Starting phenix.real_space_refine on Tue Aug 26 23:44:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8axk_15700/08_2025/8axk_15700.cif Found real_map, /net/cci-nas-00/data/ceres_data/8axk_15700/08_2025/8axk_15700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8axk_15700/08_2025/8axk_15700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8axk_15700/08_2025/8axk_15700.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8axk_15700/08_2025/8axk_15700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8axk_15700/08_2025/8axk_15700.map" } resolution = 4.05 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= 0.008 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 101 5.16 5 C 28443 2.51 5 N 7082 2.21 5 O 8515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.05s 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: 44141 Number of models: 1 Model: "" Number of chains: 85 Chain: "A" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1486 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 7, 'TRANS': 180} Chain breaks: 2 Chain: "B" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1459 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 7, 'TRANS': 177} Chain breaks: 2 Chain: "C" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1480 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 7, 'TRANS': 180} Chain breaks: 2 Chain: "D" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1438 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 7, 'TRANS': 175} Chain breaks: 2 Chain: "E" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1464 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 8, 'TRANS': 177} Chain breaks: 2 Chain: "F" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2018 Classifications: {'peptide': 256} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain: "G" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 656 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "H" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain breaks: 1 Chain: "I" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 494 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain breaks: 1 Chain: "J" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 521 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain breaks: 1 Chain: "K" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 953 Classifications: {'peptide': 113} Link IDs: {'TRANS': 112} Chain breaks: 1 Chain: "M" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 308 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "N" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 644 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "O" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 727 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "P" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 707 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 641 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "R" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 643 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain breaks: 1 Chain: "S" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 477 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "T" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 468 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "U" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 477 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "V" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 468 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "W" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 468 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "X" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "Y" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "Z" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "0" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "2" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "4" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "6" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "8" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "x" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "y" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "z" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "1" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "3" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "5" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "7" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "9" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "a" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "b" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 638 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "c" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "d" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "e" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 638 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "f" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 638 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "g" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "h" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 594 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "i" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 594 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "j" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "k" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 594 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "l" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "m" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "n" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "o" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 638 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "p" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "q" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "r" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "s" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 638 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "t" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 617 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "u" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 638 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "v" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "w" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "a0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "b0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "c0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "d0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "e0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "f0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "g0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "h0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "i0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "j0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "k0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "l0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "m0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "n0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "o0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "p0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "q0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "r0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "s0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "t0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "u0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "v0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "w0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "x0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Time building chain proxies: 8.92, per 1000 atoms: 0.20 Number of scatterers: 44141 At special positions: 0 Unit cell: (148.055, 148.055, 271.203, 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 101 16.00 O 8515 8.00 N 7082 7.00 C 28443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 158 " - pdb=" SG CYS F 164 " distance=2.03 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: 3.31 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 953.7 nanoseconds 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10836 Finding SS restraints... Secondary structure from input PDB file: 229 helices and 16 sheets defined 76.4% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 Processing helix chain 'A' and resid 16 through 25 removed outlier: 3.580A pdb=" N THR A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 41 Processing helix chain 'A' and resid 48 through 64 removed outlier: 3.513A pdb=" N LEU A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 134 through 176 Proline residue: A 140 - end of helix removed outlier: 3.687A pdb=" N LEU A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) Proline residue: A 160 - end of helix Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.848A pdb=" N VAL A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Proline residue: A 188 - end of helix Processing helix chain 'A' and resid 199 through 212 Processing helix chain 'B' and resid 3 through 16 Processing helix chain 'B' and resid 16 through 25 removed outlier: 3.543A pdb=" N THR B 25 " --> pdb=" O VAL B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 42 removed outlier: 3.579A pdb=" N GLY B 42 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 73 removed outlier: 3.788A pdb=" N LEU B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) Proline residue: B 66 - end of helix Processing helix chain 'B' and resid 95 through 106 Processing helix chain 'B' and resid 108 through 118 removed outlier: 3.649A pdb=" N ALA B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 176 Proline residue: B 140 - end of helix removed outlier: 3.682A pdb=" N LEU B 159 " --> pdb=" O PHE B 155 " (cutoff:3.500A) Proline residue: B 160 - end of helix Processing helix chain 'B' and resid 181 through 184 Processing helix chain 'B' and resid 185 through 197 removed outlier: 4.141A pdb=" N ILE B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 16 through 24 removed outlier: 3.519A pdb=" N GLY C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 41 removed outlier: 3.636A pdb=" N PHE C 30 " --> pdb=" O CYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 72 removed outlier: 3.640A pdb=" N LEU C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) Proline residue: C 66 - end of helix removed outlier: 3.541A pdb=" N TYR C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 106 Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.560A pdb=" N ALA C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 176 Proline residue: C 140 - end of helix removed outlier: 3.739A pdb=" N LEU C 159 " --> pdb=" O PHE C 155 " (cutoff:3.500A) Proline residue: C 160 - end of helix Processing helix chain 'C' and resid 181 through 197 removed outlier: 4.196A pdb=" N ILE C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Proline residue: C 188 - end of helix Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'D' and resid 5 through 16 Processing helix chain 'D' and resid 16 through 25 Processing helix chain 'D' and resid 26 through 41 Processing helix chain 'D' and resid 48 through 64 removed outlier: 3.518A pdb=" N LEU D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 71 removed outlier: 3.712A pdb=" N GLY D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 108 through 121 Processing helix chain 'D' and resid 134 through 176 Proline residue: D 140 - end of helix removed outlier: 3.640A pdb=" N LEU D 159 " --> pdb=" O PHE D 155 " (cutoff:3.500A) Proline residue: D 160 - end of helix Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.547A pdb=" N VAL D 187 " --> pdb=" O ILE D 183 " (cutoff:3.500A) Proline residue: D 188 - end of helix Processing helix chain 'D' and resid 199 through 212 Processing helix chain 'E' and resid 5 through 16 Processing helix chain 'E' and resid 16 through 24 Processing helix chain 'E' and resid 26 through 41 Processing helix chain 'E' and resid 48 through 72 Proline residue: E 66 - end of helix Processing helix chain 'E' and resid 94 through 106 Processing helix chain 'E' and resid 108 through 120 removed outlier: 3.887A pdb=" N ALA E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 176 Proline residue: E 140 - end of helix removed outlier: 3.975A pdb=" N LEU E 159 " --> pdb=" O PHE E 155 " (cutoff:3.500A) Proline residue: E 160 - end of helix Processing helix chain 'E' and resid 181 through 197 removed outlier: 4.136A pdb=" N ILE E 185 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL E 187 " --> pdb=" O ILE E 183 " (cutoff:3.500A) Proline residue: E 188 - end of helix Processing helix chain 'E' and resid 198 through 212 removed outlier: 3.631A pdb=" N ILE E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 30 Proline residue: F 26 - end of helix Processing helix chain 'F' and resid 40 through 58 removed outlier: 3.877A pdb=" N ILE F 45 " --> pdb=" O PRO F 41 " (cutoff:3.500A) Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 70 through 90 removed outlier: 4.074A pdb=" N LEU F 74 " --> pdb=" O HIS F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 108 Processing helix chain 'F' and resid 110 through 116 Processing helix chain 'F' and resid 125 through 141 Processing helix chain 'F' and resid 142 through 158 Processing helix chain 'F' and resid 167 through 172 Processing helix chain 'F' and resid 173 through 207 Proline residue: F 188 - end of helix Processing helix chain 'F' and resid 212 through 231 Processing helix chain 'F' and resid 235 through 252 removed outlier: 3.947A pdb=" N LYS F 239 " --> pdb=" O ILE F 235 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL F 240 " --> pdb=" O TYR F 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 41 removed outlier: 4.468A pdb=" N TRP G 21 " --> pdb=" O ILE G 17 " (cutoff:3.500A) Proline residue: G 22 - end of helix Processing helix chain 'G' and resid 45 through 63 removed outlier: 3.733A pdb=" N PHE G 49 " --> pdb=" O GLN G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 84 removed outlier: 3.655A pdb=" N SER G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 35 removed outlier: 3.883A pdb=" N TRP H 21 " --> pdb=" O ILE H 17 " (cutoff:3.500A) Proline residue: H 22 - end of helix Processing helix chain 'H' and resid 48 through 85 removed outlier: 5.269A pdb=" N GLY H 65 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N TRP H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER H 84 " --> pdb=" O PHE H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 25 removed outlier: 3.636A pdb=" N TRP I 21 " --> pdb=" O ILE I 17 " (cutoff:3.500A) Proline residue: I 22 - end of helix Processing helix chain 'I' and resid 49 through 85 removed outlier: 5.399A pdb=" N GLY I 65 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N TRP I 66 " --> pdb=" O LEU I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 27 removed outlier: 3.810A pdb=" N TRP J 21 " --> pdb=" O ILE J 17 " (cutoff:3.500A) Proline residue: J 22 - end of helix Processing helix chain 'J' and resid 49 through 85 removed outlier: 4.513A pdb=" N GLY J 65 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N TRP J 66 " --> pdb=" O LEU J 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 41 removed outlier: 3.816A pdb=" N PHE K 39 " --> pdb=" O LEU K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 63 Processing helix chain 'K' and resid 68 through 83 Processing helix chain 'K' and resid 132 through 155 removed outlier: 3.976A pdb=" N LYS K 136 " --> pdb=" O LYS K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 163 Processing helix chain 'K' and resid 169 through 186 removed outlier: 4.131A pdb=" N LEU K 186 " --> pdb=" O ILE K 182 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 95 Processing helix chain 'N' and resid 25 through 54 Processing helix chain 'N' and resid 55 through 58 removed outlier: 3.579A pdb=" N LEU N 58 " --> pdb=" O PRO N 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 55 through 58' Processing helix chain 'N' and resid 59 through 97 removed outlier: 3.890A pdb=" N SER N 97 " --> pdb=" O THR N 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 54 Processing helix chain 'O' and resid 59 through 96 Processing helix chain 'P' and resid 25 through 54 Processing helix chain 'P' and resid 55 through 58 removed outlier: 3.667A pdb=" N LEU P 58 " --> pdb=" O PRO P 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 55 through 58' Processing helix chain 'P' and resid 59 through 96 Processing helix chain 'Q' and resid 26 through 54 Processing helix chain 'Q' and resid 59 through 97 removed outlier: 4.144A pdb=" N SER Q 97 " --> pdb=" O THR Q 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 54 Processing helix chain 'R' and resid 59 through 97 removed outlier: 4.243A pdb=" N SER R 97 " --> pdb=" O THR R 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 40 Processing helix chain 'S' and resid 43 through 83 removed outlier: 3.813A pdb=" N ILE S 79 " --> pdb=" O ASP S 75 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN S 81 " --> pdb=" O ALA S 77 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE S 82 " --> pdb=" O ILE S 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 40 Processing helix chain 'T' and resid 43 through 83 removed outlier: 3.612A pdb=" N ILE T 79 " --> pdb=" O ASP T 75 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE T 82 " --> pdb=" O ILE T 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 40 Processing helix chain 'U' and resid 43 through 82 removed outlier: 3.680A pdb=" N ILE U 79 " --> pdb=" O ASP U 75 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN U 81 " --> pdb=" O ALA U 77 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE U 82 " --> pdb=" O ILE U 78 " (cutoff:3.500A) Processing helix chain 'V' and resid 26 through 40 Processing helix chain 'V' and resid 43 through 82 removed outlier: 3.587A pdb=" N ILE V 79 " --> pdb=" O ASP V 75 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE V 82 " --> pdb=" O ILE V 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 26 through 40 Processing helix chain 'W' and resid 43 through 83 removed outlier: 3.724A pdb=" N ILE W 79 " --> pdb=" O ASP W 75 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN W 81 " --> pdb=" O ALA W 77 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE W 82 " --> pdb=" O ILE W 78 " (cutoff:3.500A) Processing helix chain 'X' and resid 121 through 132 Processing helix chain 'X' and resid 155 through 168 Processing helix chain 'Y' and resid 121 through 132 Processing helix chain 'Y' and resid 155 through 168 Processing helix chain 'Z' and resid 121 through 132 Processing helix chain 'Z' and resid 155 through 168 Processing helix chain '0' and resid 121 through 132 Processing helix chain '0' and resid 155 through 168 Processing helix chain '2' and resid 121 through 132 Processing helix chain '2' and resid 155 through 168 Processing helix chain '4' and resid 121 through 132 Processing helix chain '4' and resid 155 through 168 Processing helix chain '6' and resid 121 through 132 Processing helix chain '6' and resid 155 through 168 Processing helix chain '8' and resid 121 through 132 Processing helix chain '8' and resid 155 through 168 Processing helix chain 'x' and resid 121 through 132 Processing helix chain 'x' and resid 155 through 168 Processing helix chain 'y' and resid 121 through 132 Processing helix chain 'y' and resid 155 through 169 Processing helix chain 'z' and resid 121 through 132 Processing helix chain 'z' and resid 155 through 168 Processing helix chain '1' and resid 121 through 132 Processing helix chain '1' and resid 155 through 168 Processing helix chain '3' and resid 121 through 132 Processing helix chain '3' and resid 155 through 168 Processing helix chain '5' and resid 121 through 132 Processing helix chain '5' and resid 155 through 169 Processing helix chain '7' and resid 121 through 132 Processing helix chain '7' and resid 155 through 168 Processing helix chain '9' and resid 121 through 132 Processing helix chain '9' and resid 155 through 168 Processing helix chain 'a' and resid 11 through 23 removed outlier: 3.648A pdb=" N THR a 23 " --> pdb=" O PHE a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 24 through 40 Processing helix chain 'a' and resid 43 through 80 Processing helix chain 'b' and resid 11 through 23 Processing helix chain 'b' and resid 24 through 40 removed outlier: 3.530A pdb=" N GLY b 28 " --> pdb=" O GLN b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 43 through 80 removed outlier: 3.514A pdb=" N GLN b 80 " --> pdb=" O ALA b 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 81 through 83 No H-bonds generated for 'chain 'b' and resid 81 through 83' Processing helix chain 'c' and resid 11 through 23 removed outlier: 3.513A pdb=" N THR c 23 " --> pdb=" O PHE c 19 " (cutoff:3.500A) Processing helix chain 'c' and resid 24 through 40 removed outlier: 3.590A