0.8135 (m-30) cc_final: 0.7860 (m-30) REVERT: B 82 ASP cc_start: 0.7969 (m-30) cc_final: 0.7448 (t70) REVERT: B 103 SER cc_start: 0.9081 (m) cc_final: 0.8441 (t) REVERT: C 82 ASP cc_start: 0.7896 (m-30) cc_final: 0.7558 (t0) REVERT: C 103 SER cc_start: 0.9018 (m) cc_final: 0.8419 (t) REVERT: C 108 ASP cc_start: 0.8132 (m-30) cc_final: 0.7828 (m-30) REVERT: D 82 ASP cc_start: 0.7760 (m-30) cc_final: 0.7335 (t70) REVERT: D 103 SER cc_start: 0.9048 (m) cc_final: 0.8439 (t) REVERT: E 95 ARG cc_start: 0.8666 (mtm180) cc_final: 0.7794 (mtt-85) REVERT: E 103 SER cc_start: 0.9114 (m) cc_final: 0.8518 (t) REVERT: F 82 ASP cc_start: 0.7871 (m-30) cc_final: 0.7371 (t0) REVERT: F 103 SER cc_start: 0.9096 (m) cc_final: 0.8524 (t) REVERT: F 108 ASP cc_start: 0.8152 (m-30) cc_final: 0.7724 (m-30) REVERT: G 82 ASP cc_start: 0.7834 (m-30) cc_final: 0.7377 (t70) REVERT: G 103 SER cc_start: 0.9009 (m) cc_final: 0.8396 (t) REVERT: G 108 ASP cc_start: 0.8060 (m-30) cc_final: 0.7770 (m-30) REVERT: H 82 ASP cc_start: 0.7817 (m-30) cc_final: 0.7403 (t0) REVERT: H 103 SER cc_start: 0.9119 (m) cc_final: 0.8459 (t) REVERT: I 32 TYR cc_start: 0.7156 (t80) cc_final: 0.6927 (t80) REVERT: I 70 GLU cc_start: 0.8488 (mp0) cc_final: 0.8257 (mp0) REVERT: I 82 ASP cc_start: 0.7899 (m-30) cc_final: 0.7457 (t70) REVERT: I 103 SER cc_start: 0.9035 (m) cc_final: 0.8377 (t) REVERT: I 115 ARG cc_start: 0.7661 (mtm180) cc_final: 0.7408 (mtm180) REVERT: J 82 ASP cc_start: 0.7858 (m-30) cc_final: 0.7425 (t0) REVERT: J 103 SER cc_start: 0.9169 (m) cc_final: 0.8607 (t) REVERT: J 108 ASP cc_start: 0.8109 (m-30) cc_final: 0.7818 (m-30) REVERT: K 103 SER cc_start: 0.9132 (m) cc_final: 0.8515 (t) REVERT: L 82 ASP cc_start: 0.7862 (m-30) cc_final: 0.7385 (t70) REVERT: L 93 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7234 (t0) REVERT: L 103 SER cc_start: 0.9015 (m) cc_final: 0.8431 (t) REVERT: L 108 ASP cc_start: 0.8149 (m-30) cc_final: 0.7789 (m-30) REVERT: M 70 GLU cc_start: 0.8351 (mp0) cc_final: 0.7827 (mp0) REVERT: M 82 ASP cc_start: 0.7852 (m-30) cc_final: 0.7446 (t0) REVERT: M 103 SER cc_start: 0.9083 (m) cc_final: 0.8469 (t) REVERT: M 108 ASP cc_start: 0.7979 (m-30) cc_final: 0.7714 (m-30) REVERT: N 82 ASP cc_start: 0.7767 (m-30) cc_final: 0.7357 (t70) REVERT: N 103 SER cc_start: 0.9075 (m) cc_final: 0.8479 (t) REVERT: O 82 ASP cc_start: 0.8030 (m-30) cc_final: 0.7484 (t0) REVERT: O 103 SER cc_start: 0.9077 (m) cc_final: 0.8484 (t) REVERT: O 108 ASP cc_start: 0.8142 (m-30) cc_final: 0.7723 (m-30) REVERT: P 32 TYR cc_start: 0.7372 (t80) cc_final: 0.6957 (t80) REVERT: P 82 ASP cc_start: 0.8005 (m-30) cc_final: 0.7556 (t70) REVERT: P 103 SER cc_start: 0.9119 (m) cc_final: 0.8514 (t) REVERT: P 108 ASP cc_start: 0.7967 (m-30) cc_final: 0.7719 (m-30) REVERT: Q 82 ASP cc_start: 0.7866 (m-30) cc_final: 0.7439 (t0) REVERT: Q 103 SER cc_start: 0.9087 (m) cc_final: 0.8453 (t) REVERT: R 82 ASP cc_start: 0.7963 (m-30) cc_final: 0.7410 (t70) REVERT: R 103 SER cc_start: 0.9072 (m) cc_final: 0.8561 (t) outliers start: 49 outliers final: 46 residues processed: 311 average time/residue: 0.1585 time to fit residues: 74.1698 Evaluate side-chains 