pdb=" N GLY c 28 " --> pdb=" O GLN c 24 " (cutoff:3.500A) Processing helix chain 'c' and resid 43 through 81 removed outlier: 3.979A pdb=" N ASN c 81 " --> pdb=" O ALA c 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 11 through 23 Processing helix chain 'd' and resid 24 through 40 Processing helix chain 'd' and resid 43 through 80 Processing helix chain 'd' and resid 81 through 83 No H-bonds generated for 'chain 'd' and resid 81 through 83' Processing helix chain 'e' and resid 11 through 22 Processing helix chain 'e' and resid 24 through 40 Processing helix chain 'e' and resid 43 through 81 removed outlier: 3.923A pdb=" N ASN e 81 " --> pdb=" O ALA e 77 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 23 removed outlier: 3.525A pdb=" N THR f 23 " --> pdb=" O PHE f 19 " (cutoff:3.500A) Processing helix chain 'f' and resid 24 through 40 Processing helix chain 'f' and resid 43 through 80 Processing helix chain 'g' and resid 11 through 23 Processing helix chain 'g' and resid 24 through 40 Processing helix chain 'g' and resid 43 through 81 removed outlier: 4.013A pdb=" N ASN g 81 " --> pdb=" O ALA g 77 " (cutoff:3.500A) Processing helix chain 'h' and resid 11 through 22 Processing helix chain 'h' and resid 24 through 40 removed outlier: 3.693A pdb=" N GLY h 28 " --> pdb=" O GLN h 24 " (cutoff:3.500A) Processing helix chain 'h' and resid 43 through 80 Processing helix chain 'h' and resid 81 through 83 No H-bonds generated for 'chain 'h' and resid 81 through 83' Processing helix chain 'i' and resid 12 through 22 Processing helix chain 'i' and resid 24 through 40 removed outlier: 3.668A pdb=" N GLY i 28 " --> pdb=" O GLN i 24 " (cutoff:3.500A) Processing helix chain 'i' and resid 43 through 81 removed outlier: 3.854A pdb=" N ASN i 81 " --> pdb=" O ALA i 77 " (cutoff:3.500A) Processing helix chain 'j' and resid 11 through 23 removed outlier: 3.593A pdb=" N THR j 23 " --> pdb=" O PHE j 19 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 40 removed outlier: 3.507A pdb=" N GLY j 28 " --> pdb=" O GLN j 24 " (cutoff:3.500A) Processing helix chain 'j' and resid 43 through 81 removed outlier: 3.925A pdb=" N ASN j 81 " --> pdb=" O ALA j 77 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 23 removed outlier: 3.804A pdb=" N THR k 23 " --> pdb=" O PHE k 19 " (cutoff:3.500A) Processing helix chain 'k' and resid 24 through 40 removed outlier: 3.557A pdb=" N GLY k 28 " --> pdb=" O GLN k 24 " (cutoff:3.500A) Processing helix chain 'k' and resid 43 through 80 Processing helix chain 'k' and resid 81 through 83 No H-bonds generated for 'chain 'k' and resid 81 through 83' Processing helix chain 'l' and resid 12 through 23 removed outlier: 3.547A pdb=" N THR l 23 " --> pdb=" O PHE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 40 removed outlier: 3.539A pdb=" N GLY l 28 " --> pdb=" O GLN l 24 " (cutoff:3.500A) Processing helix chain 'l' and resid 43 through 81 removed outlier: 3.573A pdb=" N ASN l 81 " --> pdb=" O ALA l 77 " (cutoff:3.500A) Processing helix chain 'm' and resid 11 through 23 Processing helix chain 'm' and resid 24 through 40 Processing helix chain 'm' and resid 43 through 80 Processing helix chain 'n' and resid 11 through 23 removed outlier: 3.634A pdb=" N THR n 23 " --> pdb=" O PHE n 19 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 40 Processing helix chain 'n' and resid 43 through 80 Processing helix chain 'o' and resid 11 through 23 Processing helix chain 'o' and resid 24 through 40 Processing helix chain 'o' and resid 43 through 80 Processing helix chain 'o' and resid 81 through 83 No H-bonds generated for 'chain 'o' and resid 81 through 83' Processing helix chain 'p' and resid 11 through 23 removed outlier: 3.611A pdb=" N THR p 23 " --> pdb=" O PHE p 19 " (cutoff:3.500A) Processing helix chain 'p' and resid 24 through 40 removed outlier: 3.538A pdb=" N GLY p 28 " --> pdb=" O GLN p 24 " (cutoff:3.500A) Processing helix chain 'p' and resid 43 through 81 removed outlier: 3.921A pdb=" N ASN p 81 " --> pdb=" O ALA p 77 " (cutoff:3.500A) Processing helix chain 'q' and resid 11 through 23 removed outlier: 3.876A pdb=" N THR q 23 " --> pdb=" O PHE q 19 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 40 removed outlier: 3.537A pdb=" N GLY q 28 " --> pdb=" O GLN q 24 " (cutoff:3.500A) Processing helix chain 'q' and resid 43 through 80 Processing helix chain 'r' and resid 11 through 23 removed outlier: 3.764A pdb=" N THR r 23 " --> pdb=" O PHE r 19 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 40 removed outlier: 3.686A pdb=" N GLY r 28 " --> pdb=" O GLN r 24 " (cutoff:3.500A) Processing helix chain 'r' and resid 43 through 80 Processing helix chain 's' and resid 11 through 23 Processing helix chain 's' and resid 24 through 40 Processing helix chain 's' and resid 43 through 80 removed outlier: 3.567A pdb=" N GLN s 80 " --> pdb=" O ALA s 76 " (cutoff:3.500A) Processing helix chain 's' and resid 81 through 83 No H-bonds generated for 'chain 's' and resid 81 through 83' Processing helix chain 't' and resid 11 through 23 removed outlier: 3.542A pdb=" N THR t 23 " --> pdb=" O PHE t 19 " (cutoff:3.500A) Processing helix chain 't' and resid 24 through 40 Processing helix chain 't' and resid 43 through 80 Processing helix chain 'u' and resid 11 through 23 removed outlier: 3.614A pdb=" N THR u 23 " --> pdb=" O PHE u 19 " (cutoff:3.500A) Processing helix chain 'u' and resid 24 through 40 removed outlier: 3.918A pdb=" N GLY u 28 " --> pdb=" O GLN u 24 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 80 Processing helix chain 'u' and resid 81 through 83 No H-bonds generated for 'chain 'u' and resid 81 through 83' Processing helix chain 'v' and resid 11 through 23 removed outlier: 3.986A pdb=" N THR v 23 " --> pdb=" O PHE v 19 " (cutoff:3.500A) Processing helix chain 'v' and resid 24 through 40 removed outlier: 3.644A pdb=" N GLY v 28 " --> pdb=" O GLN v 24 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 81 removed outlier: 3.517A pdb=" N GLN v 80 " --> pdb=" O ALA v 76 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN v 81 " --> pdb=" O ALA v 77 " (cutoff:3.500A) Processing helix chain 'w' and resid 11 through 23 removed outlier: 3.542A pdb=" N THR w 23 " --> pdb=" O PHE w 19 " (cutoff:3.500A) Processing helix chain 'w' and resid 24 through 40 removed outlier: 3.618A pdb=" N GLY w 28 " --> pdb=" O GLN w 24 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN w 40 " --> pdb=" O LYS w 36 " (cutoff:3.500A) Processing helix chain 'w' and resid 43 through 81 removed outlier: 3.518A pdb=" N GLN w 80 " --> pdb=" O ALA w 76 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN w 81 " --> pdb=" O ALA w 77 " (cutoff:3.500A) Processing helix chain 'a0' and resid 98 through 106 Processing helix chain 'b0' and resid 98 through 106 Processing helix chain 'c0' and resid 98 through 106 Processing helix chain 'd0' and resid 98 through 106 Processing helix chain 'e0' and resid 98 through 106 Processing helix chain 'f0' and resid 98 through 106 Processing helix chain 'g0' and resid 98 through 106 Processing helix chain 'h0' and resid 98 through 106 Processing helix chain 'i0' and resid 98 through 106 Processing helix chain 'j0' and resid 98 through 106 removed outlier: 3.520A pdb=" N GLUj0 102 " --> pdb=" O SERj0 98 " (cutoff:3.500A) Processing helix chain 'k0' and resid 98 through 106 Processing helix chain 'l0' and resid 98 through 106 Processing helix chain 'm0' and resid 98 through 106 Processing helix chain 'n0' and resid 98 through 106 Processing helix chain 'o0' and resid 98 through 106 Processing helix chain 'p0' and resid 98 through 106 Processing helix chain 'q0' and resid 98 through 106 Processing helix chain 'r0' and resid 98 through 106 Processing helix chain 's0' and resid 98 through 106 Processing helix chain 't0' and resid 98 through 106 removed outlier: 4.070A pdb=" N GLUt0 102 " --> pdb=" O SERt0 98 " (cutoff:3.500A) Processing helix chain 'u0' and resid 98 through 106 Processing helix chain 'v0' and resid 98 through 106 Processing helix chain 'w0' and resid 98 through 106 Processing helix chain 'x0' and resid 98 through 106 Processing sheet with id=AA1, first strand: chain 'N' and resid 11 through 14 Processing sheet with id=AA2, first strand: chain 'O' and resid 11 through 14 Processing sheet with id=AA3, first strand: chain 'P' and resid 11 through 14 Processing sheet with id=AA4, first strand: chain 'Q' and resid 11 through 14 Processing sheet with id=AA5, first strand: chain 'R' and resid 11 through 12 Processing sheet with id=AA6, first strand: chain 'X' and resid 111 through 116 Processing sheet with id=AA7, first strand: chain 'Z' and resid 111 through 116 Processing sheet with id=AA8, first strand: chain '2' and resid 111 through 116 Processing sheet with id=AA9, first strand: chain '4' and resid 111 through 116 Processing sheet with id=AB1, first strand: chain '8' and resid 111 through 116 Processing sheet with id=AB2, first strand: chain 'x' and resid 111 through 116 Processing sheet with id=AB3, first strand: chain 'y' and resid 111 through 116 Processing sheet with id=AB4, first strand: chain 'z' and resid 111 through 116 Processing sheet with id=AB5, first strand: chain '1' and resid 111 through 116 Processing sheet with id=AB6, first strand: chain '5' and resid 111 through 116 Processing sheet with id=AB7, first strand: chain '7' and resid 111 through 116 3327 hydrogen bonds defined for protein. 9915 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: 7.63 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 13971 1.34 - 1.46: 9401 1.46 - 1.58: 21297 1.58 - 1.69: 0 1.69 - 1.81: 189 Bond restraints: 44858 Sorted by residual: bond pdb=" C VAL B 46 " pdb=" N PRO B 47 " ideal model delta sigma weight residual 1.337 1.350 -0.013 9.80e-03 1.04e+04 1.86e+00 bond pdb=" N VALe0 96 " pdb=" CA VALe0 96 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.25e-02 6.40e+03 1.31e+00 bond pdb=" CB ILE C 153 " pdb=" CG2 ILE C 153 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.12e+00 bond pdb=" CA ILE K 33 " pdb=" CB ILE K 33 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.02e+00 bond pdb=" CA ILE K 131 " pdb=" C ILE K 131 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.27e-02 6.20e+03 9.65e-01 ... (remaining 44853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 59370 1.24 - 2.48: 1171 2.48 - 3.72: 272 3.72 - 4.96: 53 4.96 - 6.20: 24 Bond angle restraints: 60890 Sorted by residual: angle pdb=" C ILE O 4 " pdb=" N TYR O 5 " pdb=" CA TYR O 5 " ideal model delta sigma weight residual 120.09 125.08 -4.99 1.25e+00 6.40e-01 1.59e+01 angle pdb=" N VAL K 31 " pdb=" CA VAL K 31 " pdb=" C VAL K 31 " ideal model delta sigma weight residual 111.77 108.27 3.50 1.04e+00 9.25e-01 1.13e+01 angle pdb=" C SER T 42 " pdb=" N ASN T 43 " pdb=" CA ASN T 43 " ideal model delta sigma weight residual 121.61 117.19 4.42 1.39e+00 5.18e-01 1.01e+01 angle pdb=" N SERp0 94 " pdb=" CA SERp0 94 " pdb=" C SERp0 94 " ideal model delta sigma weight residual 108.19 112.16 -3.97 1.29e+00 6.01e-01 9.49e+00 angle pdb=" C PHE p 82 " pdb=" N ARG p 83 " pdb=" CA ARG p 83 " ideal model delta sigma weight residual 121.70 126.85 -5.15 1.80e+00 3.09e-01 8.19e+00 ... (remaining 60885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 26017 17.42 - 34.85: 1043 34.85 - 52.27: 240 52.27 - 69.70: 45 69.70 - 87.12: 16 Dihedral angle restraints: 27361 sinusoidal: 10773 harmonic: 16588 Sorted by residual: dihedral pdb=" CA ILE R 12 " pdb=" C ILE R 12 " pdb=" N ILE R 13 " pdb=" CA ILE R 13 " ideal model delta harmonic sigma weight residual 180.00 -155.91 -24.09 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA PRO F 32 " pdb=" C PRO F 32 " pdb=" N PHE F 33 " pdb=" CA PHE F 33 " ideal model delta harmonic sigma weight residual 180.00 155.98 24.02 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA VAL E 46 " pdb=" C VAL E 46 " pdb=" N PRO E 47 " pdb=" CA PRO E 47 " ideal model delta harmonic sigma weight residual 180.00 158.29 21.71 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 27358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 5610 0.037 - 0.073: 1324 0.073 - 0.110: 355 0.110 - 0.146: 77 0.146 - 0.183: 3 Chirality restraints: 7369 Sorted by residual: chirality pdb=" CB ILE K 131 " pdb=" CA ILE K 131 " pdb=" CG1 ILE K 131 " pdb=" CG2 ILE K 131 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.33e-01 chirality pdb=" CA PROt0 99 " pdb=" N PROt0 99 " pdb=" C PROt0 99 " pdb=" CB PROt0 99 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA ILE y 120 " pdb=" N ILE y 120 " pdb=" C ILE y 120 " pdb=" CB ILE y 120 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 7366 not shown) Planarity restraints: 7620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL P 10 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.48e+00 pdb=" C VAL P 10 " 0.044 2.00e-02 2.50e+03 pdb=" O VAL P 10 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP P 11 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHEo0 90 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PROo0 91 " -0.100 5.00e-02 4.00e+02 pdb=" CA PROo0 91 " 0.030 5.00e-02 4.00e+02 pdb=" CD PROo0 91 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL c 5 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO c 6 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO c 6 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO c 6 " 0.028 5.00e-02 4.00e+02 ... (remaining 7617 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1062 2.71 - 3.26: 45875 3.26 - 3.81: 72735 3.81 - 4.35: 79862 4.35 - 4.90: 145541 Nonbonded interactions: 345075 Sorted by model distance: nonbonded pdb=" O ALA W 38 " pdb=" OG1 THR h 23 " model vdw 2.167 3.040 nonbonded pdb=" O ALA V 38 " pdb=" OG1 THR i 23 " model vdw 2.181 3.040 nonbonded pdb=" O VAL D 21 " pdb=" OG1 THR D 25 " model vdw 2.185 3.040 nonbonded pdb=" NZ LYS Q 14 " pdb=" OD1 ASN X 164 " model vdw 2.193 3.120 nonbonded pdb=" O THR Z 149 " pdb=" OH TYR z 128 " model vdw 2.194 3.040 ... (remaining 345070 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = (chain 'A' and (resid 1 through 71 or resid 94 through 214)) selection = (chain 'B' and (resid 1 through 71 or resid 94 through 120 or resid 131 through \ 214)) selection = (chain 'C' and (resid 1 through 71 or resid 94 through 120 or resid 131 through \ 214)) selection = (chain 'D' and (resid 1 through 120 or resid 131 through 214)) selection = (chain 'E' and (resid 1 through 71 or resid 94 through 130 or resid 132 through \ 214)) } ncs_group { reference = (chain 'G' and (resid 1 through 36 or resid 47 through 85)) selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'J' and (resid 1 through 25 or resid 48 through 85)) } ncs_group { reference = (chain 'N' and (resid 8 through 14 or resid 24 through 97)) selection = (chain 'O' and (resid 8 through 14 or resid 24 through 97)) selection = (chain 'P' and (resid 8 through 14 or resid 24 through 97)) selection = (chain 'Q' and (resid 8 through 14 or resid 16 through 97)) selection = (chain 'R' and (resid 8 through 14 or resid 16 or resid 25 through 97)) } ncs_group { reference = (chain 'S' and resid 25 through 83) selection = chain 'T' selection = (chain 'U' and resid 25 through 83) selection = chain 'V' selection = chain 'W' } ncs_group { reference = (chain 'a' and resid 9 through 83) selection = (chain 'b' and resid 9 through 83) selection = (chain 'c' and resid 9 through 83) selection = (chain 'd' and resid 9 through 83) selection = (chain 'e' and resid 9 through 83) selection = (chain 'f' and resid 9 through 83) selection = (chain 'g' and resid 9 through 83) selection = chain 'h' selection = chain 'i' selection = (chain 'j' and resid 9 through 83) selection = chain 'k' selection = (chain 'l' and resid 9 through 83) selection = (chain 'm' and resid 9 through 83) selection = (chain 'n' and resid 9 through 83) selection = (chain 'o' and resid 9 through 83) selection = (chain 'p' and resid 9 through 83) selection = (chain 'q' and resid 9 through 83) selection = (chain 'r' and resid 9 through 83) selection = (chain 's' and resid 9 through 83) selection = (chain 't' and resid 9 through 83) selection = (chain 'u' and resid 9 through 83) selection = (chain 'v' and resid 9 through 83) selection = (chain 'w' and resid 9 through 83) } ncs_group { reference = chain 'a0' selection = chain 'b0' selection = chain 'c0' selection = chain 'd0' selection = chain 'e0' selection = chain 'f0' selection = chain 'g0' selection = chain 'h0' selection = chain 'i0' selection = chain 'j0' selection = chain 'k0' selection = chain 'l0' selection = chain 'm0' selection = chain 'n0' selection = chain 'o0' selection = chain 'p0' selection = chain 'q0' selection = chain 'r0' selection = chain 's0' selection = chain 't0' selection = chain 'u0' selection = chain 'v0' selection = chain 'w0' selection = chain 'x0' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.900 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: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 34.580 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 : 0.002 0.038 44859 Z= 0.114 Angle : 0.465 6.197 60892 Z= 0.262 Chirality : 0.036 0.183 7369 Planarity : 0.004 0.058 7620 Dihedral : 10.517 87.125 16522 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.27 % Allowed : 5.51 % Favored : 91.22 % 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: 3.62 (0.12), residues: 5404 helix: 3.57 (0.08), residues: 4144 sheet: 1.63 (0.33), residues: 192 loop : -2.78 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG o 61 TYR 0.012 0.001 TYR 1 151 PHE 0.018 0.001 PHE K 45 TRP 0.009 0.001 TRP K 174 HIS 0.002 0.000 HIS F 11 Details of bonding type rmsd covalent geometry : bond 0.00234 (44858) covalent geometry : angle 0.46478 (60890) SS BOND : bond 0.00180 ( 1) SS BOND : angle 0.54987 ( 2) hydrogen bonds : bond 0.09212 ( 3327) hydrogen bonds : angle 3.76748 ( 9915) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2737 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 2573 time to evaluate : 1.768 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: 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 5 MET cc_start: 0.8942 (mmm) cc_final: 0.8657 (mmm) REVERT: A 68 ILE cc_start: 0.9483 (mt) cc_final: 0.9151 (mt) REVERT: A 69 GLU cc_start: 0.7988 (tp30) cc_final: 0.7078 (mm-30) REVERT: A 96 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8956 (tt) REVERT: A 97 MET cc_start: 0.8332 (tpt) cc_final: 0.8067 (tpt) REVERT: A 98 GLU cc_start: 0.8594 (tp30) cc_final: 0.8360 (tp30) REVERT: A 101 GLN cc_start: 0.8887 (tt0) cc_final: 0.8391 (tm-30) REVERT: A 142 TYR cc_start: 0.9304 (t80) cc_final: 0.8819 (t80) REVERT: A 152 LYS cc_start: 0.9382 (tttt) cc_final: 0.9169 (ttpp) REVERT: A 179 MET cc_start: 0.8279 (mmm) cc_final: 0.7967 (mmm) REVERT: A 205 LYS cc_start: 0.9077 (mttt) cc_final: 0.8295 (tttt) REVERT: A 208 ILE cc_start: 0.8101 (mm) cc_final: 0.7808 (mm) REVERT: B 44 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8565 (mm-40) REVERT: B 65 LYS cc_start: 0.8856 (tttp) cc_final: 0.8360 (tttt) REVERT: B 67 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8262 (tp) REVERT: B 69 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7772 (mm-30) REVERT: B 96 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8361 (tt) REVERT: B 120 GLU cc_start: 0.6180 (mt-10) cc_final: 0.5883 (mp0) REVERT: B 133 TYR cc_start: 0.7513 (m-10) cc_final: 0.6846 (m-10) REVERT: B 190 LYS cc_start: 0.9217 (mtmt) cc_final: 0.8621 (mtmm) REVERT: B 211 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.7319 (t80) REVERT: C 117 ARG cc_start: 0.8447 (mtt180) cc_final: 0.8237 (tpt170) REVERT: C 146 GLU cc_start: 0.8544 (tp30) cc_final: 0.8002 (mm-30) REVERT: C 164 VAL cc_start: 0.9572 (t) cc_final: 0.9338 (t) REVERT: C 165 ASP cc_start: 0.7841 (m-30) cc_final: 0.7471 (m-30) REVERT: C 167 VAL cc_start: 0.9265 (t) cc_final: 0.9046 (p) REVERT: C 193 LEU cc_start: 0.9443 (tp) cc_final: 0.9215 (tt) REVERT: D 2 LEU cc_start: 0.9142 (mt) cc_final: 0.8739 (mt) REVERT: D 6 SER cc_start: 0.8595 (m) cc_final: 0.7909 (p) REVERT: D 27 TYR cc_start: 0.9078 (t80) cc_final: 0.8778 (t80) REVERT: D 44 GLN cc_start: 0.8300 (pm20) cc_final: 0.7846 (pm20) REVERT: D 158 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8497 (m-80) REVERT: D 170 SER cc_start: 0.8883 (m) cc_final: 0.8634 (t) REVERT: E 36 MET cc_start: 0.8695 (mmm) cc_final: 0.7872 (mmm) REVERT: E 64 MET cc_start: 0.8617 (mmm) cc_final: 0.7567 (mmm) REVERT: E 100 LYS cc_start: 0.9256 (mtpm) cc_final: 0.9021 (mtpp) REVERT: E 158 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.8181 (m-80) REVERT: E 184 THR cc_start: 0.9250 (p) cc_final: 0.8496 (t) REVERT: F 69 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7171 (pm20) REVERT: F 128 LYS cc_start: 0.8818 (tptt) cc_final: 0.8538 (ttpt) REVERT: F 140 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.6737 (t80) REVERT: F 145 VAL cc_start: 0.8664 (t) cc_final: 0.7796 (t) REVERT: F 152 GLN cc_start: 0.9178 (tt0) cc_final: 0.8578 (tp40) REVERT: F 170 ASN cc_start: 0.8365 (m-40) cc_final: 0.8141 (m-40) REVERT: G 7 MET cc_start: 0.8617 (mmm) cc_final: 0.8335 (tpp) REVERT: G 57 SER cc_start: 0.9206 (t) cc_final: 0.8862 (p) REVERT: G 74 PHE cc_start: 0.9203 (t80) cc_final: 0.8772 (t80) REVERT: G 75 CYS cc_start: 0.8613 (m) cc_final: 0.8335 (m) REVERT: H 6 TYR cc_start: 0.7253 (t80) cc_final: 0.7030 (t80) REVERT: H 58 ILE cc_start: 0.8498 (mm) cc_final: 0.8282 (mm) REVERT: H 59 SER cc_start: 0.8706 (m) cc_final: 0.8495 (m) REVERT: H 80 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.6098 (m-80) REVERT: H 81 LEU cc_start: 0.8738 (mt) cc_final: 0.8336 (mt) REVERT: H 83 LYS cc_start: 0.8699 (tptt) cc_final: 0.8494 (tppp) REVERT: I 1 MET cc_start: 0.7473 (ptm) cc_final: 0.7230 (ptp) REVERT: I 5 VAL cc_start: 0.9240 (t) cc_final: 0.8677 (p) REVERT: I 9 ASN cc_start: 0.8422 (m-40) cc_final: 0.8174 (m-40) REVERT: I 18 PHE cc_start: 0.8925 (m-10) cc_final: 0.8513 (m-10) REVERT: I 49 PHE cc_start: 0.6881 (OUTLIER) cc_final: 0.6273 (m-10) REVERT: I 53 LEU cc_start: 0.8093 (tp) cc_final: 0.7707 (tp) REVERT: I 60 LEU cc_start: 0.8698 (mt) cc_final: 0.8408 (mt) REVERT: I 82 ILE cc_start: 0.8984 (mt) cc_final: 0.8550 (mt) REVERT: J 3 ASP cc_start: 0.7523 (p0) cc_final: 0.7305 (p0) REVERT: J 66 TRP cc_start: 0.9161 (t60) cc_final: 0.8695 (t-100) REVERT: J 77 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7761 (mt-10) REVERT: K 46 SER cc_start: 0.7643 (m) cc_final: 0.6953 (t) REVERT: K 51 MET cc_start: 0.7789 (mmt) cc_final: 0.6947 (mmt) REVERT: K 132 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.6748 (mttt) REVERT: K 139 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.6819 (mm) REVERT: K 156 ARG cc_start: 0.6778 (ttp-110) cc_final: 0.6274 (ptm-80) REVERT: K 157 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7733 (pttp) REVERT: K 177 LEU cc_start: 0.9155 (tp) cc_final: 0.8871 (tp) REVERT: K 182 ILE cc_start: 0.8092 (tp) cc_final: 0.7861 (tp) REVERT: M 72 ASN cc_start: 0.8199 (m-40) cc_final: 0.7987 (t0) REVERT: N 14 LYS cc_start: 0.3229 (OUTLIER) cc_final: 0.2923 (mtmt) REVERT: N 46 SER cc_start: 0.8847 (m) cc_final: 0.8523 (p) REVERT: N 58 LEU cc_start: 0.9276 (mt) cc_final: 0.8980 (mt) REVERT: P 10 VAL cc_start: 0.6838 (OUTLIER) cc_final: 0.6311 (m) REVERT: P 12 ILE cc_start: 0.8514 (mt) cc_final: 0.8050 (mt) REVERT: P 57 SER cc_start: 0.9326 (m) cc_final: 0.8699 (p) REVERT: Q 13 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7457 (mt) REVERT: Q 49 MET cc_start: 0.9056 (mmt) cc_final: 0.8742 (mmm) REVERT: R 47 GLN cc_start: 0.8606 (tp40) cc_final: 0.8195 (tm-30) REVERT: R 51 MET cc_start: 0.8125 (ttm) cc_final: 0.7855 (ttp) REVERT: S 36 LYS cc_start: 0.9164 (mtmt) cc_final: 0.8963 (mtpt) REVERT: S 69 LYS cc_start: 0.9048 (tttp) cc_final: 0.8285 (tptm) REVERT: U 61 ARG cc_start: 0.8990 (mmt180) cc_final: 0.8498 (tpp-160) REVERT: V 32 LEU cc_start: 0.8735 (mt) cc_final: 0.8271 (tt) REVERT: V 50 TYR cc_start: 0.9196 (t80) cc_final: 0.8885 (t80) REVERT: V 59 LEU cc_start: 0.9087 (mt) cc_final: 0.8830 (mt) REVERT: V 64 GLN cc_start: 0.8626 (tt0) cc_final: 0.8373 (tt0) REVERT: V 80 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8495 (tp-100) REVERT: W 39 LYS cc_start: 0.8420 (mttt) cc_final: 0.7837 (mptt) REVERT: W 40 ASN cc_start: 0.8781 (t0) cc_final: 0.8114 (t0) REVERT: W 43 ASN cc_start: 0.8640 (t0) cc_final: 0.8040 (t0) REVERT: X 142 ARG cc_start: 0.8241 (mmt-90) cc_final: 0.7845 (mmt-90) REVERT: Y 112 SER cc_start: 0.7747 (p) cc_final: 0.7309 (m) REVERT: Y 123 ASN cc_start: 0.8639 (t0) cc_final: 0.8380 (t0) REVERT: Y 131 ASP cc_start: 0.7193 (t70) cc_final: 0.6736 (t70) REVERT: Z 111 ILE cc_start: 0.9198 (mt) cc_final: 0.8898 (pt) REVERT: Z 112 SER cc_start: 0.8622 (p) cc_final: 0.8414 (m) REVERT: Z 115 ILE cc_start: 0.9013 (mt) cc_final: 0.8800 (mp) REVERT: Z 124 TYR cc_start: 0.8350 (t80) cc_final: 0.7946 (t80) REVERT: Z 161 LEU cc_start: 0.8543 (tp) cc_final: 0.8325 (tp) REVERT: 0 133 ASN cc_start: 0.7968 (m-40) cc_final: 0.7629 (m-40) REVERT: 0 149 THR cc_start: 0.9530 (m) cc_final: 0.9305 (t) REVERT: 4 117 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.7870 (pp) REVERT: 4 150 PHE cc_start: 0.9038 (p90) cc_final: 0.8415 (p90) REVERT: 4 151 TYR cc_start: 0.8254 (t80) cc_final: 0.7576 (t80) REVERT: 6 127 GLN cc_start: 0.8904 (tp40) cc_final: 0.8425 (tp40) REVERT: 6 149 THR cc_start: 0.9167 (m) cc_final: 0.8414 (p) REVERT: 6 168 LEU cc_start: 0.9140 (tp) cc_final: 0.8850 (tt) REVERT: 8 115 ILE cc_start: 0.9094 (mt) cc_final: 0.8789 (mm) REVERT: 8 144 ASN cc_start: 0.8104 (t0) cc_final: 0.7642 (t0) REVERT: x 112 SER cc_start: 0.8674 (p) cc_final: 0.8266 (m) REVERT: x 117 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6936 (pp) REVERT: x 150 PHE cc_start: 0.9413 (p90) cc_final: 0.8466 (p90) REVERT: y 115 ILE cc_start: 0.9432 (mt) cc_final: 0.9112 (mt) REVERT: y 117 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8714 (pp) REVERT: y 148 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7068 (mtmm) REVERT: y 160 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7811 (mm-30) REVERT: z 112 SER cc_start: 0.9134 (p) cc_final: 0.8708 (m) REVERT: z 119 ASN cc_start: 0.8510 (m-40) cc_final: 0.8220 (p0) REVERT: z 148 LYS cc_start: 0.9000 (mppt) cc_final: 0.8680 (mtmt) REVERT: z 149 THR cc_start: 0.9162 (m) cc_final: 0.8676 (t) REVERT: z 151 TYR cc_start: 0.8587 (t80) cc_final: 0.8273 (t80) REVERT: z 161 LEU cc_start: 0.8891 (tp) cc_final: 0.8649 (tt) REVERT: 1 117 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6534 (pp) REVERT: 1 127 GLN cc_start: 0.7963 (tp40) cc_final: 0.7466 (tp40) REVERT: 1 133 ASN cc_start: 0.8690 (m-40) cc_final: 0.8338 (t0) REVERT: 1 147 ASP cc_start: 0.8283 (t0) cc_final: 0.8013 (m-30) REVERT: 1 148 LYS cc_start: 0.8762 (mtpt) cc_final: 0.8149 (mtpp) REVERT: 3 115 ILE cc_start: 0.8836 (mt) cc_final: 0.8130 (mt) REVERT: 3 125 LEU cc_start: 0.9252 (tp) cc_final: 0.9050 (tt) REVERT: 3 129 LEU cc_start: 0.8895 (mt) cc_final: 0.8611 (mp) REVERT: 5 112 SER cc_start: 0.8492 (p) cc_final: 0.8022 (m) REVERT: 5 117 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7660 (pp) REVERT: 5 127 GLN cc_start: 0.8868 (tp40) cc_final: 0.8578 (tp40) REVERT: 7 112 SER cc_start: 0.9031 (p) cc_final: 0.8706 (m) REVERT: 9 128 TYR cc_start: 0.8836 (t80) cc_final: 0.8554 (t80) REVERT: a 24 GLN cc_start: 0.8371 (tp40) cc_final: 0.7938 (tp40) REVERT: a 26 LEU cc_start: 0.9127 (tp) cc_final: 0.8845 (tp) REVERT: a 53 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8106 (mmtp) REVERT: a 60 TYR cc_start: 0.8548 (t80) cc_final: 0.7621 (t80) REVERT: a 61 ARG cc_start: 0.9362 (mmt180) cc_final: 0.9115 (mmt-90) REVERT: a 72 LYS cc_start: 0.9561 (tmtt) cc_final: 0.9276 (tptp) REVERT: a 80 GLN cc_start: 0.8587 (mt0) cc_final: 0.8182 (tm-30) REVERT: b 43 ASN cc_start: 0.8465 (t0) cc_final: 0.8152 (t0) REVERT: b 45 GLN cc_start: 0.8659 (tp40) cc_final: 0.7718 (tm-30) REVERT: c 19 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: c 69 LYS cc_start: 0.9354 (tptm) cc_final: 0.9092 (tptt) REVERT: d 20 ASP cc_start: 0.7870 (m-30) cc_final: 0.7581 (m-30) REVERT: d 36 LYS cc_start: 0.8713 (mttt) cc_final: 0.8487 (mttt) REVERT: d 50 TYR cc_start: 0.9078 (t80) cc_final: 0.8736 (t80) REVERT: d 57 TYR cc_start: 0.8967 (t80) cc_final: 0.8660 (t80) REVERT: f 21 ASP cc_start: 0.8419 (m-30) cc_final: 0.7125 (m-30) REVERT: f 60 TYR cc_start: 0.8308 (t80) cc_final: 0.7720 (t80) REVERT: f 75 ASP cc_start: 0.8009 (m-30) cc_final: 0.7776 (m-30) REVERT: g 14 SER cc_start: 0.8914 (m) cc_final: 0.8674 (p) REVERT: g 19 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8294 (t80) REVERT: g 25 THR cc_start: 0.8507 (p) cc_final: 0.8145 (p) REVERT: g 26 LEU cc_start: 0.9193 (tt) cc_final: 0.8833 (tt) REVERT: g 65 SER cc_start: 0.9047 (m) cc_final: 0.8822 (t) REVERT: g 79 ILE cc_start: 0.9285 (mm) cc_final: 0.9055 (mm) REVERT: h 19 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7937 (t80) REVERT: h 66 ASN cc_start: 0.9357 (m-40) cc_final: 0.9067 (m-40) REVERT: i 19 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8387 (t80) REVERT: i 50 TYR cc_start: 0.9278 (t80) cc_final: 0.9001 (t80) REVERT: i 81 ASN cc_start: 0.9352 (m-40) cc_final: 0.9051 (m-40) REVERT: j 13 SER cc_start: 0.9308 (p) cc_final: 0.9089 (m) REVERT: j 25 THR cc_start: 0.8219 (p) cc_final: 0.7692 (t) REVERT: j 26 LEU cc_start: 0.9044 (tp) cc_final: 0.8726 (tp) REVERT: j 55 SER cc_start: 0.9279 (m) cc_final: 0.8901 (p) REVERT: k 13 SER cc_start: 0.8856 (p) cc_final: 0.8171 (t) REVERT: k 37 LEU cc_start: 0.9087 (tp) cc_final: 0.8784 (tt) REVERT: k 50 TYR cc_start: 0.9096 (t80) cc_final: 0.8782 (t80) REVERT: k 64 GLN cc_start: 0.9400 (tt0) cc_final: 0.9054 (tt0) REVERT: k 72 LYS cc_start: 0.8972 (tmtp) cc_final: 0.8570 (tmmt) REVERT: k 81 ASN cc_start: 0.9170 (m-40) cc_final: 0.8871 (m-40) REVERT: l 25 THR cc_start: 0.8920 (p) cc_final: 0.8176 (p) REVERT: l 36 LYS cc_start: 0.8960 (mtpp) cc_final: 0.8552 (mtpp) REVERT: l 43 ASN cc_start: 0.8396 (t0) cc_final: 0.8170 (t0) REVERT: l 45 GLN cc_start: 0.7777 (tp40) cc_final: 0.7391 (tp40) REVERT: l 50 TYR cc_start: 0.9148 (t80) cc_final: 0.8740 (t80) REVERT: m 14 SER cc_start: 0.9324 (m) cc_final: 0.8987 (t) REVERT: m 20 ASP cc_start: 0.8104 (m-30) cc_final: 0.7629 (m-30) REVERT: m 75 ASP cc_start: 0.8146 (m-30) cc_final: 0.7690 (m-30) REVERT: n 3 VAL cc_start: 0.8611 (t) cc_final: 0.8241 (m) REVERT: n 53 LYS cc_start: 0.9131 (mmtt) cc_final: 0.8915 (mmtm) REVERT: n 75 ASP cc_start: 0.8372 (m-30) cc_final: 0.7838 (m-30) REVERT: n 80 GLN cc_start: 0.8609 (tm-30) cc_final: 0.7714 (tm-30) REVERT: o 43 ASN cc_start: 0.7823 (t0) cc_final: 0.7384 (t0) REVERT: o 50 TYR cc_start: 0.9135 (t80) cc_final: 0.8645 (t80) REVERT: o 75 ASP cc_start: 0.8507 (m-30) cc_final: 0.8292 (m-30) REVERT: p 12 LEU cc_start: 0.9513 (mt) cc_final: 0.9056 (mt) REVERT: p 14 SER cc_start: 0.8856 (m) cc_final: 0.8548 (p) REVERT: p 45 GLN cc_start: 0.8153 (tp40) cc_final: 0.7161 (mm-40) REVERT: p 58 THR cc_start: 0.9564 (m) cc_final: 0.9360 (p) REVERT: p 75 ASP cc_start: 0.8637 (m-30) cc_final: 0.8238 (m-30) REVERT: q 14 SER cc_start: 0.9333 (m) cc_final: 0.9028 (p) REVERT: q 19 PHE cc_start: 0.7951 (m-80) cc_final: 0.7672 (m-80) REVERT: q 32 LEU cc_start: 0.8506 (tp) cc_final: 0.8183 (tp) REVERT: q 36 LYS cc_start: 0.8693 (mttt) cc_final: 0.8429 (mtmt) REVERT: q 64 GLN cc_start: 0.9017 (tt0) cc_final: 0.8741 (tt0) REVERT: r 14 SER cc_start: 0.9145 (m) cc_final: 0.8939 (p) REVERT: s 7 ASN cc_start: 0.6944 (m-40) cc_final: 0.5819 (p0) REVERT: s 23 THR cc_start: 0.8699 (m) cc_final: 0.8159 (p) REVERT: s 27 GLN cc_start: 0.8430 (mt0) cc_final: 0.7712 (tm-30) REVERT: s 37 LEU cc_start: 0.8884 (tt) cc_final: 0.8488 (tt) REVERT: s 65 SER cc_start: 0.8983 (t) cc_final: 0.8634 (m) REVERT: s 69 LYS cc_start: 0.8420 (tptm) cc_final: 0.7437 (ttmt) REVERT: s 75 ASP cc_start: 0.7483 (m-30) cc_final: 0.7237 (m-30) REVERT: t 26 LEU cc_start: 0.8251 (mt) cc_final: 0.7764 (mt) REVERT: t 47 LEU cc_start: 0.9032 (mt) cc_final: 0.8826 (mt) REVERT: t 51 GLN cc_start: 0.8916 (tt0) cc_final: 0.7000 (mm-40) REVERT: t 69 LYS cc_start: 0.9132 (tptm) cc_final: 0.8549 (mttt) REVERT: u 15 LEU cc_start: 0.9185 (mt) cc_final: 0.8864 (tp) REVERT: u 26 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8960 (mt) REVERT: u 30 LEU cc_start: 0.8742 (tp) cc_final: 0.8506 (tt) REVERT: u 49 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7332 (mm-30) REVERT: u 69 LYS cc_start: 0.9102 (tptm) cc_final: 0.7645 (ttmt) REVERT: u 75 ASP cc_start: 0.8334 (m-30) cc_final: 0.8060 (m-30) REVERT: u 78 ILE cc_start: 0.9477 (mt) cc_final: 0.9248 (mt) REVERT: u 82 PHE cc_start: 0.9211 (m-10) cc_final: 0.8999 (m-80) REVERT: v 15 LEU cc_start: 0.9371 (mt) cc_final: 0.9101 (tp) REVERT: v 27 GLN cc_start: 0.8066 (mt0) cc_final: 0.7585 (tt0) REVERT: v 32 LEU cc_start: 0.9247 (tp) cc_final: 0.8932 (tp) REVERT: v 36 LYS cc_start: 0.8939 (mttt) cc_final: 0.8584 (mttm) REVERT: v 68 VAL cc_start: 0.9546 (t) cc_final: 0.9329 (m) REVERT: v 69 LYS cc_start: 0.8922 (tptm) cc_final: 0.8288 (mttm) REVERT: w 61 ARG cc_start: 0.8701 (mmt180) cc_final: 0.7209 (ttt180) REVERT: w 71 ILE cc_start: 0.9381 (mm) cc_final: 0.8621 (mm) REVERT: w 72 LYS cc_start: 0.9193 (tmtt) cc_final: 0.8540 (tptp) REVERT: w 75 ASP cc_start: 0.8255 (m-30) cc_final: 0.7457 (m-30) REVERT: a0 103 LYS cc_start: 0.8009 (tttm) cc_final: 0.7015 (tptt) REVERT: d0 103 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8100 (tttt) REVERT: e0 103 LYS cc_start: 0.8910 (ttmt) cc_final: 0.8390 (tttt) REVERT: f0 103 LYS cc_start: 0.9376 (ttmt) cc_final: 0.8412 (tptt) REVERT: g0 103 LYS cc_start: 0.8992 (mtmt) cc_final: 0.7557 (tptt) REVERT: i0 90 PHE cc_start: 0.6405 (OUTLIER) cc_final: 0.4181 (p90) REVERT: i0 93 ASP cc_start: 0.7733 (p0) cc_final: 0.7526 (p0) REVERT: i0 103 LYS cc_start: 0.8993 (tttt) cc_final: 0.8667 (tptt) REVERT: k0 103 LYS cc_start: 0.8695 (ttmm) cc_final: 0.8126 (tptt) REVERT: l0 103 LYS cc_start: 0.8941 (ttmt) cc_final: 0.8096 (tptt) REVERT: n0 97 SER cc_start: 0.9039 (m) cc_final: 0.8775 (p) REVERT: n0 103 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8428 (ttpt) REVERT: p0 103 LYS cc_start: 0.8756 (ttpt) cc_final: 0.8165 (tptt) REVERT: q0 103 LYS cc_start: 0.8848 (ttmt) cc_final: 0.8361 (tptt) REVERT: r0 102 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7995 (mt-10) REVERT: r0 103 LYS cc_start: 0.8883 (ttmt) cc_final: 0.7631 (tptt) REVERT: t0 103 LYS cc_start: 0.8791 (ttmt) cc_final: 0.8189 (tptt) REVERT: t0 105 ARG cc_start: 0.9177 (ttm110) cc_final: 0.8017 (tpm170) REVERT: u0 98 SER cc_start: 0.9091 (m) cc_final: 0.8402 (p) REVERT: u0 100 ARG cc_start: 0.8017 (ttm110) cc_final: 0.7369 (tpt170) REVERT: u0 103 LYS cc_start: 0.9042 (ttmt) cc_final: 0.8051 (tptt) REVERT: v0 92 THR cc_start: 0.8375 (m) cc_final: 0.8137 (m) REVERT: v0 100 ARG cc_start: 0.7712 (mtt180) cc_final: 0.7459 (tpt170) REVERT: v0 103 LYS cc_start: 0.9309 (mttt) cc_final: 0.8094 (tptt) REVERT: w0 103 LYS cc_start: 0.8981 (ttmt) cc_final: 0.8509 (tptt) REVERT: x0 103 LYS cc_start: 0.8489 (ttmt) cc_final: 0.7724 (tptt) outliers start: 164 outliers final: 62 residues processed: 2665 average time/residue: 0.2374 time to fit residues: 1067.3867 Evaluate side-chains 2093 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 2005 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 0.5980 chunk 497 optimal weight: 3.9990 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 0.4980 chunk 488 optimal weight: 0.8980 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 516 optimal weight: 0.0050 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 49 ASN E 44 GLN E 210 GLN F 11 HIS F 119 ASN ** F 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN F 247 HIS F 252 ASN I 76 HIS ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN O 44 GLN P 59 ASN T 80 GLN U 80 GLN ** X 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 133 ASN 4 119 ASN 4 137 HIS x 123 ASN y 123 ASN ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 64 GLN a 66 ASN c 64 GLN ** f 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 80 GLN g 81 ASN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 80 GLN ** k 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 40 ASN l 43 ASN l 62 ASN m 64 GLN n 81 ASN o 7 ASN p 80 GLN q 80 GLN r 27 GLN ** r 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 80 GLN w 64 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101166 restraints weight = 90440.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.103557 restraints weight = 54766.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.105212 restraints weight = 37604.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106404 restraints weight = 28248.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.107267 restraints weight = 22515.167| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 44859 Z= 0.155 Angle : 0.616 9.722 60892 Z= 0.310 Chirality : 0.040 0.189 7369 Planarity : 0.004 0.065 7620 Dihedral : 4.141 82.501 5953 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.42 % Allowed : 2.33 % Favored : 97.25 % 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: 3.31 (0.12), residues: 5404 helix: 3.32 (0.08), residues: 4159 sheet: 1.95 (0.32), residues: 192 loop : -2.92 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 23 TYR 0.032 0.002 TYR o 60 PHE 0.032 0.002 PHE K 45 TRP 0.010 0.001 TRP I 66 HIS 0.011 0.001 HIS I 76 Details of bonding type rmsd covalent geometry : bond 0.00357 (44858) covalent geometry : angle 0.61613 (60890) SS BOND : bond 0.00259 ( 1) SS BOND : angle 0.11153 ( 2) hydrogen bonds : bond 0.04347 ( 3327) hydrogen bonds : angle 3.63855 ( 9915) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2389 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 2368 time to evaluate : 1.428 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: 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 26 CYS cc_start: 0.8775 (p) cc_final: 0.8240 (p) REVERT: A 36 MET cc_start: 0.8888 (ttp) cc_final: 0.8306 (ttm) REVERT: A 68 ILE cc_start: 0.9516 (mt) cc_final: 0.9169 (mt) REVERT: A 69 GLU cc_start: 0.7619 (tp30) cc_final: 0.6992 (mm-30) REVERT: A 97 MET cc_start: 0.8336 (tpt) cc_final: 0.8092 (tpt) REVERT: A 101 GLN cc_start: 0.8721 (tt0) cc_final: 0.8374 (tm-30) REVERT: A 177 MET cc_start: 0.7862 (ptp) cc_final: 0.7570 (mtm) REVERT: A 205 LYS cc_start: 0.8943 (mttt) cc_final: 0.8313 (tttt) REVERT: B 111 LEU cc_start: 0.9196 (mt) cc_final: 0.8806 (mp) REVERT: B 116 GLN cc_start: 0.8839 (mm110) cc_final: 0.8537 (tp40) REVERT: B 120 GLU cc_start: 0.6479 (mt-10) cc_final: 0.5776 (mp0) REVERT: B 190 LYS cc_start: 0.9199 (mtmt) cc_final: 0.8878 (mtmm) REVERT: C 105 LYS cc_start: 0.9174 (tttp) cc_final: 0.8775 (mtpt) REVERT: C 117 ARG cc_start: 0.8502 (mtt180) cc_final: 0.8047 (tpt170) REVERT: C 119 GLU cc_start: 0.8152 (tt0) cc_final: 0.7718 (tp30) REVERT: C 164 VAL cc_start: 0.9512 (t) cc_final: 0.9280 (t) REVERT: D 2 LEU cc_start: 0.9214 (mt) cc_final: 0.8949 (mt) REVERT: D 6 SER cc_start: 0.8839 (m) cc_final: 0.8086 (p) REVERT: D 133 TYR cc_start: 0.8492 (m-10) cc_final: 0.7755 (m-10) REVERT: D 177 MET cc_start: 0.8286 (mtt) cc_final: 0.8079 (mtt) REVERT: E 59 MET cc_start: 0.8419 (mtp) cc_final: 0.8143 (mtm) REVERT: E 64 MET cc_start: 0.8672 (mmm) cc_final: 0.7520 (mmm) REVERT: E 179 MET cc_start: 0.8566 (mmp) cc_final: 0.8323 (mmp) REVERT: E 184 THR cc_start: 0.9191 (p) cc_final: 0.8742 (t) REVERT: E 194 PHE cc_start: 0.9076 (t80) cc_final: 0.8838 (t80) REVERT: F 101 SER cc_start: 0.9376 (m) cc_final: 0.9023 (t) REVERT: F 133 PHE cc_start: 0.8918 (t80) cc_final: 0.8555 (t80) REVERT: F 139 LEU cc_start: 0.9291 (tp) cc_final: 0.9038 (tp) REVERT: F 152 GLN cc_start: 0.9136 (tt0) cc_final: 0.8558 (tp40) REVERT: F 202 VAL cc_start: 0.8954 (t) cc_final: 0.8598 (t) REVERT: G 5 VAL cc_start: 0.9269 (p) cc_final: 0.8908 (p) REVERT: G 75 CYS cc_start: 0.8599 (m) cc_final: 0.8336 (m) REVERT: G 79 MET cc_start: 0.8612 (mmm) cc_final: 0.8199 (mmm) REVERT: H 81 LEU cc_start: 0.8733 (mt) cc_final: 0.8382 (mt) REVERT: H 83 LYS cc_start: 0.9048 (tptt) cc_final: 0.8815 (tppp) REVERT: I 5 VAL cc_start: 0.9136 (t) cc_final: 0.8606 (p) REVERT: I 9 ASN cc_start: 0.8397 (m-40) cc_final: 0.8137 (m-40) REVERT: I 21 TRP cc_start: 0.6333 (t-100) cc_final: 0.6000 (m100) REVERT: J 3 ASP cc_start: 0.7425 (p0) cc_final: 0.7199 (p0) REVERT: J 66 TRP cc_start: 0.9115 (t60) cc_final: 0.8641 (t-100) REVERT: K 32 VAL cc_start: 0.6837 (t) cc_final: 0.6562 (t) REVERT: K 46 SER cc_start: 0.7096 (m) cc_final: 0.6824 (t) REVERT: K 51 MET cc_start: 0.7646 (mmt) cc_final: 0.6439 (mmt) REVERT: N 46 SER cc_start: 0.8996 (m) cc_final: 0.8735 (p) REVERT: N 58 LEU cc_start: 0.9196 (mt) cc_final: 0.8894 (mt) REVERT: P 12 ILE cc_start: 0.8463 (mt) cc_final: 0.8024 (mt) REVERT: P 44 GLN cc_start: 0.8185 (tt0) cc_final: 0.7824 (tt0) REVERT: P 56 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7394 (tm-30) REVERT: P 57 SER cc_start: 0.9295 (m) cc_final: 0.8679 (p) REVERT: Q 13 ILE cc_start: 0.8005 (mt) cc_final: 0.7754 (mt) REVERT: Q 65 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8261 (mptt) REVERT: R 40 ASP cc_start: 0.8224 (t70) cc_final: 0.8007 (t70) REVERT: U 43 ASN cc_start: 0.8902 (t0) cc_final: 0.8463 (t0) REVERT: U 46 LEU cc_start: 0.9066 (mp) cc_final: 0.8414 (tt) REVERT: V 32 LEU cc_start: 0.8691 (mt) cc_final: 0.8370 (tt) REVERT: V 64 GLN cc_start: 0.8575 (tt0) cc_final: 0.8364 (tt0) REVERT: W 39 LYS cc_start: 0.8297 (mttt) cc_final: 0.7784 (mptt) REVERT: W 43 ASN cc_start: 0.8745 (t0) cc_final: 0.8181 (t0) REVERT: X 117 LEU cc_start: 0.7784 (pp) cc_final: 0.7203 (mt) REVERT: X 120 ILE cc_start: 0.9147 (pt) cc_final: 0.8940 (mt) REVERT: X 142 ARG cc_start: 0.8325 (mmt-90) cc_final: 0.7862 (mmt-90) REVERT: Y 112 SER cc_start: 0.7635 (p) cc_final: 0.7374 (m) REVERT: Y 123 ASN cc_start: 0.8660 (t0) cc_final: 0.8398 (t0) REVERT: Y 127 GLN cc_start: 0.7751 (tm-30) cc_final: 0.6706 (tm-30) REVERT: 4 150 PHE cc_start: 0.9041 (p90) cc_final: 0.8677 (p90) REVERT: 4 151 TYR cc_start: 0.8250 (t80) cc_final: 0.7773 (t80) REVERT: 6 127 GLN cc_start: 0.8969 (tp40) cc_final: 0.8326 (tp40) REVERT: 6 138 ARG cc_start: 0.8470 (mtp85) cc_final: 0.7372 (mtm110) REVERT: 6 149 THR cc_start: 0.9036 (m) cc_final: 0.8119 (p) REVERT: 8 111 ILE cc_start: 0.9295 (mt) cc_final: 0.9046 (mt) REVERT: 8 115 ILE cc_start: 0.8999 (mt) cc_final: 0.8716 (mm) REVERT: 8 144 ASN cc_start: 0.8005 (t0) cc_final: 0.7531 (t0) REVERT: x 112 SER cc_start: 0.8656 (p) cc_final: 0.8300 (m) REVERT: x 150 PHE cc_start: 0.9328 (p90) cc_final: 0.8542 (p90) REVERT: x 158 LEU cc_start: 0.8468 (tp) cc_final: 0.8134 (mm) REVERT: x 168 LEU cc_start: 0.9447 (tp) cc_final: 0.9060 (tp) REVERT: y 115 ILE cc_start: 0.9367 (mt) cc_final: 0.9145 (mt) REVERT: y 158 LEU cc_start: 0.8225 (tp) cc_final: 0.7919 (mm) REVERT: y 160 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7858 (mm-30) REVERT: z 112 SER cc_start: 0.9105 (p) cc_final: 0.8699 (m) REVERT: z 119 ASN cc_start: 0.8624 (m-40) cc_final: 0.8180 (p0) REVERT: z 139 TYR cc_start: 0.8064 (m-80) cc_final: 0.7810 (m-80) REVERT: z 149 THR cc_start: 0.9079 (m) cc_final: 0.8712 (t) REVERT: z 151 TYR cc_start: 0.8670 (t80) cc_final: 0.8388 (t80) REVERT: 1 127 GLN cc_start: 0.7738 (tp40) cc_final: 0.7512 (tp40) REVERT: 1 130 LYS cc_start: 0.8348 (mmtp) cc_final: 0.8119 (mmtp) REVERT: 1 133 ASN cc_start: 0.8685 (m-40) cc_final: 0.8219 (t0) REVERT: 1 148 LYS cc_start: 0.8739 (mtpt) cc_final: 0.8146 (mtpp) REVERT: 3 115 ILE cc_start: 0.8792 (mt) cc_final: 0.8150 (mt) REVERT: 5 112 SER cc_start: 0.8283 (p) cc_final: 0.8054 (m) REVERT: 7 128 TYR cc_start: 0.9065 (t80) cc_final: 0.8751 (t80) REVERT: 7 164 ASN cc_start: 0.8189 (m-40) cc_final: 0.7932 (m-40) REVERT: a 24 GLN cc_start: 0.8132 (tp40) cc_final: 0.7810 (tp40) REVERT: a 26 LEU cc_start: 0.9055 (tp) cc_final: 0.8593 (tp) REVERT: a 66 ASN cc_start: 0.9021 (m-40) cc_final: 0.8750 (m110) REVERT: a 72 LYS cc_start: 0.9546 (tmtt) cc_final: 0.9294 (tptp) REVERT: b 21 ASP cc_start: 0.8262 (m-30) cc_final: 0.7996 (m-30) REVERT: b 43 ASN cc_start: 0.8459 (t0) cc_final: 0.8205 (t0) REVERT: b 45 GLN cc_start: 0.9066 (tp40) cc_final: 0.8125 (tm-30) REVERT: b 49 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7536 (mm-30) REVERT: b 59 LEU cc_start: 0.9511 (mp) cc_final: 0.9288 (mp) REVERT: b 65 SER cc_start: 0.9242 (m) cc_final: 0.8564 (t) REVERT: b 72 LYS cc_start: 0.8998 (tptp) cc_final: 0.8791 (tptm) REVERT: c 9 ASP cc_start: 0.8526 (t0) cc_final: 0.8189 (t0) REVERT: d 50 TYR cc_start: 0.9076 (t80) cc_final: 0.8861 (t80) REVERT: d 57 TYR cc_start: 0.9056 (t80) cc_final: 0.8694 (t80) REVERT: d 71 ILE cc_start: 0.8860 (mm) cc_final: 0.8425 (mm) REVERT: d 75 ASP cc_start: 0.8535 (m-30) cc_final: 0.8143 (m-30) REVERT: f 17 GLU cc_start: 0.7452 (tm-30) cc_final: 0.6862 (tm-30) REVERT: f 21 ASP cc_start: 0.8378 (m-30) cc_final: 0.7954 (m-30) REVERT: f 75 ASP cc_start: 0.8227 (m-30) cc_final: 0.7987 (m-30) REVERT: g 25 THR cc_start: 0.8361 (p) cc_final: 0.8089 (p) REVERT: g 54 LEU cc_start: 0.9184 (tp) cc_final: 0.8977 (tp) REVERT: g 64 GLN cc_start: 0.8649 (tt0) cc_final: 0.8418 (tm-30) REVERT: g 79 ILE cc_start: 0.9182 (mm) cc_final: 0.8979 (mm) REVERT: h 25 THR cc_start: 0.7450 (t) cc_final: 0.7044 (t) REVERT: h 29 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8206 (mt-10) REVERT: h 59 LEU cc_start: 0.9306 (mt) cc_final: 0.9053 (mt) REVERT: h 66 ASN cc_start: 0.9384 (m-40) cc_final: 0.9166 (m-40) REVERT: i 25 THR cc_start: 0.8056 (p) cc_final: 0.7812 (p) REVERT: i 80 GLN cc_start: 0.8329 (tm130) cc_final: 0.8034 (tm-30) REVERT: i 81 ASN cc_start: 0.9260 (m-40) cc_final: 0.8959 (m-40) REVERT: j 14 SER cc_start: 0.9152 (m) cc_final: 0.8417 (t) REVERT: j 25 THR cc_start: 0.8274 (p) cc_final: 0.7836 (t) REVERT: j 55 SER cc_start: 0.9159 (m) cc_final: 0.8876 (p) REVERT: k 13 SER cc_start: 0.8803 (p) cc_final: 0.8503 (t) REVERT: k 37 LEU cc_start: 0.9047 (tp) cc_final: 0.8720 (tt) REVERT: k 50 TYR cc_start: 0.9264 (t80) cc_final: 0.8993 (t80) REVERT: l 20 ASP cc_start: 0.7946 (m-30) cc_final: 0.7472 (m-30) REVERT: l 25 THR cc_start: 0.8968 (p) cc_final: 0.8127 (p) REVERT: l 45 GLN cc_start: 0.8053 (tp40) cc_final: 0.7544 (tp40) REVERT: l 50 TYR cc_start: 0.9243 (t80) cc_final: 0.8813 (t80) REVERT: m 20 ASP cc_start: 0.8173 (m-30) cc_final: 0.7838 (m-30) REVERT: m 50 TYR cc_start: 0.8766 (t80) cc_final: 0.8382 (t80) REVERT: m 75 ASP cc_start: 0.8258 (m-30) cc_final: 0.7616 (m-30) REVERT: n 3 VAL cc_start: 0.8630 (t) cc_final: 0.8254 (m) REVERT: n 53 LYS cc_start: 0.9147 (mmtt) cc_final: 0.8866 (mmtm) REVERT: n 75 ASP cc_start: 0.8455 (m-30) cc_final: 0.8115 (m-30) REVERT: n 80 GLN cc_start: 0.8706 (tm-30) cc_final: 0.7947 (tm-30) REVERT: o 14 SER cc_start: 0.8803 (t) cc_final: 0.8312 (p) REVERT: o 37 LEU cc_start: 0.9079 (tp) cc_final: 0.8839 (tt) REVERT: o 43 ASN cc_start: 0.7573 (t0) cc_final: 0.7276 (t0) REVERT: o 75 ASP cc_start: 0.8658 (m-30) cc_final: 0.8369 (t0) REVERT: p 12 LEU cc_start: 0.9323 (mt) cc_final: 0.9001 (mt) REVERT: p 14 SER cc_start: 0.8871 (m) cc_final: 0.8573 (p) REVERT: p 75 ASP cc_start: 0.8691 (m-30) cc_final: 0.8178 (m-30) REVERT: q 14 SER cc_start: 0.9318 (m) cc_final: 0.9048 (p) REVERT: q 32 LEU cc_start: 0.8160 (tp) cc_final: 0.7798 (tp) REVERT: q 36 LYS cc_start: 0.8662 (mttt) cc_final: 0.8337 (mtmt) REVERT: s 7 ASN cc_start: 0.6830 (m-40) cc_final: 0.5856 (p0) REVERT: s 23 THR cc_start: 0.8541 (m) cc_final: 0.8102 (p) REVERT: s 27 GLN cc_start: 0.8346 (mt0) cc_final: 0.7805 (tm-30) REVERT: s 65 SER cc_start: 0.8905 (t) cc_final: 0.8587 (m) REVERT: s 69 LYS cc_start: 0.8547 (tptm) cc_final: 0.7467 (ttmt) REVERT: s 75 ASP cc_start: 0.7624 (m-30) cc_final: 0.7384 (m-30) REVERT: t 47 LEU cc_start: 0.8967 (mt) cc_final: 0.8719 (mt) REVERT: t 51 GLN cc_start: 0.8993 (tt0) cc_final: 0.7027 (mm-40) REVERT: t 55 SER cc_start: 0.9218 (m) cc_final: 0.9016 (p) REVERT: t 69 LYS cc_start: 0.9221 (tptm) cc_final: 0.8576 (mttt) REVERT: t 72 LYS cc_start: 0.9555 (tmtt) cc_final: 0.9335 (tttm) REVERT: t 75 ASP cc_start: 0.8704 (m-30) cc_final: 0.8462 (m-30) REVERT: u 15 LEU cc_start: 0.9105 (mt) cc_final: 0.8818 (tp) REVERT: u 30 LEU cc_start: 0.8836 (tp) cc_final: 0.8511 (tt) REVERT: u 69 LYS cc_start: 0.9051 (tptm) cc_final: 0.7667 (ttmt) REVERT: u 72 LYS cc_start: 0.9109 (tmtt) cc_final: 0.8713 (tmtt) REVERT: v 27 GLN cc_start: 0.7936 (mt0) cc_final: 0.7611 (tt0) REVERT: v 32 LEU cc_start: 0.9264 (tp) cc_final: 0.8960 (tp) REVERT: v 36 LYS cc_start: 0.8961 (mttt) cc_final: 0.8604 (mttm) REVERT: v 68 VAL cc_start: 0.9415 (t) cc_final: 0.9190 (m) REVERT: v 69 LYS cc_start: 0.9036 (tptm) cc_final: 0.8251 (mttm) REVERT: w 25 THR cc_start: 0.8513 (p) cc_final: 0.8097 (p) REVERT: w 57 TYR cc_start: 0.8800 (t80) cc_final: 0.8299 (t80) REVERT: w 61 ARG cc_start: 0.8528 (mmt180) cc_final: 0.6809 (ttt180) REVERT: w 69 LYS cc_start: 0.9239 (tppt) cc_final: 0.7764 (tppt) REVERT: w 72 LYS cc_start: 0.9171 (tmtt) cc_final: 0.8511 (tptp) REVERT: a0 103 LYS cc_start: 0.8316 (tttm) cc_final: 0.7149 (tptt) REVERT: d0 103 LYS cc_start: 0.9234 (ttmt) cc_final: 0.7902 (tptt) REVERT: e0 103 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8194 (tttt) REVERT: f0 103 LYS cc_start: 0.9385 (ttmt) cc_final: 0.8333 (tptt) REVERT: g0 103 LYS cc_start: 0.8991 (mtmt) cc_final: 0.7592 (tptt) REVERT: i0 103 LYS cc_start: 0.8964 (tttt) cc_final: 0.8595 (tptt) REVERT: k0 103 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8112 (tptt) REVERT: l0 103 LYS cc_start: 0.8916 (ttmt) cc_final: 0.8179 (tptt) REVERT: n0 97 SER cc_start: 0.9034 (m) cc_final: 0.8650 (p) REVERT: n0 103 LYS cc_start: 0.8974 (ttmt) cc_final: 0.8421 (ttpt) REVERT: o0 102 GLU cc_start: 0.7319 (pt0) cc_final: 0.7110 (pp20) REVERT: p0 103 LYS cc_start: 0.8939 (ttpt) cc_final: 0.8156 (tptt) REVERT: q0 103 LYS cc_start: 0.9093 (ttmt) cc_final: 0.8364 (tptt) REVERT: r0 102 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8099 (mt-10) REVERT: r0 103 LYS cc_start: 0.8823 (ttmt) cc_final: 0.7578 (tptt) REVERT: t0 103 LYS cc_start: 0.8839 (ttmt) cc_final: 0.8098 (tptt) REVERT: t0 105 ARG cc_start: 0.9174 (ttm110) cc_final: 0.7994 (tpm170) REVERT: u0 100 ARG cc_start: 0.7847 (ttm110) cc_final: 0.7356 (tpt170) REVERT: u0 103 LYS cc_start: 0.9108 (ttmt) cc_final: 0.8032 (tptt) REVERT: v0 92 THR cc_start: 0.8209 (m) cc_final: 0.7948 (m) REVERT: v0 103 LYS cc_start: 0.9265 (mttt) cc_final: 0.8034 (tptt) REVERT: w0 103 LYS cc_start: 0.8986 (ttmt) cc_final: 0.8505 (tptt) REVERT: x0 103 LYS cc_start: 0.8366 (ttmt) cc_final: 0.7680 (tptt) outliers start: 21 outliers final: 4 residues processed: 2374 average time/residue: 0.2446 time to fit residues: 986.2717 Evaluate side-chains 1992 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1988 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 271 optimal weight: 0.9980 chunk 516 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 484 optimal weight: 1.9990 chunk 459 optimal weight: 0.9980 chunk 296 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 482 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 285 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 GLN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS F 11 HIS ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN ** F 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 HIS F 252 ASN K 162 GLN O 44 GLN P 59 ASN T 80 GLN U 80 GLN U 81 ASN ** Z 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 127 GLN 4 133 ASN ** 4 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 123 ASN ** 7 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 ASN ** c 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 43 ASN f 40 ASN f 43 ASN f 51 GLN f 80 GLN g 80 GLN i 40 ASN i 43 ASN l 40 ASN l 62 ASN n 7 ASN n 24 GLN n 62 ASN n 81 ASN p 80 GLN r 27 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.115187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.100872 restraints weight = 90844.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.103261 restraints weight = 54944.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.104917 restraints weight = 37680.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106109 restraints weight = 28340.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106910 restraints weight = 22663.986| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 44859 Z= 0.152 Angle : 0.612 14.118 60892 Z= 0.306 Chirality : 0.040 0.265 7369 Planarity : 0.004 0.066 7620 Dihedral : 4.213 82.806 5953 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.28 % Allowed : 2.73 % Favored : 96.99 % 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: 3.16 (0.12), residues: 5404 helix: 3.21 (0.08), residues: 4150 sheet: 1.03 (0.33), residues: 224 loop : -2.87 (0.17), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 38 TYR 0.026 0.002 TYR C 211 PHE 0.029 0.002 PHE F 28 TRP 0.013 0.001 TRP K 174 HIS 0.007 0.001 HIS F 11 Details of bonding type rmsd covalent geometry : bond 0.00357 (44858) covalent geometry : angle 0.61223 (60890) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.06080 ( 2) hydrogen bonds : bond 0.04247 ( 3327) hydrogen bonds : angle 3.58407 ( 9915) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2290 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 2276 time to evaluate : 1.926 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 CYS cc_start: 0.8677 (p) cc_final: 0.8065 (p) REVERT: A 36 MET cc_start: 0.8922 (ttp) cc_final: 0.8451 (tpp) REVERT: A 68 ILE cc_start: 0.9525 (mt) cc_final: 0.9181 (mt) REVERT: A 69 GLU cc_start: 0.7680 (tp30) cc_final: 0.6978 (mm-30) REVERT: A 97 MET cc_start: 0.8378 (tpt) cc_final: 0.8059 (tpt) REVERT: A 101 GLN cc_start: 0.8665 (tt0) cc_final: 0.8378 (tm-30) REVERT: A 104 LYS cc_start: 0.9313 (mmmm) cc_final: 0.8993 (ttmt) REVERT: A 152 LYS cc_start: 0.9206 (tttt) cc_final: 0.8679 (ttmt) REVERT: A 158 TYR cc_start: 0.8152 (t80) cc_final: 0.7856 (t80) REVERT: A 177 MET cc_start: 0.7996 (ptp) cc_final: 0.7724 (mtt) REVERT: A 205 LYS cc_start: 0.9101 (mttt) cc_final: 0.8250 (tttt) REVERT: B 120 GLU cc_start: 0.6408 (mt-10) cc_final: 0.5745 (mp0) REVERT: B 133 TYR cc_start: 0.6999 (m-10) cc_final: 0.6781 (m-80) REVERT: B 146 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7492 (mm-30) REVERT: B 177 MET cc_start: 0.7894 (mtt) cc_final: 0.7541 (mtt) REVERT: B 190 LYS cc_start: 0.9193 (mtmt) cc_final: 0.8945 (mtmm) REVERT: C 1 MET cc_start: 0.7246 (mmm) cc_final: 0.6628 (mmm) REVERT: C 29 LYS cc_start: 0.8769 (mttp) cc_final: 0.8526 (mttm) REVERT: C 59 MET cc_start: 0.8749 (mtp) cc_final: 0.8541 (mtp) REVERT: C 105 LYS cc_start: 0.9089 (tttp) cc_final: 0.8699 (mtpt) REVERT: C 117 ARG cc_start: 0.8426 (mtt180) cc_final: 0.7916 (tpt170) REVERT: C 119 GLU cc_start: 0.8116 (tt0) cc_final: 0.7877 (tp30) REVERT: C 146 GLU cc_start: 0.8217 (tp30) cc_final: 0.7871 (tp30) REVERT: D 2 LEU cc_start: 0.9214 (mt) cc_final: 0.8986 (mt) REVERT: D 6 SER cc_start: 0.8827 (m) cc_final: 0.8110 (p) REVERT: D 17 LEU cc_start: 0.9251 (tp) cc_final: 0.8845 (tt) REVERT: D 134 SER cc_start: 0.9086 (m) cc_final: 0.8356 (t) REVERT: D 146 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8232 (mm-30) REVERT: D 159 LEU cc_start: 0.9119 (mt) cc_final: 0.8915 (mt) REVERT: E 36 MET cc_start: 0.8751 (tpp) cc_final: 0.8363 (tpp) REVERT: E 43 LEU cc_start: 0.8967 (tp) cc_final: 0.8727 (tp) REVERT: E 44 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8028 (mp10) REVERT: E 59 MET cc_start: 0.8467 (mtp) cc_final: 0.8199 (mtm) REVERT: E 64 MET cc_start: 0.8750 (mmm) cc_final: 0.7704 (mmm) REVERT: E 179 MET cc_start: 0.8631 (mmp) cc_final: 0.8370 (mmp) REVERT: E 184 THR cc_start: 0.9256 (p) cc_final: 0.8707 (t) REVERT: E 194 PHE cc_start: 0.9115 (t80) cc_final: 0.8908 (t80) REVERT: F 101 SER cc_start: 0.9284 (m) cc_final: 0.9004 (t) REVERT: F 133 PHE cc_start: 0.8916 (t80) cc_final: 0.8519 (t80) REVERT: F 152 GLN cc_start: 0.9135 (tt0) cc_final: 0.8556 (tp40) REVERT: F 170 ASN cc_start: 0.8397 (m-40) cc_final: 0.8167 (m-40) REVERT: G 5 VAL cc_start: 0.9215 (p) cc_final: 0.8856 (p) REVERT: G 73 SER cc_start: 0.8972 (p) cc_final: 0.8753 (p) REVERT: G 75 CYS cc_start: 0.8565 (m) cc_final: 0.8276 (m) REVERT: G 79 MET cc_start: 0.8637 (mmm) cc_final: 0.8023 (mmm) REVERT: H 83 LYS cc_start: 0.9043 (tptt) cc_final: 0.8698 (tppp) REVERT: I 1 MET cc_start: 0.7389 (ptp) cc_final: 0.7161 (ptp) REVERT: I 5 VAL cc_start: 0.9169 (t) cc_final: 0.8635 (p) REVERT: I 18 PHE cc_start: 0.8277 (m-80) cc_final: 0.7684 (m-80) REVERT: I 53 LEU cc_start: 0.8048 (tp) cc_final: 0.7663 (tp) REVERT: K 51 MET cc_start: 0.7625 (mmt) cc_final: 0.6582 (mmt) REVERT: K 132 LYS cc_start: 0.8624 (mmtp) cc_final: 0.8236 (mttt) REVERT: K 140 LEU cc_start: 0.9148 (tp) cc_final: 0.8877 (tt) REVERT: K 176 ARG cc_start: 0.8730 (tpt-90) cc_final: 0.8521 (tpt-90) REVERT: N 58 LEU cc_start: 0.9218 (mt) cc_final: 0.8844 (mt) REVERT: P 12 ILE cc_start: 0.8592 (mt) cc_final: 0.8104 (mt) REVERT: P 46 SER cc_start: 0.9475 (m) cc_final: 0.9133 (t) REVERT: P 56 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7408 (tm-30) REVERT: P 57 SER cc_start: 0.9140 (m) cc_final: 0.8619 (p) REVERT: Q 7 VAL cc_start: 0.8379 (m) cc_final: 0.8176 (t) REVERT: Q 13 ILE cc_start: 0.7758 (mt) cc_final: 0.7517 (mt) REVERT: R 27 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6907 (pt0) REVERT: U 43 ASN cc_start: 0.8698 (t0) cc_final: 0.8396 (t0) REVERT: U 81 ASN cc_start: 0.9133 (m-40) cc_final: 0.8830 (m110) REVERT: V 32 LEU cc_start: 0.8683 (mt) cc_final: 0.8329 (tt) REVERT: V 64 GLN cc_start: 0.8582 (tt0) cc_final: 0.8339 (tt0) REVERT: W 39 LYS cc_start: 0.8347 (mttt) cc_final: 0.7820 (mptt) REVERT: W 43 ASN cc_start: 0.8668 (t0) cc_final: 0.8190 (t0) REVERT: X 142 ARG cc_start: 0.8673 (mmt-90) cc_final: 0.8171 (mmt-90) REVERT: Y 112 SER cc_start: 0.7649 (p) cc_final: 0.7377 (m) REVERT: Y 123 ASN cc_start: 0.8758 (t0) cc_final: 0.8467 (t0) REVERT: Y 127 GLN cc_start: 0.7669 (tm-30) cc_final: 0.7209 (tm-30) REVERT: Y 131 ASP cc_start: 0.7640 (m-30) cc_final: 0.7338 (m-30) REVERT: Z 161 LEU cc_start: 0.8649 (tp) cc_final: 0.8384 (tp) REVERT: 0 128 TYR cc_start: 0.8231 (t80) cc_final: 0.7834 (t80) REVERT: 2 167 THR cc_start: 0.8683 (t) cc_final: 0.8472 (t) REVERT: 4 127 GLN cc_start: 0.7967 (tp40) cc_final: 0.7685 (tp-100) REVERT: 4 133 ASN cc_start: 0.7910 (t0) cc_final: 0.7675 (t0) REVERT: 4 150 PHE cc_start: 0.9102 (p90) cc_final: 0.8597 (p90) REVERT: 6 127 GLN cc_start: 0.8966 (tp40) cc_final: 0.8388 (tp40) REVERT: 6 138 ARG cc_start: 0.8416 (mtp85) cc_final: 0.7676 (mtm110) REVERT: 6 144 ASN cc_start: 0.8495 (m-40) cc_final: 0.8171 (m-40) REVERT: 6 149 THR cc_start: 0.9059 (m) cc_final: 0.8057 (p) REVERT: 8 115 ILE cc_start: 0.8985 (mt) cc_final: 0.8694 (mm) REVERT: 8 144 ASN cc_start: 0.7849 (t0) cc_final: 0.7427 (t0) REVERT: x 112 SER cc_start: 0.8668 (p) cc_final: 0.8463 (m) REVERT: x 150 PHE cc_start: 0.9382 (p90) cc_final: 0.8571 (p90) REVERT: x 153 SER cc_start: 0.9444 (t) cc_final: 0.9184 (p) REVERT: x 168 LEU cc_start: 0.9382 (tp) cc_final: 0.9044 (tp) REVERT: y 115 ILE cc_start: 0.9402 (mt) cc_final: 0.9168 (mt) REVERT: y 158 LEU cc_start: 0.8232 (tp) cc_final: 0.7884 (mm) REVERT: y 160 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7881 (mm-30) REVERT: y 164 ASN cc_start: 0.8668 (m-40) cc_final: 0.8364 (m-40) REVERT: z 112 SER cc_start: 0.9070 (p) cc_final: 0.8815 (m) REVERT: z 127 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7667 (tm-30) REVERT: z 149 THR cc_start: 0.9064 (m) cc_final: 0.8688 (t) REVERT: 1 133 ASN cc_start: 0.8674 (m-40) cc_final: 0.8240 (t0) REVERT: 1 148 LYS cc_start: 0.8368 (mtpt) cc_final: 0.8071 (mtpp) REVERT: 1 170 ASP cc_start: 0.7069 (m-30) cc_final: 0.5966 (m-30) REVERT: 3 115 ILE cc_start: 0.8633 (mt) cc_final: 0.8117 (mt) REVERT: 5 112 SER cc_start: 0.8286 (p) cc_final: 0.8041 (m) REVERT: 5 131 ASP cc_start: 0.8237 (p0) cc_final: 0.7944 (p0) REVERT: 9 135 TYR cc_start: 0.7560 (t80) cc_final: 0.6912 (t80) REVERT: a 26 LEU cc_start: 0.8996 (tp) cc_final: 0.8503 (tp) REVERT: a 66 ASN cc_start: 0.9031 (m-40) cc_final: 0.8700 (m110) REVERT: a 72 LYS cc_start: 0.9539 (tmtt) cc_final: 0.9112 (tptp) REVERT: b 43 ASN cc_start: 0.8482 (t0) cc_final: 0.8237 (t0) REVERT: b 45 GLN cc_start: 0.9093 (tp40) cc_final: 0.8161 (tm-30) REVERT: b 49 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7278 (mm-30) REVERT: b 59 LEU cc_start: 0.9503 (mp) cc_final: 0.9220 (mm) REVERT: b 64 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7679 (tm-30) REVERT: b 65 SER cc_start: 0.9167 (m) cc_final: 0.8559 (t) REVERT: c 9 ASP cc_start: 0.8371 (t0) cc_final: 0.7973 (t0) REVERT: c 82 PHE cc_start: 0.8787 (m-10) cc_final: 0.8534 (m-10) REVERT: d 26 LEU cc_start: 0.8327 (mt) cc_final: 0.8092 (mt) REVERT: d 57 TYR cc_start: 0.9047 (t80) cc_final: 0.8708 (t80) REVERT: d 59 LEU cc_start: 0.9670 (mt) cc_final: 0.9125 (mt) REVERT: d 75 ASP cc_start: 0.8458 (m-30) cc_final: 0.8063 (m-30) REVERT: e 56 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8312 (tt0) REVERT: f 17 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6727 (tm-30) REVERT: f 21 ASP cc_start: 0.8505 (m-30) cc_final: 0.8138 (m-30) REVERT: f 80 GLN cc_start: 0.8456 (tm130) cc_final: 0.8084 (tm-30) REVERT: g 25 THR cc_start: 0.8269 (p) cc_final: 0.8010 (p) REVERT: g 54 LEU cc_start: 0.9199 (tp) cc_final: 0.8986 (tp) REVERT: g 72 LYS cc_start: 0.9347 (tmtt) cc_final: 0.9105 (tptm) REVERT: g 79 ILE cc_start: 0.9229 (mm) cc_final: 0.8823 (mm) REVERT: g 80 GLN cc_start: 0.8653 (tp-100) cc_final: 0.8368 (tm-30) REVERT: g 81 ASN cc_start: 0.9154 (m110) cc_final: 0.8918 (m-40) REVERT: h 11 THR cc_start: 0.8873 (m) cc_final: 0.8019 (m) REVERT: h 19 PHE cc_start: 0.7427 (t80) cc_final: 0.7043 (t80) REVERT: h 66 ASN cc_start: 0.9384 (m-40) cc_final: 0.9171 (m110) REVERT: i 80 GLN cc_start: 0.8310 (tm-30) cc_final: 0.8063 (tm-30) REVERT: i 81 ASN cc_start: 0.9160 (m-40) cc_final: 0.8944 (m-40) REVERT: j 14 SER cc_start: 0.8976 (m) cc_final: 0.8299 (t) REVERT: j 55 SER cc_start: 0.9105 (m) cc_final: 0.8784 (p) REVERT: k 13 SER cc_start: 0.8773 (p) cc_final: 0.8360 (t) REVERT: k 50 TYR cc_start: 0.9282 (t80) cc_final: 0.9055 (t80) REVERT: k 72 LYS cc_start: 0.8904 (tttt) cc_final: 0.8679 (tttt) REVERT: l 20 ASP cc_start: 0.7709 (m-30) cc_final: 0.7324 (m-30) REVERT: l 25 THR cc_start: 0.8709 (p) cc_final: 0.7818 (p) REVERT: l 43 ASN cc_start: 0.8552 (t0) cc_final: 0.8255 (t0) REVERT: l 45 GLN cc_start: 0.8122 (tp40) cc_final: 0.7658 (tp40) REVERT: l 50 TYR cc_start: 0.9231 (t80) cc_final: 0.8834 (t80) REVERT: m 20 ASP cc_start: 0.8180 (m-30) cc_final: 0.7823 (m-30) REVERT: m 24 GLN cc_start: 0.8827 (tp40) cc_final: 0.8380 (tp40) REVERT: m 50 TYR cc_start: 0.8803 (t80) cc_final: 0.8380 (t80) REVERT: m 75 ASP cc_start: 0.8406 (m-30) cc_final: 0.7696 (m-30) REVERT: n 3 VAL cc_start: 0.8616 (t) cc_final: 0.8255 (m) REVERT: n 75 ASP cc_start: 0.8447 (m-30) cc_final: 0.8055 (m-30) REVERT: n 80 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8006 (tm-30) REVERT: o 14 SER cc_start: 0.8813 (t) cc_final: 0.8363 (p) REVERT: o 43 ASN cc_start: 0.7510 (t0) cc_final: 0.7220 (t0) REVERT: o 50 TYR cc_start: 0.9243 (t80) cc_final: 0.8982 (t80) REVERT: o 72 LYS cc_start: 