307 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 260 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 26 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain F residue 35 GLN 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 40 ILE Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain L residue 26 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 L residue 93 ASP Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 40 ILE 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 121 SER Chi-restraints excluded: chain R residue 35 GLN Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R 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: 4.9990 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.186620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.118759 restraints weight = 20757.853| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.70 r_work: 0.3182 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19296 Z= 0.110 Angle : 0.450 4.825 26262 Z= 0.247 Chirality : 0.041 0.121 2880 Planarity : 0.004 0.033 3348 Dihedral : 3.918 15.362 2466 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.37 % Allowed : 16.71 % Favored : 80.92 % 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 aren not related in a simple way. whole: 1.50 (0.17), residues: 2268 helix: 2.25 (0.19), residues: 720 sheet: 1.40 (0.25), residues: 378 loop : 0.11 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 95 TYR 0.023 0.001 TYR F 32 PHE 0.011 0.001 PHE R 94 TRP 0.011 0.001 TRP E 88 HIS 0.002 0.001 HIS Q 49 Details of bonding type rmsd covalent geometry : bond 0.00262 (19296) covalent geometry : angle 0.45034 (26262) hydrogen bonds : bond 0.03647 ( 918) hydrogen bonds : angle 3.72250 ( 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 320 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 0.749 Fit side-chains REVERT: A 81 LYS cc_start: 0.8665 (ttmt) cc_final: 0.8448 (ttmt) REVERT: A 82 ASP cc_start: 0.7822 (m-30) cc_final: 0.7345 (t0) REVERT: A 103 SER cc_start: 0.9097 (m) cc_final: 0.8540 (t) REVERT: A 108 ASP cc_start: 0.8129 (m-30) cc_final: 0.7851 (m-30) REVERT: B 82 ASP cc_start: 0.7908 (m-30) cc_final: 0.7407 (t70) REVERT: B 103 SER cc_start: 0.9061 (m) cc_final: 0.8396 (t) REVERT: C 70 GLU cc_start: 0.8334 (mp0) cc_final: 0.7921 (mp0) REVERT: C 82 ASP cc_start: 0.7872 (m-30) cc_final: 0.7539 (t0) REVERT: C 103 SER cc_start: 0.9014 (m) cc_final: 0.8405 (t) REVERT: C 108 ASP cc_start: 0.8118 (m-30) cc_final: 0.7803 (m-30) REVERT: D 82 ASP cc_start: 0.7758 (m-30) cc_final: 0.7335 (t70) REVERT: D 103 SER cc_start: 0.9049 (m) cc_final: 0.8424 (t) REVERT: E 95 ARG cc_start: 0.8639 (mtm180) cc_final: 0.7760 (mtt-85) REVERT: E 103 SER cc_start: 0.9128 (m) cc_final: 0.8528 (t) REVERT: F 82 ASP cc_start: 0.7842 (m-30) cc_final: 0.7354 (t0) REVERT: F 103 SER cc_start: 0.9077 (m) cc_final: 0.8511 (t) REVERT: F 108 ASP cc_start: 0.8107 (m-30) cc_final: 0.7712 (m-30) REVERT: G 32 TYR cc_start: 0.7189 (t80) cc_final: 0.6964 (t80) REVERT: G 82 ASP cc_start: 0.7832 (m-30) cc_final: 0.7391 (t70) REVERT: G 103 SER cc_start: 0.8998 (m) cc_final: 0.8384 (t) REVERT: G 108 ASP