0.9429 (tmtt) cc_final: 0.9010 (tmtt) REVERT: p 12 LEU cc_start: 0.9362 (mt) cc_final: 0.9054 (mt) REVERT: p 46 LEU cc_start: 0.9363 (tp) cc_final: 0.9080 (tt) REVERT: p 75 ASP cc_start: 0.8671 (m-30) cc_final: 0.8023 (m-30) REVERT: q 14 SER cc_start: 0.9329 (m) cc_final: 0.9059 (p) REVERT: q 32 LEU cc_start: 0.8197 (tp) cc_final: 0.7848 (tp) REVERT: q 36 LYS cc_start: 0.8629 (mttt) cc_final: 0.8280 (mtmt) REVERT: r 59 LEU cc_start: 0.8825 (mt) cc_final: 0.8548 (mt) REVERT: s 7 ASN cc_start: 0.6799 (m-40) cc_final: 0.5846 (p0) REVERT: s 23 THR cc_start: 0.8609 (m) cc_final: 0.8328 (m) REVERT: s 24 GLN cc_start: 0.8252 (tp40) cc_final: 0.7918 (mm-40) REVERT: s 27 GLN cc_start: 0.8443 (mt0) cc_final: 0.7952 (tm-30) REVERT: s 65 SER cc_start: 0.8979 (t) cc_final: 0.8677 (m) REVERT: s 69 LYS cc_start: 0.8577 (tptm) cc_final: 0.7497 (ttmt) REVERT: t 26 LEU cc_start: 0.7882 (mt) cc_final: 0.7578 (mt) REVERT: t 47 LEU cc_start: 0.8948 (mt) cc_final: 0.8711 (mt) REVERT: t 51 GLN cc_start: 0.8974 (tt0) cc_final: 0.6850 (mm-40) REVERT: t 52 SER cc_start: 0.8839 (m) cc_final: 0.8492 (t) REVERT: t 69 LYS cc_start: 0.9222 (tptm) cc_final: 0.8617 (mttt) REVERT: t 72 LYS cc_start: 0.9559 (tmtt) cc_final: 0.9334 (tttm) REVERT: t 75 ASP cc_start: 0.8709 (m-30) cc_final: 0.8439 (m-30) REVERT: u 15 LEU cc_start: 0.9113 (mt) cc_final: 0.8873 (tp) REVERT: u 30 LEU cc_start: 0.8816 (tp) cc_final: 0.8503 (tt) REVERT: u 49 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7133 (tp30) REVERT: u 69 LYS cc_start: 0.9049 (tptm) cc_final: 0.7672 (ttmt) REVERT: u 72 LYS cc_start: 0.9113 (tmtt) cc_final: 0.8568 (tmtt) REVERT: u 75 ASP cc_start: 0.8962 (m-30) cc_final: 0.8262 (m-30) REVERT: v 18 THR cc_start: 0.8166 (m) cc_final: 0.7854 (m) REVERT: v 32 LEU cc_start: 0.9267 (tp) cc_final: 0.8960 (tp) REVERT: v 36 LYS cc_start: 0.9030 (mttt) cc_final: 0.8716 (mttm) REVERT: v 69 LYS cc_start: 0.9071 (tptm) cc_final: 0.8276 (mttm) REVERT: w 25 THR cc_start: 0.8670 (p) cc_final: 0.8287 (p) REVERT: w 57 TYR cc_start: 0.8850 (t80) cc_final: 0.8390 (t80) REVERT: w 61 ARG cc_start: 0.8484 (mmt180) cc_final: 0.6917 (ttp-170) REVERT: a0 103 LYS cc_start: 0.8208 (tttm) cc_final: 0.7133 (tptt) REVERT: b0 96 VAL cc_start: 0.8204 (t) cc_final: 0.7863 (t) REVERT: d0 103 LYS cc_start: 0.9258 (ttmt) cc_final: 0.7834 (tptt) REVERT: e0 103 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8176 (tttt) REVERT: f0 103 LYS cc_start: 0.9246 (ttmt) cc_final: 0.8313 (tptt) REVERT: g0 103 LYS cc_start: 0.9004 (mtmt) cc_final: 0.7653 (tptt) REVERT: i0 103 LYS cc_start: 0.8923 (tttt) cc_final: 0.8562 (tptt) REVERT: k0 103 LYS cc_start: 0.8792 (ttmm) cc_final: 0.8127 (tptt) REVERT: l0 103 LYS cc_start: 0.8947 (ttmt) cc_final: 0.8189 (tptt) REVERT: n0 97 SER cc_start: 0.9079 (m) cc_final: 0.8632 (p) REVERT: n0 103 LYS cc_start: 0.8983 (ttmt) cc_final: 0.8460 (ttpt) REVERT: p0 103 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8069 (tptt) REVERT: q0 103 LYS cc_start: 0.9108 (ttmt) cc_final: 0.8376 (tptt) REVERT: r0 102 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8174 (mt-10) REVERT: r0 103 LYS cc_start: 0.8814 (ttmt) cc_final: 0.7534 (tptt) REVERT: t0 103 LYS cc_start: 0.8886 (ttmt) cc_final: 0.8096 (tptt) REVERT: t0 105 ARG cc_start: 0.9173 (ttm110) cc_final: 0.7993 (tpm170) REVERT: u0 100 ARG cc_start: 0.7825 (ttm110) cc_final: 0.7323 (tpt170) REVERT: u0 103 LYS cc_start: 0.9067 (ttmt) cc_final: 0.8048 (tptt) REVERT: v0 92 THR cc_start: 0.8224 (m) cc_final: 0.7957 (m) REVERT: v0 103 LYS cc_start: 0.9266 (mttt) cc_final: 0.7901 (tptt) REVERT: w0 103 LYS cc_start: 0.8968 (ttmt) cc_final: 0.8471 (tptt) REVERT: x0 98 SER cc_start: 0.9082 (t) cc_final: 0.8670 (p) REVERT: x0 103 LYS cc_start: 0.8451 (ttmt) cc_final: 0.7718 (tptt) outliers start: 14 outliers final: 1 residues processed: 2278 average time/residue: 0.2398 time to fit residues: 928.3941 Evaluate side-chains 1958 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1957 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 481 optimal weight: 1.9990 chunk 435 optimal weight: 0.7980 chunk 483 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 360 optimal weight: 0.9990 chunk 157 optimal weight: 7.9990 chunk 269 optimal weight: 0.9980 chunk 502 optimal weight: 0.0670 chunk 442 optimal weight: 0.6980 chunk 388 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS E 44 GLN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 170 ASN F 247 HIS F 252 ASN I 9 ASN K 162 GLN O 9 GLN O 44 GLN P 59 ASN R 19 GLN R 44 GLN T 80 GLN U 80 GLN V 40 ASN Z 137 HIS ** 4 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 123 ASN ** y 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 ASN ** c 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 64 GLN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 81 ASN p 80 GLN q 81 ASN r 27 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102291 restraints weight = 90194.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104691 restraints weight = 54710.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106366 restraints weight = 37604.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.107529 restraints weight = 28266.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108396 restraints weight = 22689.605| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 44859 Z= 0.136 Angle : 0.612 9.815 60892 Z= 0.304 Chirality : 0.040 0.195 7369 Planarity : 0.004 0.068 7620 Dihedral : 4.242 83.313 5953 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.12 % Allowed : 2.20 % Favored : 97.69 % 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: 3.08 (0.12), residues: 5404 helix: 3.14 (0.08), residues: 4152 sheet: 1.12 (0.32), residues: 224 loop : -2.87 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGv0 100 TYR 0.028 0.001 TYR C 211 PHE 0.025 0.002 PHE g 19 TRP 0.010 0.001 TRP I 66 HIS 0.007 0.001 HIS F 11 Details of bonding type rmsd covalent geometry : bond 0.00306 (44858) covalent geometry : angle 0.61222 (60890) SS BOND : bond 0.00093 ( 1) SS BOND : angle 0.33617 ( 2) hydrogen bonds : bond 0.04078 ( 3327) hydrogen bonds : angle 3.53427 ( 9915) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2260 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 2254 time to evaluate : 1.491 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 CYS cc_start: 0.8646 (p) cc_final: 0.7918 (p) REVERT: A 36 MET cc_start: 0.8869 (ttp) cc_final: 0.8449 (tpp) REVERT: A 48 SER cc_start: 0.8897 (t) cc_final: 0.8573 (p) REVERT: A 50 MET cc_start: 0.8049 (ttp) cc_final: 0.7797 (ttm) REVERT: A 68 ILE cc_start: 0.9528 (mt) cc_final: 0.9178 (mt) REVERT: A 69 GLU cc_start: 0.7645 (tp30) cc_final: 0.7149 (mm-30) REVERT: A 97 MET cc_start: 0.8299 (tpt) cc_final: 0.7892 (tpt) REVERT: A 101 GLN cc_start: 0.8639 (tt0) cc_final: 0.8344 (tm-30) REVERT: A 104 LYS cc_start: 0.9285 (mmmm) cc_final: 0.8931 (ttmt) REVERT: A 152 LYS cc_start: 0.9175 (tttt) cc_final: 0.8658 (ttmt) REVERT: A 205 LYS cc_start: 0.9124 (mttt) cc_final: 0.8257 (tttt) REVERT: B 110 GLU cc_start: 0.8516 (pm20) cc_final: 0.7920 (pm20) REVERT: B 120 GLU cc_start: 0.6390 (mt-10) cc_final: 0.5865 (mp0) REVERT: B 177 MET cc_start: 0.7900 (mtt) cc_final: 0.7571 (mtt) REVERT: B 190 LYS cc_start: 0.9212 (mtmt) cc_final: 0.8923 (mtmm) REVERT: C 29 LYS cc_start: 0.8956 (mttp) cc_final: 0.8479 (mttm) REVERT: C 105 LYS cc_start: 0.9070 (tttp) cc_final: 0.8682 (mtpt) REVERT: C 117 ARG cc_start: 0.8335 (mtt180) cc_final: 0.7904 (tpt170) REVERT: C 119 GLU cc_start: 0.8044 (tt0) cc_final: 0.7833 (tp30) REVERT: C 146 GLU cc_start: 0.8239 (tp30) cc_final: 0.7935 (tp30) REVERT: D 2 LEU cc_start: 0.9213 (mt) cc_final: 0.8928 (mt) REVERT: D 6 SER cc_start: 0.8744 (m) cc_final: 0.7987 (p) REVERT: D 27 TYR cc_start: 0.9089 (t80) cc_final: 0.8810 (t80) REVERT: D 134 SER cc_start: 0.9162 (m) cc_final: 0.8354 (t) REVERT: E 36 MET cc_start: 0.8695 (tpp) cc_final: 0.8245 (tpp) REVERT: E 43 LEU cc_start: 0.8914 (tp) cc_final: 0.8675 (tp) REVERT: E 44 GLN cc_start: 0.8503 (mm110) cc_final: 0.8302 (mt0) REVERT: E 59 MET cc_start: 0.8654 (mtm) cc_final: 0.8448 (mtp) REVERT: E 64 MET cc_start: 0.8654 (mmm) cc_final: 0.7585 (mmm) REVERT: E 184 THR cc_start: 0.9272 (p) cc_final: 0.9016 (p) REVERT: F 36 ASN cc_start: 0.7959 (t0) cc_final: 0.7494 (t0) REVERT: F 101 SER cc_start: 0.9258 (m) cc_final: 0.8985 (t) REVERT: F 104 ASP cc_start: 0.8201 (t0) cc_final: 0.7961 (t0) REVERT: F 128 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8482 (ttpt) REVERT: F 133 PHE cc_start: 0.8889 (t80) cc_final: 0.8438 (t80) REVERT: F 139 LEU cc_start: 0.9237 (tp) cc_final: 0.9027 (tp) REVERT: F 152 GLN cc_start: 0.9090 (tt0) cc_final: 0.8533 (tp40) REVERT: G 7 MET cc_start: 0.8559 (tpp) cc_final: 0.8251 (tpp) REVERT: G 73 SER cc_start: 0.8963 (p) cc_final: 0.8587 (p) REVERT: G 79 MET cc_start: 0.8733 (mmm) cc_final: 0.8016 (mmm) REVERT: H 77 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7851 (tm-30) REVERT: I 1 MET cc_start: 0.7267 (ptp) cc_final: 0.7013 (ptp) REVERT: I 5 VAL cc_start: 0.8837 (t) cc_final: 0.8599 (p) REVERT: I 18 PHE cc_start: 0.8286 (m-80) cc_final: 0.7669 (m-80) REVERT: I 53 LEU cc_start: 0.8058 (tp) cc_final: 0.7857 (tp) REVERT: I 77 GLU cc_start: 0.8227 (tt0) cc_final: 0.7963 (tt0) REVERT: K 32 VAL cc_start: 0.6827 (t) cc_final: 0.6617 (t) REVERT: K 51 MET cc_start: 0.7530 (mmt) cc_final: 0.6749 (mmt) REVERT: K 132 LYS cc_start: 0.8599 (mmtp) cc_final: 0.8229 (mttt) REVERT: K 140 LEU cc_start: 0.9132 (tp) cc_final: 0.8884 (tt) REVERT: K 176 ARG cc_start: 0.8715 (tpt-90) cc_final: 0.8490 (tpt-90) REVERT: N 58 LEU cc_start: 0.9196 (mt) cc_final: 0.8821 (mt) REVERT: N 89 SER cc_start: 0.9311 (t) cc_final: 0.8930 (p) REVERT: N 92 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7467 (tm-30) REVERT: O 41 THR cc_start: 0.8784 (t) cc_final: 0.8450 (m) REVERT: P 56 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7218 (tm-30) REVERT: P 57 SER cc_start: 0.9195 (m) cc_final: 0.8594 (p) REVERT: Q 13 ILE cc_start: 0.7658 (mt) cc_final: 0.7401 (mt) REVERT: R 27 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6917 (pt0) REVERT: S 37 LEU cc_start: 0.9051 (tp) cc_final: 0.8730 (tp) REVERT: S 45 GLN cc_start: 0.8833 (tp40) cc_final: 0.8258 (tp-100) REVERT: T 30 LEU cc_start: 0.9159 (tp) cc_final: 0.8862 (tp) REVERT: T 50 TYR cc_start: 0.9151 (t80) cc_final: 0.8946 (t80) REVERT: T 56 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7659 (tt0) REVERT: U 43 ASN cc_start: 0.8693 (t0) cc_final: 0.8377 (t0) REVERT: U 46 LEU cc_start: 0.9037 (mp) cc_final: 0.8350 (tt) REVERT: V 32 LEU cc_start: 0.8665 (mt) cc_final: 0.8313 (tt) REVERT: V 64 GLN cc_start: 0.8551 (tt0) cc_final: 0.8315 (tt0) REVERT: W 39 LYS cc_start: 0.8281 (mttt) cc_final: 0.7731 (mptt) REVERT: W 43 ASN cc_start: 0.8447 (t0) cc_final: 0.8080 (t0) REVERT: X 142 ARG cc_start: 0.8604 (mmt-90) cc_final: 0.8168 (mmt-90) REVERT: Y 112 SER cc_start: 0.7598 (p) cc_final: 0.7275 (m) REVERT: Y 123 ASN cc_start: 0.8747 (t0) cc_final: 0.8447 (t0) REVERT: Y 127 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7519 (tm-30) REVERT: Y 131 ASP cc_start: 0.7551 (m-30) cc_final: 0.7273 (m-30) REVERT: Y 144 ASN cc_start: 0.7168 (m-40) cc_final: 0.5657 (m110) REVERT: Z 117 LEU cc_start: 0.7949 (pp) cc_final: 0.7659 (mt) REVERT: Z 158 LEU cc_start: 0.8999 (tt) cc_final: 0.8685 (mm) REVERT: Z 161 LEU cc_start: 0.8649 (tp) cc_final: 0.8394 (tp) REVERT: 0 128 TYR cc_start: 0.8173 (t80) cc_final: 0.7772 (t80) REVERT: 0 164 ASN cc_start: 0.8844 (m-40) cc_final: 0.8532 (m110) REVERT: 2 127 GLN cc_start: 0.8261 (tp40) cc_final: 0.7953 (tp40) REVERT: 4 133 ASN cc_start: 0.7980 (t0) cc_final: 0.7684 (t0) REVERT: 4 150 PHE cc_start: 0.9091 (p90) cc_final: 0.8593 (p90) REVERT: 4 151 TYR cc_start: 0.8329 (t80) cc_final: 0.8076 (t80) REVERT: 4 167 THR cc_start: 0.8815 (m) cc_final: 0.8532 (t) REVERT: 6 127 GLN cc_start: 0.8966 (tp40) cc_final: 0.8361 (tp40) REVERT: 6 149 THR cc_start: 0.8993 (m) cc_final: 0.8224 (p) REVERT: 8 111 ILE cc_start: 0.9296 (mt) cc_final: 0.9049 (mt) REVERT: 8 115 ILE cc_start: 0.8968 (mt) cc_final: 0.8675 (mm) REVERT: 8 144 ASN cc_start: 0.8047 (t0) cc_final: 0.7527 (t0) REVERT: x 127 GLN cc_start: 0.8688 (tp-100) cc_final: 0.8468 (tp-100) REVERT: x 150 PHE cc_start: 0.9362 (p90) cc_final: 0.8664 (p90) REVERT: x 153 SER cc_start: 0.9355 (t) cc_final: 0.9114 (p) REVERT: y 115 ILE cc_start: 0.9396 (mt) cc_final: 0.9183 (mt) REVERT: y 130 LYS cc_start: 0.8353 (mttt) cc_final: 0.8138 (mtmt) REVERT: y 158 LEU cc_start: 0.8232 (tp) cc_final: 0.7903 (mm) REVERT: y 160 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7749 (mm-30) REVERT: y 164 ASN cc_start: 0.8674 (m-40) cc_final: 0.8384 (m-40) REVERT: z 112 SER cc_start: 0.9160 (p) cc_final: 0.8870 (m) REVERT: z 127 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7637 (tm-30) REVERT: z 149 THR cc_start: 0.9014 (m) cc_final: 0.8675 (t) REVERT: 1 133 ASN cc_start: 0.8596 (m-40) cc_final: 0.8308 (t0) REVERT: 1 148 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8116 (mtpp) REVERT: 3 115 ILE cc_start: 0.8564 (mt) cc_final: 0.7956 (mt) REVERT: 5 112 SER cc_start: 0.8229 (p) cc_final: 0.8011 (m) REVERT: 5 131 ASP cc_start: 0.8261 (p0) cc_final: 0.7874 (p0) REVERT: 7 168 LEU cc_start: 0.9118 (tp) cc_final: 0.8904 (tp) REVERT: 9 135 TYR cc_start: 0.7516 (t80) cc_final: 0.6968 (t80) REVERT: a 26 LEU cc_start: 0.8934 (tp) cc_final: 0.8496 (tp) REVERT: a 31 THR cc_start: 0.7715 (m) cc_final: 0.7378 (m) REVERT: a 66 ASN cc_start: 0.9040 (m-40) cc_final: 0.8787 (m110) REVERT: a 72 LYS cc_start: 0.9570 (tmtt) cc_final: 0.9095 (tptp) REVERT: b 43 ASN cc_start: 0.8438 (t0) cc_final: 0.8232 (t0) REVERT: b 45 GLN cc_start: 0.8999 (tp40) cc_final: 0.7972 (tm-30) REVERT: b 49 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7212 (mm-30) REVERT: b 59 LEU cc_start: 0.9360 (mp) cc_final: 0.9126 (mp) REVERT: b 64 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7593 (tm-30) REVERT: b 65 SER cc_start: 0.9191 (m) cc_final: 0.8622 (t) REVERT: b 75 ASP cc_start: 0.8534 (t0) cc_final: 0.8146 (t0) REVERT: c 9 ASP cc_start: 0.8090 (t0) cc_final: 0.7840 (t0) REVERT: c 20 ASP cc_start: 0.8129 (t0) cc_final: 0.7797 (t0) REVERT: c 82 PHE cc_start: 0.8765 (m-10) cc_final: 0.8553 (m-10) REVERT: d 50 TYR cc_start: 0.8999 (t80) cc_final: 0.8770 (t80) REVERT: d 57 TYR cc_start: 0.8985 (t80) cc_final: 0.8513 (t80) REVERT: d 71 ILE cc_start: 0.8732 (mm) cc_final: 0.8208 (mm) REVERT: d 75 ASP cc_start: 0.8392 (m-30) cc_final: 0.7953 (m-30) REVERT: e 56 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8283 (tt0) REVERT: f 17 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6992 (tm-30) REVERT: f 20 ASP cc_start: 0.8492 (t70) cc_final: 0.8155 (t70) REVERT: f 21 ASP cc_start: 0.8465 (m-30) cc_final: 0.8008 (p0) REVERT: f 80 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8062 (tm-30) REVERT: g 25 THR cc_start: 0.8218 (p) cc_final: 0.8000 (p) REVERT: g 54 LEU cc_start: 0.9222 (tp) cc_final: 0.8972 (tp) REVERT: g 59 LEU cc_start: 0.9488 (mt) cc_final: 0.9265 (mt) REVERT: g 79 ILE cc_start: 0.9223 (mm) cc_final: 0.8821 (mm) REVERT: g 80 GLN cc_start: 0.8675 (tp-100) cc_final: 0.8356 (tm-30) REVERT: g 81 ASN cc_start: 0.9138 (m110) cc_final: 0.8910 (m-40) REVERT: h 20 ASP cc_start: 0.8003 (t70) cc_final: 0.7618 (t70) REVERT: h 59 LEU cc_start: 0.9162 (mt) cc_final: 0.8817 (mt) REVERT: i 80 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8141 (tm-30) REVERT: i 81 ASN cc_start: 0.9167 (m-40) cc_final: 0.8946 (m-40) REVERT: j 14 SER cc_start: 0.8966 (m) cc_final: 0.8341 (t) REVERT: j 55 SER cc_start: 0.9064 (m) cc_final: 0.8790 (p) REVERT: k 50 TYR cc_start: 0.9226 (t80) cc_final: 0.8999 (t80) REVERT: l 16 SER cc_start: 0.9078 (m) cc_final: 0.8202 (t) REVERT: l 20 ASP cc_start: 0.7585 (m-30) cc_final: 0.7178 (m-30) REVERT: l 25 THR cc_start: 0.8683 (p) cc_final: 0.8057 (p) REVERT: l 43 ASN cc_start: 0.8694 (t0) cc_final: 0.8455 (t0) REVERT: l 45 GLN cc_start: 0.8219 (tp40) cc_final: 0.7525 (tp40) REVERT: l 50 TYR cc_start: 0.9206 (t80) cc_final: 0.8805 (t80) REVERT: m 20 ASP cc_start: 0.8287 (m-30) cc_final: 0.7820 (m-30) REVERT: m 24 GLN cc_start: 0.9086 (tp40) cc_final: 0.8808 (tp40) REVERT: m 27 GLN cc_start: 0.7908 (pt0) cc_final: 0.7287 (pt0) REVERT: m 50 TYR cc_start: 0.8804 (t80) cc_final: 0.8453 (t80) REVERT: m 75 ASP cc_start: 0.8334 (m-30) cc_final: 0.7704 (m-30) REVERT: n 3 VAL cc_start: 0.8593 (t) cc_final: 0.8304 (m) REVERT: n 23 THR cc_start: 0.8757 (t) cc_final: 0.8518 (m) REVERT: n 29 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7012 (tm-30) REVERT: n 75 ASP cc_start: 0.8478 (m-30) cc_final: 0.8083 (m-30) REVERT: n 80 GLN cc_start: 0.8710 (tm-30) cc_final: 0.7986 (tm-30) REVERT: o 14 SER cc_start: 0.8786 (t) cc_final: 0.8360 (p) REVERT: o 24 GLN cc_start: 0.8807 (tp40) cc_final: 0.8600 (mm110) REVERT: o 29 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7389 (mt-10) REVERT: o 50 TYR cc_start: 0.9206 (t80) cc_final: 0.8821 (t80) REVERT: o 72 LYS cc_start: 0.9439 (tmtt) cc_final: 0.8991 (tmtt) REVERT: p 12 LEU cc_start: 0.9384 (mt) cc_final: 0.9049 (mt) REVERT: p 25 THR cc_start: 0.8379 (p) cc_final: 0.7743 (t) REVERT: p 46 LEU cc_start: 0.9246 (tp) cc_final: 0.9040 (tt) REVERT: p 75 ASP cc_start: 0.8621 (m-30) cc_final: 0.8013 (m-30) REVERT: q 12 LEU cc_start: 0.9464 (mt) cc_final: 0.9222 (mt) REVERT: q 14 SER cc_start: 0.9297 (m) cc_final: 0.9070 (p) REVERT: q 32 LEU cc_start: 0.8187 (tp) cc_final: 0.7848 (tp) REVERT: q 36 LYS cc_start: 0.8657 (mttt) cc_final: 0.8350 (mtmt) REVERT: r 27 GLN cc_start: 0.8779 (mt0) cc_final: 0.8547 (mt0) REVERT: r 59 LEU cc_start: 0.8836 (mt) cc_final: 0.8560 (mt) REVERT: s 7 ASN cc_start: 0.6699 (m-40) cc_final: 0.5685 (p0) REVERT: s 23 THR cc_start: 0.8566 (m) cc_final: 0.8299 (m) REVERT: s 24 GLN cc_start: 0.8180 (tp40) cc_final: 0.7804 (mm-40) REVERT: s 27 GLN cc_start: 0.8456 (mt0) cc_final: 0.8015 (tm-30) REVERT: s 65 SER cc_start: 0.8978 (t) cc_final: 0.8682 (m) REVERT: s 69 LYS cc_start: 0.7810 (tptm) cc_final: 0.7411 (ttmt) REVERT: t 49 GLU cc_start: 0.7684 (tp30) cc_final: 0.7452 (tp30) REVERT: t 69 LYS cc_start: 0.9216 (tptm) cc_final: 0.8556 (mttt) REVERT: t 72 LYS cc_start: 0.9533 (tmtt) cc_final: 0.9189 (tttp) REVERT: t 75 ASP cc_start: 0.8660 (m-30) cc_final: 0.8382 (m-30) REVERT: u 30 LEU cc_start: 0.8905 (tp) cc_final: 0.8594 (tt) REVERT: u 69 LYS cc_start: 0.9003 (tptm) cc_final: 0.7632 (ttmt) REVERT: u 72 LYS cc_start: 0.9163 (tmtt) cc_final: 0.8663 (tmtt) REVERT: u 75 ASP cc_start: 0.8929 (m-30) cc_final: 0.8142 (m-30) REVERT: v 32 LEU cc_start: 0.9283 (tp) cc_final: 0.9017 (tp) REVERT: v 36 LYS cc_start: 0.9014 (mttt) cc_final: 0.8702 (mttp) REVERT: v 69 LYS cc_start: 0.9114 (tptm) cc_final: 0.8197 (mttm) REVERT: w 25 THR cc_start: 0.8715 (p) cc_final: 0.8336 (p) REVERT: w 57 TYR cc_start: 0.8829 (t80) cc_final: 0.8318 (t80) REVERT: w 61 ARG cc_start: 0.8451 (mmt180) cc_final: 0.6774 (ttp-170) REVERT: a0 103 LYS cc_start: 0.8119 (tttm) cc_final: 0.7063 (tptt) REVERT: d0 103 LYS cc_start: 0.9246 (ttmt) cc_final: 0.7898 (tptt) REVERT: e0 103 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8282 (tttt) REVERT: f0 103 LYS cc_start: 0.9230 (ttmt) cc_final: 0.8298 (tptt) REVERT: g0 103 LYS cc_start: 0.9017 (mtmt) cc_final: 0.7652 (tptt) REVERT: i0 103 LYS cc_start: 0.8955 (tttt) cc_final: 0.8581 (tptt) REVERT: k0 103 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8125 (tptt) REVERT: l0 103 LYS cc_start: 0.8944 (ttmt) cc_final: 0.8171 (tptt) REVERT: m0 103 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8130 (tptt) REVERT: n0 97 SER cc_start: 0.9082 (m) cc_final: 0.8598 (p) REVERT: n0 103 LYS cc_start: 0.9023 (ttmt) cc_final: 0.8500 (ttpt) REVERT: p0 103 LYS cc_start: 0.8864 (ttpt) cc_final: 0.8013 (tptt) REVERT: q0 103 LYS cc_start: 0.9054 (ttmt) cc_final: 0.8298 (tptt) REVERT: r0 102 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8134 (mt-10) REVERT: r0 103 LYS cc_start: 0.8811 (ttmt) cc_final: 0.7528 (tptt) REVERT: t0 103 LYS cc_start: 0.8869 (ttmt) cc_final: 0.8089 (tptt) REVERT: t0 105 ARG cc_start: 0.9156 (ttm110) cc_final: 0.7984 (tpm170) REVERT: u0 100 ARG cc_start: 0.7826 (ttm110) cc_final: 0.7313 (tpt170) REVERT: u0 103 LYS cc_start: 0.9072 (ttmt) cc_final: 0.8046 (tptt) REVERT: v0 92 THR cc_start: 0.8346 (m) cc_final: 0.8098 (m) REVERT: v0 103 LYS cc_start: 0.9261 (mttt) cc_final: 0.7854 (tptt) REVERT: w0 103 LYS cc_start: 0.8942 (ttmt) cc_final: 0.8413 (tptt) REVERT: x0 103 LYS cc_start: 0.8454 (ttmt) cc_final: 0.7706 (tptt) outliers start: 6 outliers final: 0 residues processed: 2256 average time/residue: 0.2330 time to fit residues: 894.1350 Evaluate side-chains 1944 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1944 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 192 optimal weight: 1.9990 chunk 467 optimal weight: 0.9990 chunk 321 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 389 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 298 optimal weight: 7.9990 chunk 69 optimal weight: 0.1980 chunk 338 optimal weight: 1.9990 chunk 502 optimal weight: 0.6980 chunk 289 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 170 ASN F 247 HIS F 252 ASN I 9 ASN K 162 GLN N 8 ASN O 44 GLN P 59 ASN R 19 GLN T 80 GLN U 80 GLN W 81 ASN 4 127 GLN ** 4 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 123 ASN ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 ASN c 64 GLN h 66 ASN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 40 ASN n 7 ASN n 81 ASN p 80 GLN t 24 GLN u 40 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.101471 restraints weight = 90393.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.103842 restraints weight = 54866.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105502 restraints weight = 37723.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106698 restraints weight = 28336.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107565 restraints weight = 22669.473| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 44859 Z= 0.154 Angle : 0.626 9.589 60892 Z= 0.312 Chirality : 0.040 0.177 7369 Planarity : 0.004 0.071 7620 Dihedral : 4.265 84.180 5953 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.16 % Allowed : 1.88 % Favored : 97.96 % 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: 2.99 (0.12), residues: 5404 helix: 3.07 (0.08), residues: 4151 sheet: 1.20 (0.31), residues: 224 loop : -2.88 (0.17), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG z 138 TYR 0.028 0.002 TYR E 158 PHE 0.025 0.002 PHE l 19 TRP 0.011 0.001 TRP I 66 HIS 0.006 0.001 HIS F 11 Details of bonding type rmsd covalent geometry : bond 0.00361 (44858) covalent geometry : angle 0.62569 (60890) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.23098 ( 2) hydrogen bonds : bond 0.04124 ( 3327) hydrogen bonds : angle 3.57878 ( 9915) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2220 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 2212 time to evaluate : 2.165 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: 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 26 CYS cc_start: 0.8676 (p) cc_final: 0.7957 (p) REVERT: A 36 MET cc_start: 0.8723 (ttp) cc_final: 0.8360 (tpp) REVERT: A 48 SER cc_start: 0.8922 (t) cc_final: 0.8694 (p) REVERT: A 50 MET cc_start: 0.8183 (ttp) cc_final: 0.7891 (ttm) REVERT: A 68 ILE cc_start: 0.9517 (mt) cc_final: 0.9207 (mt) REVERT: A 69 GLU cc_start: 0.7787 (tp30) cc_final: 0.7195 (mm-30) REVERT: A 101 GLN cc_start: 0.8632 (tt0) cc_final: 0.8377 (tm-30) REVERT: A 104 LYS cc_start: 0.9301 (mmmm) cc_final: 0.8928 (ttmt) REVERT: A 152 LYS cc_start: 0.9230 (tttt) cc_final: 0.8769 (ttmt) REVERT: A 177 MET cc_start: 0.7976 (mtt) cc_final: 0.7727 (mtt) REVERT: A 205 LYS cc_start: 0.9142 (mttt) cc_final: 0.8256 (tttt) REVERT: A 209 GLU cc_start: 0.7883 (pt0) cc_final: 0.7647 (pt0) REVERT: B 65 LYS cc_start: 0.8621 (tttp) cc_final: 0.8103 (tmtt) REVERT: B 120 GLU cc_start: 0.6339 (mt-10) cc_final: 0.5823 (mp0) REVERT: B 146 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7726 (mm-30) REVERT: B 177 MET cc_start: 0.7959 (mtt) cc_final: 0.7631 (mtt) REVERT: B 190 LYS cc_start: 0.9222 (mtmt) cc_final: 0.8554 (mtmm) REVERT: C 25 THR cc_start: 0.9188 (p) cc_final: 0.8873 (t) REVERT: C 29 LYS cc_start: 0.9034 (mttp) cc_final: 0.8588 (mttm) REVERT: C 59 MET cc_start: 0.8407 (mtp) cc_final: 0.8189 (mtp) REVERT: C 105 LYS cc_start: 0.9010 (tttp) cc_final: 0.8720 (mtpp) REVERT: C 117 ARG cc_start: 0.8350 (mtt180) cc_final: 0.7858 (tpt170) REVERT: C 146 GLU cc_start: 0.8229 (tp30) cc_final: 0.7955 (tp30) REVERT: C 178 MET cc_start: 0.8608 (mmp) cc_final: 0.8387 (mmm) REVERT: D 2 LEU cc_start: 0.9222 (mt) cc_final: 0.8946 (mt) REVERT: D 6 SER cc_start: 0.8756 (m) cc_final: 0.7996 (p) REVERT: D 17 LEU cc_start: 0.9261 (tp) cc_final: 0.8861 (tt) REVERT: E 36 MET cc_start: 0.8830 (tpp) cc_final: 0.8353 (tpp) REVERT: E 162 VAL cc_start: 0.9371 (t) cc_final: 0.9111 (p) REVERT: F 110 THR cc_start: 0.8156 (t) cc_final: 0.7946 (t) REVERT: F 133 PHE cc_start: 0.8908 (t80) cc_final: 0.8488 (t80) REVERT: F 152 GLN cc_start: 0.9077 (tt0) cc_final: 0.8507 (tp40) REVERT: F 202 VAL cc_start: 0.8894 (t) cc_final: 0.8673 (t) REVERT: G 73 SER cc_start: 0.8982 (p) cc_final: 0.8736 (p) REVERT: G 79 MET cc_start: 0.8712 (mmm) cc_final: 0.7953 (mmm) REVERT: H 77 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7792 (tm-30) REVERT: I 5 VAL cc_start: 0.9068 (t) cc_final: 0.8519 (p) REVERT: I 6 TYR cc_start: 0.8598 (t80) cc_final: 0.8299 (t80) REVERT: I 53 LEU cc_start: 0.8071 (tp) cc_final: 0.7861 (tp) REVERT: I 60 LEU cc_start: 0.8569 (mt) cc_final: 0.8354 (mt) REVERT: J 70 VAL cc_start: 0.9622 (t) cc_final: 0.9384 (p) REVERT: K 32 VAL cc_start: 0.6972 (t) cc_final: 0.6605 (t) REVERT: K 51 MET cc_start: 0.7487 (mmt) cc_final: 0.6856 (mmt) REVERT: K 132 LYS cc_start: 0.8588 (mmtp) cc_final: 0.8221 (mttt) REVERT: K 176 ARG cc_start: 0.8734 (tpt-90) cc_final: 0.8509 (tpt-90) REVERT: N 58 LEU cc_start: 0.9176 (mt) cc_final: 0.8849 (mt) REVERT: N 68 THR cc_start: 0.8967 (m) cc_final: 0.8694 (t) REVERT: N 89 SER cc_start: 0.9230 (t) cc_final: 0.9025 (p) REVERT: O 41 THR cc_start: 0.8820 (t) cc_final: 0.8436 (m) REVERT: P 56 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7221 (tm-30) REVERT: P 57 SER cc_start: 0.9209 (m) cc_final: 0.8568 (p) REVERT: R 27 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6936 (pt0) REVERT: R 47 GLN cc_start: 0.8298 (tp40) cc_final: 0.7663 (tm-30) REVERT: R 51 MET cc_start: 0.7740 (mtt) cc_final: 0.7319 (mtm) REVERT: S 25 THR cc_start: 0.7860 (t) cc_final: 0.7639 (t) REVERT: S 37 LEU cc_start: 0.9052 (tp) cc_final: 0.8705 (tp) REVERT: T 30 LEU cc_start: 0.9176 (tp) cc_final: 0.8898 (tp) REVERT: T 50 TYR cc_start: 0.9165 (t80) cc_final: 0.8928 (t80) REVERT: U 43 ASN cc_start: 0.8585 (t0) cc_final: 0.8336 (t0) REVERT: U 46 LEU cc_start: 0.9037 (mp) cc_final: 0.8448 (tt) REVERT: V 32 LEU cc_start: 0.8683 (mt) cc_final: 0.8337 (tt) REVERT: V 64 GLN cc_start: 0.8597 (tt0) cc_final: 0.8308 (tt0) REVERT: W 39 LYS cc_start: 0.8357 (mttt) cc_final: 0.7780 (mptt) REVERT: W 43 ASN cc_start: 0.8646 (t0) cc_final: 0.8073 (t0) REVERT: X 142 ARG cc_start: 0.8608 (mmt-90) cc_final: 0.8215 (mmt-90) REVERT: Y 112 SER cc_start: 0.7945 (p) cc_final: 0.7613 (m) REVERT: Y 123 ASN cc_start: 0.8684 (t0) cc_final: 0.8419 (t0) REVERT: Y 127 GLN cc_start: 0.7629 (tm-30) cc_final: 0.7346 (tm-30) REVERT: Y 131 ASP cc_start: 0.7576 (m-30) cc_final: 0.7246 (m-30) REVERT: Z 117 LEU cc_start: 0.7955 (pp) cc_final: 0.7732 (mt) REVERT: Z 133 ASN cc_start: 0.9245 (t0) cc_final: 0.8923 (t0) REVERT: Z 161 LEU cc_start: 0.8650 (tp) cc_final: 0.8418 (tp) REVERT: 0 128 TYR cc_start: 0.8178 (t80) cc_final: 0.7740 (t80) REVERT: 2 127 GLN cc_start: 0.8288 (tp40) cc_final: 0.7945 (tp40) REVERT: 4 133 ASN cc_start: 0.7957 (t0) cc_final: 0.7571 (t0) REVERT: 4 150 PHE cc_start: 0.9046 (p90) cc_final: 0.8551 (p90) REVERT: 4 167 THR cc_start: 0.8811 (m) cc_final: 0.8517 (t) REVERT: 6 127 GLN cc_start: 0.8922 (tp40) cc_final: 0.8331 (tp40) REVERT: 6 138 ARG cc_start: 0.8391 (mtp85) cc_final: 0.7408 (mtm110) REVERT: 6 149 THR cc_start: 0.8959 (m) cc_final: 0.8166 (p) REVERT: 8 111 ILE cc_start: 0.9321 (mt) cc_final: 0.9105 (mt) REVERT: 8 115 ILE cc_start: 0.8950 (mt) cc_final: 0.8673 (mm) REVERT: 8 144 ASN cc_start: 0.7813 (t0) cc_final: 0.7534 (t0) REVERT: 8 150 PHE cc_start: 0.9250 (p90) cc_final: 0.8742 (p90) REVERT: x 150 PHE cc_start: 0.9362 (p90) cc_final: 0.8658 (p90) REVERT: x 153 SER cc_start: 0.9553 (t) cc_final: 0.9043 (p) REVERT: y 115 ILE cc_start: 0.9432 (mt) cc_final: 0.9207 (mt) REVERT: y 158 LEU cc_start: 0.8233 (tp) cc_final: 0.7882 (mm) REVERT: y 160 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7744 (mm-30) REVERT: z 112 SER cc_start: 0.9124 (p) cc_final: 0.8863 (m) REVERT: z 127 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7739 (tm-30) REVERT: z 138 ARG cc_start: 0.8107 (ttp-170) cc_final: 0.7803 (ttp-110) REVERT: z 149 THR cc_start: 0.9033 (m) cc_final: 0.8711 (t) REVERT: 1 130 LYS cc_start: 0.8445 (mmmt) cc_final: 0.7928 (mmtt) REVERT: 1 133 ASN cc_start: 0.8677 (m-40) cc_final: 0.8274 (t0) REVERT: 1 148 LYS cc_start: 0.8476 (mtpt) cc_final: 0.8159 (mtpp) REVERT: 1 170 ASP cc_start: 0.7414 (m-30) cc_final: 0.6368 (m-30) REVERT: 3 115 ILE cc_start: 0.8568 (mt) cc_final: 0.7913 (mt) REVERT: 5 131 ASP cc_start: 0.8239 (p0) cc_final: 0.7934 (p0) REVERT: 9 135 TYR cc_start: 0.7638 (t80) cc_final: 0.7059 (t80) REVERT: a 26 LEU cc_start: 0.8953 (tp) cc_final: 0.8632 (tp) REVERT: a 66 ASN cc_start: 0.9076 (m-40) cc_final: 0.8743 (m110) REVERT: b 14 SER cc_start: 0.8858 (m) cc_final: 0.8588 (p) REVERT: b 43 ASN cc_start: 0.8475 (t0) cc_final: 0.8235 (t0) REVERT: b 45 GLN cc_start: 0.9035 (tp40) cc_final: 0.8000 (tm-30) REVERT: b 49 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7251 (mm-30) REVERT: b 59 LEU cc_start: 0.9277 (mp) cc_final: 0.8997 (mp) REVERT: b 64 GLN cc_start: 0.8504 (tm-30) cc_final: 0.7822 (tm-30) REVERT: b 65 SER cc_start: 0.9251 (m) cc_final: 0.8859 (t) REVERT: b 75 ASP cc_start: 0.8584 (t0) cc_final: 0.8175 (t0) REVERT: c 9 ASP cc_start: 0.8295 (t0) cc_final: 0.7938 (t0) REVERT: c 20 ASP cc_start: 0.7934 (t0) cc_final: 0.7617 (t0) REVERT: d 57 TYR cc_start: 0.8992 (t80) cc_final: 0.8593 (t80) REVERT: d 71 ILE cc_start: 0.8786 (mm) cc_final: 0.8269 (mm) REVERT: d 75 ASP cc_start: 0.8379 (m-30) cc_final: 0.8002 (m-30) REVERT: e 40 ASN cc_start: 0.8487 (p0) cc_final: 0.8095 (p0) REVERT: e 56 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8235 (tt0) REVERT: f 20 ASP cc_start: 0.8493 (t70) cc_final: 0.8265 (t70) REVERT: f 80 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8172 (tm-30) REVERT: g 8 ASP cc_start: 0.6046 (p0) cc_final: 0.5843 (p0) REVERT: g 17 GLU cc_start: 0.7823 (mp0) cc_final: 0.7537 (mp0) REVERT: g 54 LEU cc_start: 0.9229 (tp) cc_final: 0.9000 (tp) REVERT: g 79 ILE cc_start: 0.9209 (mm) cc_final: 0.8760 (mm) REVERT: g 80 GLN cc_start: 0.8734 (tp-100) cc_final: 0.8381 (tm-30) REVERT: g 81 ASN cc_start: 0.9176 (m110) cc_final: 0.8938 (m-40) REVERT: h 59 LEU cc_start: 0.9282 (mt) cc_final: 0.8906 (mt) REVERT: i 80 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8161 (tm-30) REVERT: i 81 ASN cc_start: 0.9245 (m-40) cc_final: 0.8979 (m-40) REVERT: j 14 SER cc_start: 0.8927 (m) cc_final: 0.8592 (t) REVERT: j 80 GLN cc_start: 0.8920 (tp-100) cc_final: 0.8592 (tp40) REVERT: k 50 TYR cc_start: 0.9244 (t80) cc_final: 0.9026 (t80) REVERT: k 72 LYS cc_start: 0.8862 (tttt) cc_final: 0.8594 (tttt) REVERT: l 16 SER cc_start: 0.9064 (m) cc_final: 0.8283 (t) REVERT: l 20 ASP cc_start: 0.7625 (m-30) cc_final: 0.7277 (m-30) REVERT: l 25 THR cc_start: 0.8887 (p) cc_final: 0.8150 (p) REVERT: l 26 LEU cc_start: 0.9253 (tt) cc_final: 0.9023 (tt) REVERT: l 43 ASN cc_start: 0.8784 (t0) cc_final: 0.8532 (t0) REVERT: l 45 GLN cc_start: 0.8257 (tp40) cc_final: 0.7571 (tp40) REVERT: l 50 TYR cc_start: 0.9219 (t80) cc_final: 0.8806 (t80) REVERT: m 20 ASP cc_start: 0.8317 (m-30) cc_final: 0.7925 (m-30) REVERT: m 27 GLN cc_start: 0.8016 (pt0) cc_final: 0.7627 (pt0) REVERT: m 50 TYR cc_start: 0.8833 (t80) cc_final: 0.8473 (t80) REVERT: m 75 ASP cc_start: 0.8421 (m-30) cc_final: 0.7530 (m-30) REVERT: n 3 VAL cc_start: 0.8604 (t) cc_final: 0.8276 (m) REVERT: n 29 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7138 (tm-30) REVERT: n 75 ASP cc_start: 0.8496 (m-30) cc_final: 0.8120 (m-30) REVERT: n 80 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8026 (tm-30) REVERT: o 14 SER cc_start: 0.8698 (t) cc_final: 0.8309 (p) REVERT: o 29 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7453 (mt-10) REVERT: o 39 LYS cc_start: 0.7853 (mmpt) cc_final: 0.7333 (mmpt) REVERT: o 43 ASN cc_start: 0.7700 (t0) cc_final: 0.7387 (t0) REVERT: o 53 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8704 (mmpt) REVERT: o 72 LYS cc_start: 0.9439 (tmtt) cc_final: 0.8956 (tmtt) REVERT: p 25 THR cc_start: 0.8343 (p) cc_final: 0.7684 (t) REVERT: p 46 LEU cc_start: 0.9277 (tp) cc_final: 0.9070 (tt) REVERT: p 75 ASP cc_start: 0.8616 (m-30) cc_final: 0.8051 (m-30) REVERT: q 14 SER cc_start: 0.9344 (m) cc_final: 0.9108 (p) REVERT: q 32 LEU cc_start: 0.8225 (tp) cc_final: 0.7812 (tp) REVERT: q 36 LYS cc_start: 0.8708 (mttt) cc_final: 0.8436 (mtmt) REVERT: q 50 TYR cc_start: 0.8642 (t80) cc_final: 0.8349 (t80) REVERT: r 59 LEU cc_start: 0.8853 (mt) cc_final: 0.8554 (mt) REVERT: s 7 ASN cc_start: 0.6658 (m-40) cc_final: 0.5598 (p0) REVERT: s 23 THR cc_start: 0.8586 (m) cc_final: 0.8334 (m) REVERT: s 24 GLN cc_start: 0.8105 (tp40) cc_final: 0.7728 (mm-40) REVERT: s 27 GLN cc_start: 0.8468 (mt0) cc_final: 0.8031 (tm-30) REVERT: s 65 SER cc_start: 0.9068 (t) cc_final: 0.8707 (m) REVERT: s 69 LYS cc_start: 0.8593 (tptm) cc_final: 0.7420 (ttmt) REVERT: t 51 GLN cc_start: 0.8825 (tt0) cc_final: 0.6641 (mm-40) REVERT: t 52 SER cc_start: 0.8458 (m) cc_final: 0.8182 (t) REVERT: t 69 LYS cc_start: 0.9258 (tptm) cc_final: 0.8587 (mttt) REVERT: t 72 LYS cc_start: 0.9512 (tmtt) cc_final: 0.9208 (tttp) REVERT: u 30 LEU cc_start: 0.8813 (tp) cc_final: 0.8581 (tt) REVERT: u 49 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7055 (tp30) REVERT: u 69 LYS cc_start: 0.9050 (tptm) cc_final: 0.7607 (ttmt) REVERT: u 75 ASP cc_start: 0.8921 (m-30) cc_final: 0.8167 (m-30) REVERT: v 18 THR cc_start: 0.8135 (m) cc_final: 0.7715 (m) REVERT: v 32 LEU cc_start: 0.9295 (tp) cc_final: 0.9035 (tp) REVERT: v 36 LYS cc_start: 0.9045 (mttt) cc_final: 0.8751 (mttm) REVERT: v 69 LYS cc_start: 0.9162 (tptm) cc_final: 0.8224 (mttm) REVERT: w 25 THR cc_start: 0.8676 (p) cc_final: 0.8271 (p) REVERT: w 57 TYR cc_start: 0.8886 (t80) cc_final: 0.8414 (t80) REVERT: w 61 ARG cc_start: 0.8464 (mmt180) cc_final: 0.6811 (ttp-170) REVERT: w 69 LYS cc_start: 0.9135 (tppt) cc_final: 0.7673 (tppt) REVERT: a0 103 LYS cc_start: 0.8165 (tttm) cc_final: 0.7109 (tptt) REVERT: d0 103 LYS cc_start: 0.9263 (ttmt) cc_final: 0.7919 (tptt) REVERT: e0 103 LYS cc_start: 0.8790 (ttmt) cc_final: 0.8175 (tttt) REVERT: f0 103 LYS cc_start: 0.9228 (ttmt) cc_final: 0.8311 (tptt) REVERT: g0 103 LYS cc_start: 0.9083 (mtmt) cc_final: 0.7744 (tptt) REVERT: i0 103 LYS cc_start: 0.8966 (tttt) cc_final: 0.8601 (tptt) REVERT: k0 103 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8068 (tptt) REVERT: l0 103 LYS cc_start: 0.8933 (ttmt) cc_final: 0.8145 (tptt) REVERT: m0 103 LYS cc_start: 0.9063 (mtpt) cc_final: 0.8161 (tptt) REVERT: n0 97 SER cc_start: 0.9112 (m) cc_final: 0.8818 (t) REVERT: n0 103 LYS cc_start: 0.8990 (ttmt) cc_final: 0.8483 (ttpt) REVERT: p0 103 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8041 (tptt) REVERT: q0 103 LYS cc_start: 0.8943 (ttmt) cc_final: 0.8328 (tptt) REVERT: r0 102 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8149 (mt-10) REVERT: r0 103 LYS cc_start: 0.8816 (ttmt) cc_final: 0.7541 (tptt) REVERT: t0 103 LYS cc_start: 0.8906 (ttmt) cc_final: 0.8142 (tptt) REVERT: t0 105 ARG cc_start: 0.9197 (ttm110) cc_final: 0.8000 (tpm170) REVERT: u0 100 ARG cc_start: 0.7794 (ttm110) cc_final: 0.7332 (tpt170) REVERT: u0 103 LYS cc_start: 0.9105 (ttmt) cc_final: 0.8044 (tptt) REVERT: v0 92 THR cc_start: 0.8376 (m) cc_final: 0.8138 (m) REVERT: v0 103 LYS cc_start: 0.9233 (mttt) cc_final: 0.7855 (tptt) REVERT: w0 103 LYS cc_start: 0.8893 (ttmt) cc_final: 0.8386 (tptt) REVERT: x0 103 LYS cc_start: 0.8421 (ttmt) cc_final: 0.7816 (tptt) outliers start: 8 outliers final: 0 residues processed: 2213 average time/residue: 0.2202 time to fit residues: 828.1767 Evaluate side-chains 1907 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1907 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 61 optimal weight: 0.9990 chunk 257 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 484 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 300 optimal weight: 2.9990 chunk 144 optimal weight: 0.0870 chunk 382 optimal weight: 0.9990 chunk 288 optimal weight: 0.0970 chunk 92 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 77 ASN A 106 HIS ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN E 106 HIS ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 170 ASN F 247 HIS J 76 HIS N 8 ASN O 44 GLN P 59 ASN R 19 GLN T 80 GLN V 40 ASN W 81 ASN Y 144 ASN 2 137 HIS 4 127 GLN 4 137 HIS ** 4 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 123 ASN ** y 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 123 ASN 9 123 ASN b 24 GLN e 45 GLN f 40 ASN f 51 GLN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 40 ASN n 81 ASN p 80 GLN t 24 GLN u 40 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.116960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.102565 restraints weight = 90278.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.104953 restraints weight = 55036.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.106650 restraints weight = 38041.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107849 restraints weight = 28625.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108663 restraints weight = 22995.748| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 44859 Z= 0.136 Angle : 0.625 13.370 60892 Z= 0.309 Chirality : 0.040 0.199 7369 Planarity : 0.004 0.072 7620 Dihedral : 4.283 84.754 5953 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.12 % Allowed : 1.84 % Favored : 98.04 % 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: 3.00 (0.12), residues: 5404 helix: 3.07 (0.08), residues: 4150 sheet: 1.20 (0.31), residues: 224 loop : -2.86 (0.17), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 85 TYR 0.024 0.001 TYR O 3 PHE 0.036 0.002 PHE u 19 TRP 0.010 0.001 TRP I 66 HIS 0.006 0.001 HIS F 11 Details of bonding type rmsd covalent geometry : bond 0.00314 (44858) covalent geometry : angle 0.62527 (60890) SS BOND : bond 0.00056 ( 1) SS BOND : angle 0.27118 ( 2) hydrogen bonds : bond 0.03985 ( 3327) hydrogen bonds : angle 3.52897 ( 9915) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2239 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 2233 time to evaluate : 1.833 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: 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 26 CYS cc_start: 0.8608 (p) cc_final: 0.7871 (p) REVERT: A 36 MET cc_start: 0.8797 (ttp) cc_final: 0.8399 (tpp) REVERT: A 50 MET cc_start: 0.8195 (ttp) cc_final: 0.7842 (ttm) REVERT: A 68 ILE cc_start: 0.9524 (mt) cc_final: 0.9212 (mt) REVERT: A 69 GLU cc_start: 0.7796 (tp30) cc_final: 0.7165 (mm-30) REVERT: A 101 GLN cc_start: 0.8632 (tt0) cc_final: 0.8381 (tm-30) REVERT: A 104 LYS cc_start: 0.9374 (mmmm) cc_final: 0.9040 (ttmt) REVERT: A 152 LYS cc_start: 0.9203 (tttt) cc_final: 0.8736 (mtmt) REVERT: A 177 MET cc_start: 0.7843 (mtt) cc_final: 0.7569 (mtt) REVERT: A 205 LYS cc_start: 0.9000 (mttt) cc_final: 0.8040 (tttt) REVERT: B 65 LYS cc_start: 0.8567 (tttp) cc_final: 0.7976 (tttt) REVERT: B 120 GLU cc_start: 0.6264 (mt-10) cc_final: 0.5815 (mp0) REVERT: B 146 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7666 (mm-30) REVERT: B 177 MET cc_start: 0.8019 (mtt) cc_final: 0.7714 (mtt) REVERT: B 178 MET cc_start: 0.8282 (mtm) cc_final: 0.8048 (mtp) REVERT: B 190 LYS cc_start: 0.9190 (mtmt) cc_final: 0.8482 (mtmm) REVERT: C 25 THR cc_start: 0.9111 (p) cc_final: 0.8645 (t) REVERT: C 29 LYS cc_start: 0.9012 (mttp) cc_final: 0.8542 (mttm) REVERT: C 105 LYS cc_start: 0.9022 (tttp) cc_final: 0.8745 (mtpp) REVERT: C 117 ARG cc_start: 0.8418 (mtt180) cc_final: 0.7947 (tpt170) REVERT: C 119 GLU cc_start: 0.7752 (tp30) cc_final: 0.7512 (tp30) REVERT: C 146 GLU cc_start: 0.8266 (tp30) cc_final: 0.7886 (tp30) REVERT: D 2 LEU cc_start: 0.9199 (mt) cc_final: 0.8909 (mt) REVERT: D 6 SER cc_start: 0.8722 (m) cc_final: 0.7899 (p) REVERT: D 17 LEU cc_start: 0.9229 (tp) cc_final: 0.8836 (tt) REVERT: D 105 LYS cc_start: 0.9270 (ttmt) cc_final: 0.8944 (ttmm) REVERT: D 117 ARG cc_start: 0.8794 (tmm-80) cc_final: 0.8498 (ttt180) REVERT: E 146 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8573 (mm-30) REVERT: F 36 ASN cc_start: 0.7807 (t0) cc_final: 0.7383 (t0) REVERT: F 58 SER cc_start: 0.8772 (m) cc_final: 0.8417 (p) REVERT: F 104 ASP cc_start: 0.8442 (t0) cc_final: 0.8188 (t0) REVERT: F 133 PHE cc_start: 0.8881 (t80) cc_final: 0.8358 (t80) REVERT: F 152 GLN cc_start: 0.9038 (tt0) cc_final: 0.8491 (tp40) REVERT: F 202 VAL cc_start: 0.9098 (t) cc_final: 0.8891 (t) REVERT: G 73 SER cc_start: 0.8927 (p) cc_final: 0.8685 (p) REVERT: G 79 MET cc_start: 0.8559 (mmm) cc_final: 0.8051 (mmm) REVERT: H 77 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7908 (tm-30) REVERT: I 5 VAL cc_start: 0.9142 (t) cc_final: 0.8547 (p) REVERT: I 60 LEU cc_start: 0.8519 (mt) cc_final: 0.8304 (mt) REVERT: I 69 GLU cc_start: 0.7667 (tp30) cc_final: 0.6543 (tp30) REVERT: J 70 VAL cc_start: 0.9681 (t) cc_final: 0.9377 (p) REVERT: K 51 MET cc_start: 0.7433 (mmt) cc_final: 0.6946 (mmt) REVERT: K 132 LYS cc_start: 0.8573 (mmtp) cc_final: 0.8206 (mttt) REVERT: K 176 ARG cc_start: 0.8749 (tpt-90) cc_final: 0.8491 (tpt-90) REVERT: N 33 LYS cc_start: 0.8616 (mmmm) cc_final: 0.7981 (mmtt) REVERT: N 58 LEU cc_start: 0.9137 (mt) cc_final: 0.8787 (mt) REVERT: N 89 SER cc_start: 0.9321 (t) cc_final: 0.8943 (p) REVERT: O 