cc_start: 0.8061 (m-30) cc_final: 0.7765 (m-30) REVERT: H 82 ASP cc_start: 0.7802 (m-30) cc_final: 0.7396 (t0) REVERT: H 103 SER cc_start: 0.9096 (m) cc_final: 0.8413 (t) REVERT: I 32 TYR cc_start: 0.7200 (t80) cc_final: 0.6950 (t80) REVERT: I 82 ASP cc_start: 0.7940 (m-30) cc_final: 0.7466 (t70) REVERT: I 103 SER cc_start: 0.9026 (m) cc_final: 0.8341 (t) REVERT: I 115 ARG cc_start: 0.7632 (mtm180) cc_final: 0.7380 (mtm180) REVERT: J 82 ASP cc_start: 0.7841 (m-30) cc_final: 0.7413 (t0) REVERT: J 103 SER cc_start: 0.9140 (m) cc_final: 0.8586 (t) REVERT: J 108 ASP cc_start: 0.8071 (m-30) cc_final: 0.7799 (m-30) REVERT: K 32 TYR cc_start: 0.7401 (t80) cc_final: 0.6993 (t80) REVERT: K 103 SER cc_start: 0.9110 (m) cc_final: 0.8491 (t) REVERT: L 82 ASP cc_start: 0.7901 (m-30) cc_final: 0.7438 (t70) REVERT: L 93 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7163 (t0) REVERT: L 103 SER cc_start: 0.9008 (m) cc_final: 0.8414 (t) REVERT: L 108 ASP cc_start: 0.8124 (m-30) cc_final: 0.7821 (m-30) REVERT: M 70 GLU cc_start: 0.8305 (mp0) cc_final: 0.7864 (mp0) REVERT: M 82 ASP cc_start: 0.7838 (m-30) cc_final: 0.7431 (t0) REVERT: M 103 SER cc_start: 0.9129 (m) cc_final: 0.8510 (t) REVERT: M 108 ASP cc_start: 0.7959 (m-30) cc_final: 0.7662 (m-30) REVERT: N 82 ASP cc_start: 0.7751 (m-30) cc_final: 0.7347 (t70) REVERT: N 103 SER cc_start: 0.9073 (m) cc_final: 0.8463 (t) REVERT: O 82 ASP cc_start: 0.8044 (m-30) cc_final: 0.7489 (t0) REVERT: O 103 SER cc_start: 0.9082 (m) cc_final: 0.8490 (t) REVERT: O 108 ASP cc_start: 0.8115 (m-30) cc_final: 0.7692 (m-30) REVERT: P 103 SER cc_start: 0.9111 (m) cc_final: 0.8506 (t) REVERT: P 108 ASP cc_start: 0.7956 (m-30) cc_final: 0.7725 (m-30) REVERT: Q 82 ASP cc_start: 0.7844 (m-30) cc_final: 0.7418 (t0) REVERT: Q 103 SER cc_start: 0.9115 (m) cc_final: 0.8464 (t) REVERT: R 103 SER cc_start: 0.9031 (m) cc_final: 0.8513 (t) outliers start: 49 outliers final: 45 residues processed: 318 average time/residue: 0.1688 time to fit residues: 78.5416 Evaluate side-chains 308 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 262 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 40 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 121 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 40 ILE Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain L residue 26 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 L residue 93 ASP Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 84 THR 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 121 SER Chi-restraints excluded: chain R residue 35 GLN Chi-restraints excluded: chain R 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: 0.5980 chunk 201 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 147 optimal weight: 0.0570 chunk 142 optimal weight: 1.