41 THR cc_start: 0.8707 (t) cc_final: 0.8336 (m) REVERT: P 44 GLN cc_start: 0.8318 (tt0) cc_final: 0.7984 (tt0) REVERT: P 56 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7160 (tm-30) REVERT: P 57 SER cc_start: 0.9087 (m) cc_final: 0.8513 (p) REVERT: R 27 GLU cc_start: 0.6972 (tm-30) cc_final: 0.6768 (pt0) REVERT: R 47 GLN cc_start: 0.8273 (tp40) cc_final: 0.7926 (tm-30) REVERT: R 51 MET cc_start: 0.7500 (mtt) cc_final: 0.7227 (mtp) REVERT: S 25 THR cc_start: 0.7788 (t) cc_final: 0.7585 (t) REVERT: S 37 LEU cc_start: 0.9074 (tp) cc_final: 0.8694 (tp) REVERT: T 30 LEU cc_start: 0.9173 (tp) cc_final: 0.8895 (tp) REVERT: T 50 TYR cc_start: 0.9152 (t80) cc_final: 0.8910 (t80) REVERT: U 43 ASN cc_start: 0.8615 (t0) cc_final: 0.7948 (t0) REVERT: U 46 LEU cc_start: 0.9021 (mp) cc_final: 0.8440 (tt) REVERT: U 55 SER cc_start: 0.9074 (m) cc_final: 0.8275 (m) REVERT: V 32 LEU cc_start: 0.8691 (mt) cc_final: 0.8330 (tt) REVERT: V 64 GLN cc_start: 0.8573 (tt0) cc_final: 0.8288 (tt0) REVERT: W 39 LYS cc_start: 0.8363 (mttt) cc_final: 0.7719 (mptt) REVERT: W 43 ASN cc_start: 0.8630 (t0) cc_final: 0.8074 (t0) REVERT: X 141 ILE cc_start: 0.9204 (mm) cc_final: 0.8963 (mm) REVERT: X 142 ARG cc_start: 0.8588 (mmt-90) cc_final: 0.8190 (mmt-90) REVERT: Y 112 SER cc_start: 0.7915 (p) cc_final: 0.7576 (m) REVERT: Y 123 ASN cc_start: 0.8675 (t0) cc_final: 0.8419 (t0) REVERT: Y 131 ASP cc_start: 0.7582 (m-30) cc_final: 0.7158 (m-30) REVERT: Z 133 ASN cc_start: 0.9181 (t0) cc_final: 0.8861 (t0) REVERT: Z 161 LEU cc_start: 0.8629 (tp) cc_final: 0.8428 (tp) REVERT: 0 128 TYR cc_start: 0.8192 (t80) cc_final: 0.7726 (t80) REVERT: 0 164 ASN cc_start: 0.8927 (m-40) cc_final: 0.8684 (m-40) REVERT: 2 127 GLN cc_start: 0.8287 (tp40) cc_final: 0.7955 (tp40) REVERT: 2 167 THR cc_start: 0.8676 (t) cc_final: 0.8472 (t) REVERT: 4 150 PHE cc_start: 0.9019 (p90) cc_final: 0.8577 (p90) REVERT: 4 167 THR cc_start: 0.8781 (m) cc_final: 0.8516 (t) REVERT: 6 127 GLN cc_start: 0.8942 (tp40) cc_final: 0.8277 (tp40) REVERT: 6 138 ARG cc_start: 0.8368 (mtp85) cc_final: 0.7398 (mtm110) REVERT: 6 149 THR cc_start: 0.8874 (m) cc_final: 0.7971 (p) REVERT: 6 168 LEU cc_start: 0.9098 (tp) cc_final: 0.8840 (tt) REVERT: 8 111 ILE cc_start: 0.9279 (mt) cc_final: 0.9073 (mt) REVERT: 8 115 ILE cc_start: 0.8953 (mt) cc_final: 0.8677 (mm) REVERT: 8 144 ASN cc_start: 0.7657 (t0) cc_final: 0.7432 (t0) REVERT: 8 150 PHE cc_start: 0.9241 (p90) cc_final: 0.8739 (p90) REVERT: x 150 PHE cc_start: 0.9339 (p90) cc_final: 0.8654 (p90) REVERT: x 153 SER cc_start: 0.9529 (t) cc_final: 0.9024 (p) REVERT: y 158 LEU cc_start: 0.8253 (tp) cc_final: 0.7876 (mm) REVERT: y 160 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7791 (mm-30) REVERT: y 164 ASN cc_start: 0.8685 (m-40) cc_final: 0.8394 (m-40) REVERT: z 112 SER cc_start: 0.9164 (p) cc_final: 0.8754 (m) REVERT: z 127 GLN cc_start: 0.8432 (tm-30) cc_final: 0.7788 (tm-30) REVERT: z 149 THR cc_start: 0.9031 (m) cc_final: 0.8691 (t) REVERT: z 151 TYR cc_start: 0.8596 (t80) cc_final: 0.8171 (t80) REVERT: 1 127 GLN cc_start: 0.7979 (tp40) cc_final: 0.7495 (tp40) REVERT: 1 130 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8096 (mmtt) REVERT: 1 133 ASN cc_start: 0.8614 (m-40) cc_final: 0.8302 (t0) REVERT: 1 148 LYS cc_start: 0.8501 (mtpt) cc_final: 0.8166 (mtpp) REVERT: 1 170 ASP cc_start: 0.7412 (m-30) cc_final: 0.6969 (m-30) REVERT: 3 115 ILE cc_start: 0.8421 (mt) cc_final: 0.8176 (mt) REVERT: 5 131 ASP cc_start: 0.8201 (p0) cc_final: 0.7853 (p0) REVERT: 7 168 LEU cc_start: 0.9084 (tp) cc_final: 0.8859 (tp) REVERT: 9 135 TYR cc_start: 0.7587 (t80) cc_final: 0.7055 (t80) REVERT: a 26 LEU cc_start: 0.8802 (tp) cc_final: 0.8544 (tp) REVERT: a 31 THR cc_start: 0.7663 (m) cc_final: 0.7270 (m) REVERT: a 66 ASN cc_start: 0.9044 (m-40) cc_final: 0.8686 (m110) REVERT: a 80 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8403 (tm-30) REVERT: b 14 SER cc_start: 0.8899 (m) cc_final: 0.8601 (p) REVERT: b 43 ASN cc_start: 0.8451 (t0) cc_final: 0.8207 (t0) REVERT: b 45 GLN cc_start: 0.9007 (tp40) cc_final: 0.8001 (tm-30) REVERT: b 49 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7093 (mm-30) REVERT: b 59 LEU cc_start: 0.9328 (mp) cc_final: 0.9067 (mp) REVERT: b 64 GLN cc_start: 0.8429 (tm-30) cc_final: 0.7662 (tm-30) REVERT: b 72 LYS cc_start: 0.8834 (tptm) cc_final: 0.8605 (tptm) REVERT: b 75 ASP cc_start: 0.8529 (t0) cc_final: 0.8118 (t0) REVERT: c 20 ASP cc_start: 0.7789 (t0) cc_final: 0.7480 (t0) REVERT: c 59 LEU cc_start: 0.9414 (mt) cc_final: 0.9211 (mt) REVERT: d 57 TYR cc_start: 0.8968 (t80) cc_final: 0.8565 (t80) REVERT: d 71 ILE cc_start: 0.8720 (mm) cc_final: 0.8197 (mm) REVERT: d 75 ASP cc_start: 0.8344 (m-30) cc_final: 0.7968 (m-30) REVERT: e 40 ASN cc_start: 0.8379 (p0) cc_final: 0.7991 (p0) REVERT: e 56 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8096 (tt0) REVERT: f 14 SER cc_start: 0.9102 (p) cc_final: 0.8443 (t) REVERT: f 80 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8126 (tm-30) REVERT: g 26 LEU cc_start: 0.9224 (tt) cc_final: 0.8583 (mm) REVERT: g 54 LEU cc_start: 0.9279 (tp) cc_final: 0.9062 (tp) REVERT: g 65 SER cc_start: 0.9067 (t) cc_final: 0.8823 (t) REVERT: g 79 ILE cc_start: 0.9213 (mm) cc_final: 0.8811 (mm) REVERT: g 80 GLN cc_start: 0.8803 (tp-100) cc_final: 0.8436 (tm-30) REVERT: g 81 ASN cc_start: 0.9153 (m110) cc_final: 0.8937 (m-40) REVERT: h 29 GLU cc_start: 0.8505 (mp0) cc_final: 0.8295 (mp0) REVERT: h 59 LEU cc_start: 0.9184 (mt) cc_final: 0.8750 (mt) REVERT: i 72 LYS cc_start: 0.8991 (ttpt) cc_final: 0.8751 (ttpt) REVERT: i 80 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8200 (tm-30) REVERT: i 81 ASN cc_start: 0.9303 (m-40) cc_final: 0.9009 (m-40) REVERT: j 14 SER cc_start: 0.8809 (m) cc_final: 0.8574 (t) REVERT: j 80 GLN cc_start: 0.9053 (tp-100) cc_final: 0.8629 (tp40) REVERT: k 50 TYR cc_start: 0.9247 (t80) cc_final: 0.9033 (t80) REVERT: l 16 SER cc_start: 0.9021 (m) cc_final: 0.8303 (t) REVERT: l 20 ASP cc_start: 0.7584 (m-30) cc_final: 0.7162 (m-30) REVERT: l 25 THR cc_start: 0.8675 (p) cc_final: 0.7971 (p) REVERT: l 43 ASN cc_start: 0.8714 (t0) cc_final: 0.8473 (t0) REVERT: l 45 GLN cc_start: 0.8235 (tp40) cc_final: 0.7567 (tp40) REVERT: l 50 TYR cc_start: 0.9182 (t80) cc_final: 0.8811 (t80) REVERT: m 20 ASP cc_start: 0.8277 (m-30) cc_final: 0.7825 (m-30) REVERT: m 50 TYR cc_start: 0.8819 (t80) cc_final: 0.8457 (t80) REVERT: m 75 ASP cc_start: 0.8326 (m-30) cc_final: 0.7443 (m-30) REVERT: n 3 VAL cc_start: 0.8595 (t) cc_final: 0.8287 (m) REVERT: n 29 GLU cc_start: 0.7330 (tm-30) cc_final: 0.7014 (tm-30) REVERT: n 75 ASP cc_start: 0.8483 (m-30) cc_final: 0.8121 (m-30) REVERT: n 80 GLN cc_start: 0.8739 (tm-30) cc_final: 0.8047 (tm-30) REVERT: o 29 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7471 (mt-10) REVERT: o 43 ASN cc_start: 0.7606 (t0) cc_final: 0.7391 (t0) REVERT: o 50 TYR cc_start: 0.9280 (t80) cc_final: 0.8970 (t80) REVERT: o 53 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8707 (mmpt) REVERT: p 12 LEU cc_start: 0.9415 (mt) cc_final: 0.9074 (mt) REVERT: p 25 THR cc_start: 0.8286 (p) cc_final: 0.7661 (t) REVERT: p 75 ASP cc_start: 0.8581 (m-30) cc_final: 0.8083 (m-30) REVERT: q 14 SER cc_start: 0.9449 (m) cc_final: 0.9130 (p) REVERT: q 32 LEU cc_start: 0.8191 (tp) cc_final: 0.7833 (tp) REVERT: q 36 LYS cc_start: 0.8689 (mttt) cc_final: 0.8451 (mtmt) REVERT: r 25 THR cc_start: 0.8190 (p) cc_final: 0.7686 (p) REVERT: r 59 LEU cc_start: 0.8887 (mt) cc_final: 0.8575 (mt) REVERT: s 7 ASN cc_start: 0.6624 (m-40) cc_final: 0.5562 (p0) REVERT: s 23 THR cc_start: 0.8540 (m) cc_final: 0.8255 (m) REVERT: s 24 GLN cc_start: 0.8110 (tp40) cc_final: 0.7890 (mm-40) REVERT: s 27 GLN cc_start: 0.8473 (mt0) cc_final: 0.7954 (tm-30) REVERT: s 65 SER cc_start: 0.9048 (t) cc_final: 0.8693 (m) REVERT: s 69 LYS cc_start: 0.8558 (tptm) cc_final: 0.7422 (ttmt) REVERT: t 51 GLN cc_start: 0.8712 (tt0) cc_final: 0.6647 (mm-40) REVERT: t 69 LYS cc_start: 0.9257 (tptm) cc_final: 0.8603 (mttt) REVERT: t 72 LYS cc_start: 0.9515 (tmtt) cc_final: 0.9205 (tttp) REVERT: u 30 LEU cc_start: 0.8911 (tp) cc_final: 0.8664 (tt) REVERT: u 49 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7104 (tp30) REVERT: u 69 LYS cc_start: 0.8908 (tptm) cc_final: 0.7484 (ttmt) REVERT: u 82 PHE cc_start: 0.8938 (m-80) cc_final: 0.8598 (m-80) REVERT: v 32 LEU cc_start: 0.9289 (tp) cc_final: 0.9024 (tp) REVERT: v 36 LYS cc_start: 0.9027 (mttt) cc_final: 0.8738 (mttm) REVERT: v 69 LYS cc_start: 0.9113 (tptm) cc_final: 0.8210 (mttt) REVERT: w 25 THR cc_start: 0.8614 (p) cc_final: 0.8172 (p) REVERT: w 57 TYR cc_start: 0.8879 (t80) cc_final: 0.8440 (t80) REVERT: w 61 ARG cc_start: 0.8378 (mmt180) cc_final: 0.6676 (ttp-170) REVERT: w 69 LYS cc_start: 0.8991 (tppt) cc_final: 0.7427 (tppt) REVERT: a0 103 LYS cc_start: 0.8099 (tttm) cc_final: 0.6999 (tptt) REVERT: d0 103 LYS cc_start: 0.9254 (ttmt) cc_final: 0.7912 (tptt) REVERT: e0 103 LYS cc_start: 0.8728 (ttmt) cc_final: 0.7799 (tttt) REVERT: f0 100 ARG cc_start: 0.8350 (ttm170) cc_final: 0.7946 (ttm170) REVERT: f0 103 LYS cc_start: 0.9238 (ttmt) cc_final: 0.8292 (tptt) REVERT: g0 103 LYS cc_start: 0.9081 (mtmt) cc_final: 0.7747 (tptt) REVERT: i0 103 LYS cc_start: 0.8942 (tttt) cc_final: 0.8616 (tptt) REVERT: k0 103 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8099 (tptt) REVERT: l0 103 LYS cc_start: 0.8926 (ttmt) cc_final: 0.8158 (tptt) REVERT: m0 103 LYS cc_start: 0.9058 (mtpt) cc_final: 0.8134 (tptt) REVERT: n0 97 SER cc_start: 0.9017 (m) cc_final: 0.8772 (t) REVERT: p0 103 LYS cc_start: 0.8869 (ttpt) cc_final: 0.8026 (tptt) REVERT: q0 103 LYS cc_start: 0.9063 (ttmt) cc_final: 0.8292 (tptt) REVERT: r0 102 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8094 (mt-10) REVERT: r0 103 LYS cc_start: 0.8828 (ttmt) cc_final: 0.7541 (tptt) REVERT: t0 103 LYS cc_start: 0.8886 (ttmt) cc_final: 0.8092 (tptt) REVERT: t0 105 ARG cc_start: 0.9179 (ttm110) cc_final: 0.7988 (tpm170) REVERT: u0 100 ARG cc_start: 0.7797 (ttm110) cc_final: 0.7322 (tpt170) REVERT: u0 103 LYS cc_start: 0.9109 (ttmt) cc_final: 0.8027 (tptt) REVERT: v0 92 THR cc_start: 0.8361 (m) cc_final: 0.8129 (m) REVERT: v0 103 LYS cc_start: 0.9229 (mttt) cc_final: 0.7811 (tptt) REVERT: w0 103 LYS cc_start: 0.8868 (ttmt) cc_final: 0.8355 (tptt) REVERT: x0 103 LYS cc_start: 0.8392 (ttmt) cc_final: 0.7810 (tptt) outliers start: 6 outliers final: 0 residues processed: 2234 average time/residue: 0.2243 time to fit residues: 851.7244 Evaluate side-chains 1922 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1922 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 179 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 366 optimal weight: 0.5980 chunk 360 optimal weight: 2.9990 chunk 396 optimal weight: 2.9990 chunk 451 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 259 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 313 optimal weight: 3.9990 chunk 379 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 106 HIS B 210 GLN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS ** F 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 170 ASN F 247 HIS F 252 ASN I 9 ASN J 76 HIS K 162 GLN O 44 GLN P 59 ASN R 19 GLN ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 80 GLN U 80 GLN W 81 ASN Y 144 ASN 2 137 HIS ** 4 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 123 ASN ** y 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 ASN b 81 ASN c 64 GLN d 66 ASN f 40 ASN f 51 GLN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 40 ASN ** m 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 81 ASN p 80 GLN t 24 GLN u 40 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102239 restraints weight = 89994.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.104804 restraints weight = 53072.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106601 restraints weight = 35813.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107904 restraints weight = 26547.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108834 restraints weight = 20969.190| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 44859 Z= 0.141 Angle : 0.642 10.859 60892 Z= 0.319 Chirality : 0.041 0.259 7369 Planarity : 0.004 0.073 7620 Dihedral : 4.309 85.590 5953 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.12 % Allowed : 1.04 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.96 (0.11), residues: 5404 helix: 3.04 (0.08), residues: 4150 sheet: 1.19 (0.31), residues: 224 loop : -2.84 (0.17), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 113 TYR 0.040 0.002 TYR K 171 PHE 0.034 0.002 PHE v 19 TRP 0.009 0.001 TRP t 10 HIS 0.006 0.001 HIS F 11 Details of bonding type rmsd covalent geometry : bond 0.00328 (44858) covalent geometry : angle 0.64174 (60890) SS BOND : bond 0.00084 ( 1) SS BOND : angle 0.10745 ( 2) hydrogen bonds : bond 0.04035 ( 3327) hydrogen bonds : angle 3.56662 ( 9915) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2212 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 2206 time to evaluate : 1.810 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: 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: symmetry clash REVERT: A 26 CYS cc_start: 0.8721 (p) cc_final: 0.7985 (p) REVERT: A 36 MET cc_start: 0.8782 (ttp) cc_final: 0.8399 (tpp) REVERT: A 50 MET cc_start: 0.8179 (ttp) cc_final: 0.7871 (ttm) REVERT: A 68 ILE cc_start: 0.9518 (mt) cc_final: 0.9198 (mt) REVERT: A 69 GLU cc_start: 0.7822 (tp30) cc_final: 0.7123 (mm-30) REVERT: A 101 GLN cc_start: 0.8710 (tt0) cc_final: 0.8454 (tm-30) REVERT: A 152 LYS cc_start: 0.9136 (tttt) cc_final: 0.8680 (mtmt) REVERT: A 205 LYS cc_start: 0.9100 (mttt) cc_final: 0.8140 (tttt) REVERT: B 65 LYS cc_start: 0.8543 (tttp) cc_final: 0.8028 (tttt) REVERT: B 120 GLU cc_start: 0.6190 (mt-10) cc_final: 0.5750 (mp0) REVERT: B 162 VAL cc_start: 0.8941 (m) cc_final: 0.8737 (p) REVERT: B 173 LEU cc_start: 0.9106 (mt) cc_final: 0.8636 (mp) REVERT: B 177 MET cc_start: 0.8080 (mtt) cc_final: 0.7728 (mtt) REVERT: B 178 MET cc_start: 0.8350 (mtm) cc_final: 0.8036 (mtp) REVERT: B 190 LYS cc_start: 0.9211 (mtmt) cc_final: 0.8305 (mtmm) REVERT: C 29 LYS cc_start: 0.9033 (mttp) cc_final: 0.8801 (mttp) REVERT: C 105 LYS cc_start: 0.8969 (tttp) cc_final: 0.8679 (mtpp) REVERT: C 117 ARG cc_start: 0.8371 (mtt180) cc_final: 0.7847 (tpt170) REVERT: D 1 MET cc_start: 0.1679 (ptt) cc_final: 0.1404 (ptt) REVERT: D 2 LEU cc_start: 0.9212 (mt) cc_final: 0.8924 (mt) REVERT: D 6 SER cc_start: 0.8769 (m) cc_final: 0.7919 (p) REVERT: D 17 LEU cc_start: 0.9265 (tp) cc_final: 0.8874 (tt) REVERT: D 105 LYS cc_start: 0.9303 (ttmt) cc_final: 0.9084 (tttm) REVERT: E 44 GLN cc_start: 0.8610 (mp10) cc_final: 0.8330 (mp10) REVERT: F 58 SER cc_start: 0.8751 (m) cc_final: 0.8450 (p) REVERT: F 104 ASP cc_start: 0.8546 (t0) cc_final: 0.8243 (t0) REVERT: F 133 PHE cc_start: 0.8934 (t80) cc_final: 0.8426 (t80) REVERT: F 152 GLN cc_start: 0.9106 (tt0) cc_final: 0.8455 (tp-100) REVERT: F 153 LEU cc_start: 0.9514 (tp) cc_final: 0.9302 (tp) REVERT: G 79 MET cc_start: 0.8594 (mmm) cc_final: 0.8387 (mmm) REVERT: H 60 LEU cc_start: 0.8894 (mm) cc_final: 0.8647 (mm) REVERT: H 77 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8027 (tm-30) REVERT: I 53 LEU cc_start: 0.7936 (tp) cc_final: 0.7716 (tp) REVERT: I 60 LEU cc_start: 0.8593 (mt) cc_final: 0.8370 (mt) REVERT: I 69 GLU cc_start: 0.7764 (tp30) cc_final: 0.6646 (tp30) REVERT: J 70 VAL cc_start: 0.9670 (t) cc_final: 0.9409 (p) REVERT: K 46 SER cc_start: 0.7114 (m) cc_final: 0.6493 (t) REVERT: K 51 MET cc_start: 0.7448 (mmt) cc_final: 0.7025 (mmt) REVERT: K 132 LYS cc_start: 0.8572 (mmtp) cc_final: 0.8178 (mttt) REVERT: K 176 ARG cc_start: 0.8699 (tpt-90) cc_final: 0.8458 (tpt-90) REVERT: N 58 LEU cc_start: 0.9192 (mt) cc_final: 0.8865 (mt) REVERT: N 68 THR cc_start: 0.8923 (m) cc_final: 0.8676 (t) REVERT: N 88 VAL cc_start: 0.9320 (t) cc_final: 0.9078 (p) REVERT: N 89 SER cc_start: 0.9351 (t) cc_final: 0.9088 (p) REVERT: O 41 THR cc_start: 0.8740 (t) cc_final: 0.8376 (m) REVERT: P 44 GLN cc_start: 0.8290 (tt0) cc_final: 0.7957 (tt0) REVERT: P 56 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7139 (tm-30) REVERT: P 57 SER cc_start: 0.9145 (m) cc_final: 0.8610 (p) REVERT: R 27 GLU cc_start: 0.6933 (tm-30) cc_final: 0.6691 (pt0) REVERT: R 47 GLN cc_start: 0.8232 (tp40) cc_final: 0.7851 (tm-30) REVERT: R 51 MET cc_start: 0.7685 (mtt) cc_final: 0.7220 (mtp) REVERT: S 37 LEU cc_start: 0.9030 (tp) cc_final: 0.8671 (tp) REVERT: T 30 LEU cc_start: 0.9176 (tp) cc_final: 0.8885 (tp) REVERT: U 43 ASN cc_start: 0.8583 (t0) cc_final: 0.8001 (m-40) REVERT: U 55 SER cc_start: 0.9179 (m) cc_final: 0.8531 (m) REVERT: V 32 LEU cc_start: 0.8694 (mt) cc_final: 0.8350 (tt) REVERT: V 64 GLN cc_start: 0.8642 (tt0) cc_final: 0.8359 (tt0) REVERT: W 39 LYS cc_start: 0.8343 (mttt) cc_final: 0.7718 (mptt) REVERT: W 43 ASN cc_start: 0.8646 (t0) cc_final: 0.8098 (t0) REVERT: Y 112 SER cc_start: 0.8115 (p) cc_final: 0.7688 (m) REVERT: Y 123 ASN cc_start: 0.8743 (t0) cc_final: 0.8466 (t0) REVERT: Y 138 ARG cc_start: 0.8690 (mtp85) cc_final: 0.8455 (mtp85) REVERT: Z 133 ASN cc_start: 0.9199 (t0) cc_final: 0.8866 (t0) REVERT: 0 128 TYR cc_start: 0.8229 (t80) cc_final: 0.7898 (t80) REVERT: 2 127 GLN cc_start: 0.8355 (tp40) cc_final: 0.7993 (tp40) REVERT: 2 131 ASP cc_start: 0.8062 (t0) cc_final: 0.7851 (t0) REVERT: 4 150 PHE cc_start: 0.9027 (p90) cc_final: 0.8597 (p90) REVERT: 4 167 THR cc_start: 0.8762 (m) cc_final: 0.8497 (t) REVERT: 6 127 GLN cc_start: 0.8983 (tp40) cc_final: 0.8347 (tp40) REVERT: 6 138 ARG cc_start: 0.8432 (mtp85) cc_final: 0.7465 (mtm110) REVERT: 6 149 THR cc_start: 0.8897 (m) cc_final: 0.8015 (p) REVERT: 6 168 LEU cc_start: 0.9117 (tp) cc_final: 0.8824 (tt) REVERT: 8 115 ILE cc_start: 0.8919 (mt) cc_final: 0.8626 (mm) REVERT: 8 144 ASN cc_start: 0.7761 (t0) cc_final: 0.7492 (t0) REVERT: 8 150 PHE cc_start: 0.9257 (p90) cc_final: 0.8703 (p90) REVERT: x 127 GLN cc_start: 0.8932 (tp-100) cc_final: 0.8669 (tp-100) REVERT: x 150 PHE cc_start: 0.9231 (p90) cc_final: 0.8585 (p90) REVERT: x 153 SER cc_start: 0.9440 (t) cc_final: 0.9033 (p) REVERT: x 168 LEU cc_start: 0.9577 (tt) cc_final: 0.9349 (tp) REVERT: y 158 LEU cc_start: 0.8194 (tp) cc_final: 0.7808 (mm) REVERT: y 160 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7847 (mm-30) REVERT: y 164 ASN cc_start: 0.8684 (m-40) cc_final: 0.8435 (m-40) REVERT: z 112 SER cc_start: 0.9162 (p) cc_final: 0.8817 (m) REVERT: z 127 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8118 (tm-30) REVERT: z 149 THR cc_start: 0.9029 (m) cc_final: 0.8722 (t) REVERT: 1 130 LYS cc_start: 0.8421 (mmmt) cc_final: 0.8040 (mmtt) REVERT: 1 133 ASN cc_start: 0.8643 (m-40) cc_final: 0.8277 (t0) REVERT: 3 115 ILE cc_start: 0.8431 (mt) cc_final: 0.8142 (mt) REVERT: 9 135 TYR cc_start: 0.7677 (t80) cc_final: 0.7127 (t80) REVERT: a 26 LEU cc_start: 0.8830 (tp) cc_final: 0.8539 (tp) REVERT: a 31 THR cc_start: 0.7923 (m) cc_final: 0.7528 (m) REVERT: a 66 ASN cc_start: 0.9081 (m-40) cc_final: 0.8840 (m110) REVERT: a 73 ASP cc_start: 0.7544 (t70) cc_final: 0.7321 (t70) REVERT: a 80 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8362 (tm-30) REVERT: b 14 SER cc_start: 0.8865 (m) cc_final: 0.8603 (p) REVERT: b 43 ASN cc_start: 0.8459 (t0) cc_final: 0.8190 (t0) REVERT: b 45 GLN cc_start: 0.9016 (tp40) cc_final: 0.7935 (tm-30) REVERT: b 49 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7293 (mm-30) REVERT: b 59 LEU cc_start: 0.9311 (mp) cc_final: 0.9058 (mp) REVERT: b 64 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7451 (tm-30) REVERT: b 67 THR cc_start: 0.9258 (m) cc_final: 0.8886 (p) REVERT: b 72 LYS cc_start: 0.8838 (tptm) cc_final: 0.8480 (tptp) REVERT: b 75 ASP cc_start: 0.8603 (t0) cc_final: 0.8157 (t0) REVERT: c 20 ASP cc_start: 0.7996 (t0) cc_final: 0.7711 (t0) REVERT: d 57 TYR cc_start: 0.9072 (t80) cc_final: 0.8721 (t80) REVERT: d 71 ILE cc_start: 0.8710 (mm) cc_final: 0.8156 (mm) REVERT: d 75 ASP cc_start: 0.8422 (m-30) cc_final: 0.8016 (m-30) REVERT: d 80 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7314 (tm-30) REVERT: e 40 ASN cc_start: 0.8416 (p0) cc_final: 0.8001 (p0) REVERT: e 56 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8227 (tt0) REVERT: f 14 SER cc_start: 0.9011 (p) cc_final: 0.8400 (t) REVERT: f 80 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8062 (tm-30) REVERT: g 17 GLU cc_start: 0.7966 (mp0) cc_final: 0.7295 (mp0) REVERT: g 26 LEU cc_start: 0.9156 (tt) cc_final: 0.8529 (mm) REVERT: g 54 LEU cc_start: 0.9325 (tp) cc_final: 0.9070 (tp) REVERT: g 79 ILE cc_start: 0.9228 (mm) cc_final: 0.8827 (mm) REVERT: g 80 GLN cc_start: 0.8801 (tp-100) cc_final: 0.8433 (tm-30) REVERT: g 81 ASN cc_start: 0.9222 (m110) cc_final: 0.9003 (m-40) REVERT: h 59 LEU cc_start: 0.9190 (mt) cc_final: 0.8746 (mt) REVERT: i 72 LYS cc_start: 0.8931 (ttpt) cc_final: 0.8682 (ttpt) REVERT: i 80 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8269 (tm-30) REVERT: i 81 ASN cc_start: 0.9349 (m-40) cc_final: 0.9084 (m-40) REVERT: j 14 SER cc_start: 0.8744 (m) cc_final: 0.8472 (t) REVERT: j 42 SER