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.186535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.119402 restraints weight = 20812.074| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.66 r_work: 0.3198 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 19296 Z= 0.100 Angle : 0.448 6.222 26262 Z= 0.248 Chirality : 0.041 0.121 2880 Planarity : 0.004 0.033 3348 Dihedral : 3.812 14.071 2466 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.27 % Allowed : 17.49 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.17), residues: 2268 helix: 2.32 (0.19), residues: 720 sheet: 1.56 (0.26), residues: 378 loop : 0.17 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 95 TYR 0.023 0.001 TYR M 32 PHE 0.012 0.001 PHE R 94 TRP 0.011 0.001 TRP E 88 HIS 0.002 0.001 HIS Q 49 Details of bonding type rmsd covalent geometry : bond 0.00228 (19296) covalent geometry : angle 0.44753 (26262) hydrogen bonds : bond 0.03459 ( 918) hydrogen bonds : angle 3.66283 ( 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 331 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 284 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.7815 (m-30) cc_final: 0.7351 (t0) REVERT: A 103 SER cc_start: 0.9099 (m) cc_final: 0.8535 (t) REVERT: A 108 ASP cc_start: 0.8126 (m-30) cc_final: 0.7844 (m-30) REVERT: B 82 ASP cc_start: 0.7903 (m-30) cc_final: 0.7403 (t70) REVERT: B 103 SER cc_start: 0.9071 (m) cc_final: 0.8404 (t) REVERT: C 41 ASP cc_start: 0.8284 (t0) cc_final: 0.8026 (t0) REVERT: C 70 GLU cc_start: 0.8298 (mp0) cc_final: 0.7949 (mp0) REVERT: C 82 ASP cc_start: 0.7848 (m-30) cc_final: 0.7525 (t0) REVERT: C 103 SER cc_start: 0.9033 (m) cc_final: 0.8419 (t) REVERT: C 108 ASP cc_start: 0.8094 (m-30) cc_final: 0.7797 (m-30) REVERT: D 82 ASP cc_start: 0.7751 (m-30) cc_final: 0.7336 (t70) REVERT: D 103 SER cc_start: 0.9028 (m) cc_final: 0.8406 (t) REVERT: E 70 GLU cc_start: 0.8242 (mp0) cc_final: 0.7866 (mp0) REVERT: E 95 ARG cc_start: 0.8629 (mtm180) cc_final: 0.7750 (mtt-85) REVERT: E 103 SER cc_start: 0.9087 (m) cc_final: 0.8482 (t) REVERT: F 82 ASP cc_start: 0.7839 (m-30) cc_final: 0.7355 (t0) REVERT: F 103 SER cc_start: 0.9068 (m) cc_final: 0.8499 (t) REVERT: F 108 ASP cc_start: 0.8099 (m-30) cc_final: 0.7703 (m-30) REVERT: G 70 GLU cc_start: 0.8301 (mp0) cc_final: 0.8084 (mp0) REVERT: G 82 ASP cc_start: 0.7829 (m-30) cc_final: 0.7395 (t70) REVERT: G 95 ARG cc_start: 0.8609 (mtm180) cc_final: 0.8008 (mtm-85) REVERT: G 103 SER cc_start: 0.8998 (m) cc_final: 0.8374 (t) REVERT: G 108 ASP cc_start: 0.8055 (m-30) cc_final: 0.7760 (m-30) REVERT: H 82 ASP cc_start: 0.7784 (m-30) cc_final: 0.7392 (t0) REVERT: H 103 SER cc_start: 0.9086 (m) cc_final: 0.8395 (t) REVERT: I 82 ASP cc_start: 0.8005 (m-30) cc_final: 0.7488 (t70) REVERT: I 103 SER cc_start: 0.8991 (m) cc_final: 0.8350 (t) REVERT: I 115 ARG cc_start: 0.7616 (mtm180) cc_final: 0.7354 (mtm180) REVERT: J 82 ASP cc_start: 0.7828 (m-30) cc_final: 0.7413 (t0) REVERT: J 103 SER cc_start: 0.9132 (m) cc_final: 0.8572 (t) REVERT: J 108 ASP cc_start: 0.8029 (m-30) cc_final: 0.7753 (m-30) REVERT: K 103 SER cc_start: 0.9098 (m) cc_final: 0.8472 (t) REVERT: L 82 ASP cc_start: 0.7895 (m-30) cc_final: 0.7444 (t70) REVERT: L 93 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.7119 (t0) REVERT: L 103 SER cc_start: 0.9007 (m) cc_final: 0.8399 (t) REVERT: L 108 ASP cc_start: 0.8085 (m-30) cc_final: 0.7778 (m-30) REVERT: M 70 GLU cc_start: 0.8275 (mp0) cc_final: 0.7867 (mp0) REVERT: M 82 ASP cc_start: 0.7749 (m-30) cc_final: 0.7344 (t0) REVERT: M 103 SER cc_start: 0.9113 (m) cc_final: 0.8485 (t) REVERT: M 108 ASP cc_start: 0.7932 (m-30) cc_final: 0.7625 (m-30) REVERT: N 82 ASP cc_start: 0.7739 (m-30) cc_final: 0.7348 (t70) REVERT: N 103 SER cc_start: 0.9060 (m) cc_final: 0.8435 (t) REVERT: O 82 ASP cc_start: 0.8083 (m-30) cc_final: 0.7532 (t0) REVERT: O 103 SER cc_start: 0.9089 (m) cc_final: 0.8490 (t) REVERT: O 108 ASP cc_start: 0.8078 (m-30) cc_final: 0.7647 (m-30) REVERT: P 32 TYR cc_start: 0.7308 (t80) cc_final: 0.7093 (t80) REVERT: P 70 GLU cc_start: 0.8301 (mp0) cc_final: 0.8045 (mp0) REVERT: P 103 SER cc_start: 0.9094 (m) cc_final: 0.8483 (t) REVERT: P 108 ASP cc_start: 0.7951 (m-30) cc_final: 0.7471 (m-30) REVERT: Q 82 ASP cc_start: 0.7844 (m-30) cc_final: 0.7410 (t0) REVERT: Q 103 SER cc_start: 0.9080 (m) cc_final: 0.8441 (t) REVERT: R 95 ARG cc_start: 0.8539 (mtm180) cc_final: 0.7990 (mtm-85) REVERT: R 103 SER cc_start: 0.8994 (m) cc_final: 0.8472 (t) outliers start: 47 outliers final: 45 residues processed: 330 average time/residue: 0.1503 time to fit residues: 73.4601 Evaluate side-chains 317 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 271 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 121 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 40 ILE Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 35 GLN Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 84 THR 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 35 GLN Chi-restraints excluded: chain R residue 40 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 66 optimal weight: 0.6980 chunk 175 optimal weight: 0.6980 chunk 115 optimal weight: 0.0370 chunk 209 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 25 optimal weight: 0.0040 chunk 97 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 188 optimal weight: 0.5980 chunk 154 optimal weight: 0.9980 overall best weight: 0.4070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN M 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.189589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121640 restraints weight = 20923.844| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.79 r_work: 0.3214 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 19296 Z= 0.089 Angle : 0.443 6.188 26262 Z= 0.245 Chirality : 0.040 0.136 2880 Planarity : 0.004 0.032 3348 Dihedral : 3.701 13.040 2466 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.59 % Allowed : 18.70 % Favored : 79.71 % 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 aren not related in a simple way. whole: 1.81 (0.17), residues: 2268 helix: 2.45 (0.19), residues: 720 sheet: 1.73 (0.26), residues: 378 loop : 0.28 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 95 TYR 0.021 0.001 TYR K 32 PHE 0.011 0.001 PHE R 94 TRP 0.011 0.001 TRP E 88 HIS 0.001 0.000 HIS I 18 Details of bonding type rmsd covalent geometry : bond 0.00191 (19296) covalent geometry : angle 0.44333 (26262) hydrogen bonds : bond 0.03156 ( 918) hydrogen bonds : angle 3.58980 ( 2484) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4624.85 seconds wall clock time: 80 minutes 39.16 seconds (4839.16 seconds total)