cc_start: 0.9371 (m) cc_final: 0.8984 (p) REVERT: j 80 GLN cc_start: 0.9132 (tp-100) cc_final: 0.8823 (tp-100) REVERT: k 50 TYR cc_start: 0.9296 (t80) cc_final: 0.9095 (t80) REVERT: l 16 SER cc_start: 0.9101 (m) cc_final: 0.8297 (t) REVERT: l 20 ASP cc_start: 0.7608 (m-30) cc_final: 0.7256 (m-30) REVERT: l 25 THR cc_start: 0.8871 (p) cc_final: 0.7963 (p) REVERT: l 26 LEU cc_start: 0.9224 (tt) cc_final: 0.8944 (tt) REVERT: l 45 GLN cc_start: 0.8240 (tp40) cc_final: 0.7599 (tp40) REVERT: l 50 TYR cc_start: 0.9262 (t80) cc_final: 0.8889 (t80) REVERT: m 20 ASP cc_start: 0.8295 (m-30) cc_final: 0.7886 (m-30) REVERT: m 50 TYR cc_start: 0.8885 (t80) cc_final: 0.8544 (t80) REVERT: m 75 ASP cc_start: 0.8444 (m-30) cc_final: 0.7522 (m-30) REVERT: n 3 VAL cc_start: 0.8599 (t) cc_final: 0.8335 (m) REVERT: n 75 ASP cc_start: 0.8521 (m-30) cc_final: 0.8100 (m-30) REVERT: n 80 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8096 (tm-30) REVERT: o 14 SER cc_start: 0.8756 (t) cc_final: 0.8372 (p) REVERT: o 39 LYS cc_start: 0.7891 (mmpt) cc_final: 0.7517 (mmpt) REVERT: o 50 TYR cc_start: 0.9291 (t80) cc_final: 0.9053 (t80) REVERT: p 25 THR cc_start: 0.8299 (p) cc_final: 0.7640 (t) REVERT: p 75 ASP cc_start: 0.8696 (m-30) cc_final: 0.8111 (m-30) REVERT: q 14 SER cc_start: 0.9457 (m) cc_final: 0.9139 (p) REVERT: q 32 LEU cc_start: 0.8178 (tp) cc_final: 0.7798 (tp) REVERT: q 36 LYS cc_start: 0.8656 (mttt) cc_final: 0.8406 (mtmt) REVERT: q 50 TYR cc_start: 0.8435 (t80) cc_final: 0.8176 (t80) REVERT: r 24 GLN cc_start: 0.8298 (mm110) cc_final: 0.7803 (mp10) REVERT: r 25 THR cc_start: 0.8327 (p) cc_final: 0.8020 (p) REVERT: r 29 GLU cc_start: 0.8950 (pm20) cc_final: 0.8682 (pm20) REVERT: r 59 LEU cc_start: 0.8810 (mt) cc_final: 0.8496 (mt) REVERT: s 7 ASN cc_start: 0.6853 (m-40) cc_final: 0.5902 (p0) REVERT: s 23 THR cc_start: 0.8554 (m) cc_final: 0.8274 (m) REVERT: s 24 GLN cc_start: 0.8137 (tp40) cc_final: 0.7917 (mm-40) REVERT: s 27 GLN cc_start: 0.8473 (mt0) cc_final: 0.7874 (tm-30) REVERT: s 65 SER cc_start: 0.9000 (t) cc_final: 0.8697 (m) REVERT: s 69 LYS cc_start: 0.7799 (tptm) cc_final: 0.7342 (ttmt) REVERT: t 49 GLU cc_start: 0.7286 (tp30) cc_final: 0.7080 (tp30) REVERT: t 51 GLN cc_start: 0.8770 (tt0) cc_final: 0.6808 (mm110) REVERT: t 69 LYS cc_start: 0.9302 (tptm) cc_final: 0.8552 (mttt) REVERT: t 72 LYS cc_start: 0.9494 (tmtt) cc_final: 0.9220 (tttp) REVERT: u 30 LEU cc_start: 0.8792 (tp) cc_final: 0.8534 (tt) REVERT: u 49 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7080 (tp30) REVERT: u 67 THR cc_start: 0.8983 (m) cc_final: 0.8694 (m) REVERT: u 69 LYS cc_start: 0.8937 (tptm) cc_final: 0.7464 (ttmt) REVERT: u 82 PHE cc_start: 0.9027 (m-80) cc_final: 0.8504 (m-80) REVERT: v 32 LEU cc_start: 0.9337 (tp) cc_final: 0.9071 (tp) REVERT: v 36 LYS cc_start: 0.8931 (mttt) cc_final: 0.8618 (mttm) REVERT: v 69 LYS cc_start: 0.9103 (tptm) cc_final: 0.8139 (mttt) REVERT: w 25 THR cc_start: 0.8637 (p) cc_final: 0.8139 (p) REVERT: w 57 TYR cc_start: 0.8890 (t80) cc_final: 0.8466 (t80) REVERT: w 61 ARG cc_start: 0.8339 (mmt180) cc_final: 0.6623 (ttp-170) REVERT: w 69 LYS cc_start: 0.8831 (tppt) cc_final: 0.7338 (tppt) REVERT: a0 103 LYS cc_start: 0.8070 (tttm) cc_final: 0.6982 (tptt) REVERT: d0 103 LYS cc_start: 0.9251 (ttmt) cc_final: 0.7897 (tptt) REVERT: e0 103 LYS cc_start: 0.8737 (ttmt) cc_final: 0.7797 (tttt) REVERT: f0 100 ARG cc_start: 0.8451 (ttm170) cc_final: 0.7988 (ttm170) REVERT: f0 103 LYS cc_start: 0.9230 (ttmt) cc_final: 0.8308 (tptt) REVERT: g0 103 LYS cc_start: 0.9112 (mtmt) cc_final: 0.7757 (tptt) REVERT: i0 103 LYS cc_start: 0.8916 (tttt) cc_final: 0.8528 (tptt) REVERT: k0 103 LYS cc_start: 0.8906 (ttmm) cc_final: 0.8085 (tptt) REVERT: l0 103 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8115 (tptt) REVERT: m0 103 LYS cc_start: 0.9086 (mtpt) cc_final: 0.8126 (tptt) REVERT: n0 97 SER cc_start: 0.9040 (m) cc_final: 0.8796 (t) REVERT: n0 103 LYS cc_start: 0.8807 (ttpt) cc_final: 0.8290 (ttpt) REVERT: p0 103 LYS cc_start: 0.8801 (ttpt) cc_final: 0.7970 (tptt) REVERT: p0 105 ARG cc_start: 0.6820 (tmt170) cc_final: 0.6497 (tpt170) REVERT: q0 103 LYS cc_start: 0.9087 (ttmt) cc_final: 0.8272 (tptt) REVERT: r0 102 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8130 (mt-10) REVERT: r0 103 LYS cc_start: 0.8836 (ttmt) cc_final: 0.7502 (tptt) REVERT: t0 103 LYS cc_start: 0.8899 (ttmt) cc_final: 0.8076 (tptt) REVERT: t0 105 ARG cc_start: 0.9249 (ttm110) cc_final: 0.7728 (tpm170) REVERT: u0 100 ARG cc_start: 0.7770 (ttm110) cc_final: 0.7279 (tpt170) REVERT: u0 103 LYS cc_start: 0.9065 (ttmt) cc_final: 0.7966 (tptt) REVERT: v0 92 THR cc_start: 0.8417 (m) cc_final: 0.8210 (m) REVERT: v0 103 LYS cc_start: 0.9241 (mttt) cc_final: 0.7811 (tptt) REVERT: w0 103 LYS cc_start: 0.8873 (ttmt) cc_final: 0.8322 (tptt) REVERT: x0 103 LYS cc_start: 0.8462 (ttmt) cc_final: 0.7832 (tptt) outliers start: 6 outliers final: 1 residues processed: 2206 average time/residue: 0.2224 time to fit residues: 833.0688 Evaluate side-chains 1924 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1923 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 429 optimal weight: 0.7980 chunk 352 optimal weight: 0.9980 chunk 377 optimal weight: 0.7980 chunk 421 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 359 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 493 optimal weight: 0.6980 chunk 337 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 HIS B 210 GLN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN E 116 GLN ** F 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 170 ASN F 247 HIS F 252 ASN J 76 HIS O 44 GLN P 59 ASN R 19 GLN W 81 ASN Y 144 ASN 2 137 HIS ** 4 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 123 ASN ** y 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 ASN b 24 GLN ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 51 GLN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 40 ASN ** m 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 7 ASN n 81 ASN p 80 GLN t 24 GLN u 40 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.101933 restraints weight = 90731.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104486 restraints weight = 53263.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106267 restraints weight = 35980.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107543 restraints weight = 26766.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.108412 restraints weight = 21259.488| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 44859 Z= 0.146 Angle : 0.649 9.864 60892 Z= 0.324 Chirality : 0.041 0.209 7369 Planarity : 0.004 0.076 7620 Dihedral : 4.331 86.662 5953 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.14 % Allowed : 0.86 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.89 (0.11), residues: 5404 helix: 2.99 (0.08), residues: 4150 sheet: 1.89 (0.31), residues: 160 loop : -2.75 (0.16), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 113 TYR 0.031 0.002 TYR T 50 PHE 0.035 0.002 PHE o 19 TRP 0.011 0.001 TRP j 10 HIS 0.006 0.001 HIS F 11 Details of bonding type rmsd covalent geometry : bond 0.00335 (44858) covalent geometry : angle 0.64866 (60890) SS BOND : bond 0.00002 ( 1) SS BOND : angle 0.29185 ( 2) hydrogen bonds : bond 0.04060 ( 3327) hydrogen bonds : angle 3.60935 ( 9915) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2195 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 2188 time to evaluate : 1.600 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 CYS cc_start: 0.8675 (p) cc_final: 0.7914 (p) REVERT: A 50 MET cc_start: 0.8218 (ttp) cc_final: 0.7959 (ttm) REVERT: A 68 ILE cc_start: 0.9537 (mt) cc_final: 0.9249 (mt) REVERT: A 69 GLU cc_start: 0.7824 (tp30) cc_final: 0.7222 (mm-30) REVERT: A 101 GLN cc_start: 0.8832 (tt0) cc_final: 0.8420 (tm-30) REVERT: A 152 LYS cc_start: 0.9150 (tttt) cc_final: 0.8705 (mtmt) REVERT: A 177 MET cc_start: 0.7912 (mmt) cc_final: 0.7548 (mmt) REVERT: A 205 LYS cc_start: 0.9093 (mttt) cc_final: 0.8110 (tttt) REVERT: B 27 TYR cc_start: 0.8800 (t80) cc_final: 0.8583 (t80) REVERT: B 65 LYS cc_start: 0.8509 (tttp) cc_final: 0.8181 (tmtt) REVERT: B 110 GLU cc_start: 0.8551 (pm20) cc_final: 0.8297 (pm20) REVERT: B 146 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7874 (mm-30) REVERT: B 177 MET cc_start: 0.8103 (mtt) cc_final: 0.7811 (mtt) REVERT: B 178 MET cc_start: 0.8256 (mtm) cc_final: 0.7943 (mtp) REVERT: B 190 LYS cc_start: 0.9161 (mtmt) cc_final: 0.8503 (mtmm) REVERT: C 29 LYS cc_start: 0.9095 (mttp) cc_final: 0.8859 (mttm) REVERT: C 72 TYR cc_start: 0.5413 (t80) cc_final: 0.5160 (m-10) REVERT: C 105 LYS cc_start: 0.9006 (tttp) cc_final: 0.8737 (mtpp) REVERT: C 117 ARG cc_start: 0.8378 (mtt180) cc_final: 0.7836 (tpt170) REVERT: D 1 MET cc_start: 0.1703 (ptt) cc_final: 0.1439 (ptt) REVERT: D 2 LEU cc_start: 0.9196 (mt) cc_final: 0.8920 (mt) REVERT: D 6 SER cc_start: 0.8751 (m) cc_final: 0.7903 (p) REVERT: D 17 LEU cc_start: 0.9263 (tp) cc_final: 0.8895 (tt) REVERT: D 105 LYS cc_start: 0.9305 (ttmt) cc_final: 0.9101 (tttm) REVERT: D 183 ILE cc_start: 0.8946 (mm) cc_final: 0.8566 (tp) REVERT: E 36 MET cc_start: 0.8993 (tpp) cc_final: 0.8775 (tpp) REVERT: E 59 MET cc_start: 0.8378 (mtm) cc_final: 0.8175 (mtp) REVERT: F 36 ASN cc_start: 0.7977 (t0) cc_final: 0.7519 (t0) REVERT: F 58 SER cc_start: 0.8638 (m) cc_final: 0.8406 (p) REVERT: F 104 ASP cc_start: 0.8533 (t0) cc_final: 0.8287 (t0) REVERT: F 133 PHE cc_start: 0.9087 (t80) cc_final: 0.8498 (t80) REVERT: F 152 GLN cc_start: 0.9087 (tt0) cc_final: 0.8493 (tp-100) REVERT: F 153 LEU cc_start: 0.9502 (tp) cc_final: 0.9273 (tp) REVERT: F 181 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8405 (mm110) REVERT: G 79 MET cc_start: 0.8578 (mmm) cc_final: 0.8211 (mmm) REVERT: G 83 LYS cc_start: 0.8465 (mmmm) cc_final: 0.8059 (mmmm) REVERT: H 60 LEU cc_start: 0.8912 (mm) cc_final: 0.8662 (mm) REVERT: H 77 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7953 (tm-30) REVERT: I 53 LEU cc_start: 0.7905 (tp) cc_final: 0.7603 (tp) REVERT: I 60 LEU cc_start: 0.8613 (mt) cc_final: 0.8367 (mt) REVERT: I 69 GLU cc_start: 0.7779 (tp30) cc_final: 0.6671 (tp30) REVERT: K 46 SER cc_start: 0.7202 (m) cc_final: 0.6962 (t) REVERT: K 51 MET cc_start: 0.7437 (mmt) cc_final: 0.6871 (mmt) REVERT: K 132 LYS cc_start: 0.8613 (mmtp) cc_final: 0.8114 (mttt) REVERT: K 176 ARG cc_start: 0.8726 (tpt-90) cc_final: 0.8464 (tpt-90) REVERT: N 33 LYS cc_start: 0.8660 (mmmm) cc_final: 0.8032 (mmtt) REVERT: N 58 LEU cc_start: 0.9219 (mt) cc_final: 0.8854 (mt) REVERT: N 89 SER cc_start: 0.9370 (t) cc_final: 0.8989 (p) REVERT: O 41 THR cc_start: 0.8729 (t) cc_final: 0.8373 (m) REVERT: P 54 ASN cc_start: 0.8739 (t0) cc_final: 0.8519 (t0) REVERT: P 56 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7090 (tm-30) REVERT: P 57 SER cc_start: 0.9121 (m) cc_final: 0.8604 (p) REVERT: R 27 GLU cc_start: 0.6794 (tm-30) cc_final: 0.6556 (pt0) REVERT: R 47 GLN cc_start: 0.8208 (tp40) cc_final: 0.7748 (tm-30) REVERT: R 51 MET cc_start: 0.7523 (mtt) cc_final: 0.7140 (mtp) REVERT: S 25 THR cc_start: 0.7724 (t) cc_final: 0.7310 (t) REVERT: S 27 GLN cc_start: 0.8057 (pm20) cc_final: 0.7769 (pm20) REVERT: S 37 LEU cc_start: 0.8927 (tp) cc_final: 0.8562 (tp) REVERT: T 30 LEU cc_start: 0.9078 (tp) cc_final: 0.8853 (tp) REVERT: U 55 SER cc_start: 0.9118 (m) cc_final: 0.8515 (m) REVERT: V 32 LEU cc_start: 0.8685 (mt) cc_final: 0.8323 (tt) REVERT: V 64 GLN cc_start: 0.8629 (tt0) cc_final: 0.8361 (tt0) REVERT: W 39 LYS cc_start: 0.8445 (mttt) cc_final: 0.7809 (mptt) REVERT: W 43 ASN cc_start: 0.8645 (t0) cc_final: 0.8211 (t0) REVERT: Y 112 SER cc_start: 0.8130 (p) cc_final: 0.7684 (m) REVERT: Y 123 ASN cc_start: 0.8747 (t0) cc_final: 0.8448 (t0) REVERT: Y 130 LYS cc_start: 0.8177 (mttt) cc_final: 0.7973 (mttm) REVERT: 0 128 TYR cc_start: 0.8260 (t80) cc_final: 0.7934 (t80) REVERT: 2 127 GLN cc_start: 0.8354 (tp40) cc_final: 0.7989 (tp40) REVERT: 2 131 ASP cc_start: 0.8045 (t0) cc_final: 0.7844 (t0) REVERT: 4 150 PHE cc_start: 0.9004 (p90) cc_final: 0.8578 (p90) REVERT: 4 167 THR cc_start: 0.8842 (m) cc_final: 0.8520 (t) REVERT: 6 127 GLN cc_start: 0.8956 (tp40) cc_final: 0.8287 (tp40) REVERT: 6 138 ARG cc_start: 0.8397 (mtp85) cc_final: 0.7352 (mtm110) REVERT: 6 149 THR cc_start: 0.8910 (m) cc_final: 0.8047 (p) REVERT: 8 111 ILE cc_start: 0.9311 (mt) cc_final: 0.9104 (mt) REVERT: 8 115 ILE cc_start: 0.8919 (mt) cc_final: 0.8641 (mm) REVERT: 8 144 ASN cc_start: 0.7735 (t0) cc_final: 0.7389 (t0) REVERT: 8 150 PHE cc_start: 0.9243 (p90) cc_final: 0.8695 (p90) REVERT: x 127 GLN cc_start: 0.8915 (tp-100) cc_final: 0.8517 (tp-100) REVERT: x 150 PHE cc_start: 0.9248 (p90) cc_final: 0.8456 (p90) REVERT: x 153 SER cc_start: 0.9445 (t) cc_final: 0.9008 (p) REVERT: x 168 LEU cc_start: 0.9575 (tt) cc_final: 0.9347 (tp) REVERT: y 115 ILE cc_start: 0.9263 (mt) cc_final: 0.8974 (mt) REVERT: y 158 LEU cc_start: 0.8219 (tp) cc_final: 0.7813 (mm) REVERT: y 160 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7844 (mm-30) REVERT: z 112 SER cc_start: 0.9160 (p) cc_final: 0.8801 (m) REVERT: z 127 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8167 (tm-30) REVERT: z 138 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7596 (ttp-110) REVERT: z 149 THR cc_start: 0.9033 (m) cc_final: 0.8701 (t) REVERT: 1 130 LYS cc_start: 0.8421 (mmmt) cc_final: 0.8056 (mmtt) REVERT: 1 133 ASN cc_start: 0.8584 (m-40) cc_final: 0.8289 (t0) REVERT: 3 115 ILE cc_start: 0.8397 (mt) cc_final: 0.8159 (mt) REVERT: 9 126 ILE cc_start: 0.8950 (mm) cc_final: 0.8718 (mt) REVERT: 9 135 TYR cc_start: 0.7656 (t80) cc_final: 0.7159 (t80) REVERT: a 31 THR cc_start: 0.7939 (m) cc_final: 0.7585 (m) REVERT: a 73 ASP cc_start: 0.7557 (t70) cc_final: 0.7354 (t70) REVERT: a 80 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8347 (tm-30) REVERT: b 43 ASN cc_start: 0.8483 (t0) cc_final: 0.8214 (t0) REVERT: b 45 GLN cc_start: 0.8971 (tp40) cc_final: 0.7826 (tm-30) REVERT: b 49 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7266 (mm-30) REVERT: b 64 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7586 (tm-30) REVERT: b 67 THR cc_start: 0.9247 (m) cc_final: 0.8867 (p) REVERT: d 57 TYR cc_start: 0.9088 (t80) cc_final: 0.8720 (t80) REVERT: d 75 ASP cc_start: 0.8421 (m-30) cc_final: 0.7977 (m-30) REVERT: d 80 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7401 (tm-30) REVERT: e 40 ASN cc_start: 0.8437 (p0) cc_final: 0.8011 (p0) REVERT: f 14 SER cc_start: 0.9016 (p) cc_final: 0.8380 (t) REVERT: f 80 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8205 (tm-30) REVERT: g 17 GLU cc_start: 0.7735 (mp0) cc_final: 0.7214 (mp0) REVERT: g 26 LEU cc_start: 0.9128 (tt) cc_final: 0.8384 (mm) REVERT: g 54 LEU cc_start: 0.9334 (tp) cc_final: 0.9079 (tp) REVERT: g 65 SER cc_start: 0.9063 (t) cc_final: 0.8857 (t) REVERT: g 79 ILE cc_start: 0.9236 (mm) cc_final: 0.8981 (mm) REVERT: g 80 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8447 (tm-30) REVERT: g 81 ASN cc_start: 0.9291 (m110) cc_final: 0.8981 (m-40) REVERT: g 82 PHE cc_start: 0.9136 (m-10) cc_final: 0.8909 (m-80) REVERT: h 29 GLU cc_start: 0.8636 (mp0) cc_final: 0.8261 (mp0) REVERT: h 79 ILE cc_start: 0.9212 (mm) cc_final: 0.8915 (mm) REVERT: i 80 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8251 (tm-30) REVERT: i 81 ASN cc_start: 0.9361 (m-40) cc_final: 0.9069 (m-40) REVERT: j 14 SER cc_start: 0.8820 (m) cc_final: 0.8611 (p) REVERT: j 80 GLN cc_start: 0.9207 (tp-100) cc_final: 0.8770 (tp40) REVERT: k 50 TYR cc_start: 0.9294 (t80) cc_final: 0.9091 (t80) REVERT: k 80 GLN cc_start: 0.8716 (tp40) cc_final: 0.8483 (tp40) REVERT: l 16 SER cc_start: 0.9069 (m) cc_final: 0.8324 (t) REVERT: l 20 ASP cc_start: 0.7644 (m-30) cc_final: 0.7173 (m-30) REVERT: l 25 THR cc_start: 0.8876 (p) cc_final: 0.8265 (p) REVERT: l 45 GLN cc_start: 0.8041 (tp40) cc_final: 0.7733 (tp40) REVERT: l 50 TYR cc_start: 0.9228 (t80) cc_final: 0.8819 (t80) REVERT: l 80 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8051 (tm-30) REVERT: m 20 ASP cc_start: 0.8251 (m-30) cc_final: 0.7795 (m-30) REVERT: m 50 TYR cc_start: 0.8874 (t80) cc_final: 0.8551 (t80) REVERT: m 75 ASP cc_start: 0.8406 (m-30) cc_final: 0.7483 (m-30) REVERT: n 3 VAL cc_start: 0.8664 (t) cc_final: 0.8391 (m) REVERT: n 5 VAL cc_start: 0.8221 (p) cc_final: 0.7909 (p) REVERT: n 75 ASP cc_start: 0.8560 (m-30) cc_final: 0.8151 (m-30) REVERT: n 80 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8054 (tm-30) REVERT: o 37 LEU cc_start: 0.8941 (tt) cc_final: 0.8731 (tt) REVERT: o 39 LYS cc_start: 0.8002 (mmpt) cc_final: 0.7759 (mmpt) REVERT: p 25 THR cc_start: 0.8256 (p) cc_final: 0.7599 (t) REVERT: p 71 ILE cc_start: 0.8859 (mm) cc_final: 0.8646 (mm) REVERT: p 75 ASP cc_start: 0.8660 (m-30) cc_final: 0.8014 (m-30) REVERT: q 14 SER cc_start: 0.9482 (m) cc_final: 0.9176 (p) REVERT: q 32 LEU cc_start: 0.8170 (tp) cc_final: 0.7813 (tp) REVERT: q 36 LYS cc_start: 0.8587 (mttt) cc_final: 0.8344 (mtmt) REVERT: r 59 LEU cc_start: 0.8816 (mt) cc_final: 0.8489 (mt) REVERT: s 7 ASN cc_start: 0.6923 (m-40) cc_final: 0.6001 (p0) REVERT: s 23 THR cc_start: 0.8580 (m) cc_final: 0.8266 (m) REVERT: s 24 GLN cc_start: 0.8102 (tp40) cc_final: 0.7887 (mm-40) REVERT: s 27 GLN cc_start: 0.8488 (mt0) cc_final: 0.7849 (tm-30) REVERT: s 65 SER cc_start: 0.9054 (t) cc_final: 0.8704 (m) REVERT: s 69 LYS cc_start: 0.8520 (tptm) cc_final: 0.7359 (ttmt) REVERT: t 51 GLN cc_start: 0.8716 (tt0) cc_final: 0.6634 (mm-40) REVERT: t 69 LYS cc_start: 0.9292 (tptm) cc_final: 0.8582 (mttt) REVERT: t 72 LYS cc_start: 0.9500 (tmtt) cc_final: 0.9192 (tttp) REVERT: u 30 LEU cc_start: 0.8925 (tp) cc_final: 0.8690 (tt) REVERT: u 49 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7078 (tp30) REVERT: u 69 LYS cc_start: 0.8963 (tptm) cc_final: 0.7461 (ttmt) REVERT: u 82 PHE cc_start: 0.9036 (m-80) cc_final: 0.8536 (m-80) REVERT: v 32 LEU cc_start: 0.9345 (tp) cc_final: 0.9085 (tp) REVERT: v 36 LYS cc_start: 0.8921 (mttt) cc_final: 0.8625 (mttm) REVERT: v 69 LYS cc_start: 0.9115 (tptm) cc_final: 0.8221 (mttt) REVERT: w 25 THR cc_start: 0.8638 (p) cc_final: 0.8145 (p) REVERT: w 47 LEU cc_start: 0.9125 (mm) cc_final: 0.8827 (mm) REVERT: w 57 TYR cc_start: 0.8938 (t80) cc_final: 0.8526 (t80) REVERT: w 61 ARG cc_start: 0.8337 (mmt180) cc_final: 0.6647 (ttp-170) REVERT: w 69 LYS cc_start: 0.8864 (tppt) cc_final: 0.7338 (tppt) REVERT: a0 103 LYS cc_start: 0.8071 (tttm) cc_final: 0.6981 (tptt) REVERT: d0 103 LYS cc_start: 0.9250 (ttmt) cc_final: 0.7901 (tptt) REVERT: e0 103 LYS cc_start: 0.8729 (ttmt) cc_final: 0.7800 (tttt) REVERT: f0 100 ARG cc_start: 0.8497 (ttm170) cc_final: 0.8034 (ttm170) REVERT: f0 103 LYS cc_start: 0.9247 (ttmt) cc_final: 0.8319 (tptt) REVERT: g0 103 LYS cc_start: 0.9124 (mtmt) cc_final: 0.7762 (tptt) REVERT: i0 103 LYS cc_start: 0.8922 (tttt) cc_final: 0.8555 (tptt) REVERT: k0 103 LYS cc_start: 0.8919 (ttmm) cc_final: 0.8086 (tptt) REVERT: l0 103 LYS cc_start: 0.8899 (ttmt) cc_final: 0.8172 (tptt) REVERT: m0 103 LYS cc_start: 0.9080 (mtpt) cc_final: 0.8110 (tptt) REVERT: n0 97 SER cc_start: 0.9082 (m) cc_final: 0.8835 (t) REVERT: n0 103 LYS cc_start: 0.8857 (ttpt) cc_final: 0.8321 (ttpt) REVERT: p0 103 LYS cc_start: 0.8814 (ttpt) cc_final: 0.7989 (tptt) REVERT: p0 105 ARG cc_start: 0.6818 (tmt170) cc_final: 0.6567 (tpt170) REVERT: q0 103 LYS cc_start: 0.9096 (ttmt) cc_final: 0.8288 (tptt) REVERT: r0 102 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8131 (mt-10) REVERT: r0 103 LYS cc_start: 0.8847 (ttmt) cc_final: 0.7521 (tptt) REVERT: t0 103 LYS cc_start: 0.8910 (ttmt) cc_final: 0.8083 (tptt) REVERT: t0 105 ARG cc_start: 0.9248 (ttm110) cc_final: 0.7736 (tpm170) REVERT: u0 98 SER cc_start: 0.8726 (m) cc_final: 0.8074 (p) REVERT: u0 100 ARG cc_start: 0.7791 (ttm110) cc_final: 0.7257 (tpt170) REVERT: u0 103 LYS cc_start: 0.9083 (ttmt) cc_final: 0.7972 (tptt) REVERT: v0 92 THR cc_start: 0.8460 (m) cc_final: 0.8233 (m) REVERT: v0 103 LYS cc_start: 0.9250 (mttt) cc_final: 0.7809 (tptt) REVERT: w0 103 LYS cc_start: 0.8867 (ttmt) cc_final: 0.8303 (tptt) REVERT: x0 103 LYS cc_start: 0.8439 (ttmt) cc_final: 0.7757 (tptt) outliers start: 7 outliers final: 2 residues processed: 2189 average time/residue: 0.2334 time to fit residues: 867.9655 Evaluate side-chains 1897 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1895 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 52 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 195 optimal weight: 0.0470 chunk 471 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 297 optimal weight: 0.9990 chunk 286 optimal weight: 0.9980 chunk 522 optimal weight: 0.8980 chunk 190 optimal weight: 0.5980 chunk 366 optimal weight: 0.8980 chunk 247 optimal weight: 3.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** F 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 170 ASN F 247 HIS F 252 ASN ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS O 44 GLN P 59 ASN R 19 GLN R 44 GLN ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 81 ASN Y 144 ASN 2 137 HIS 4 127 GLN ** 4 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 123 ASN y 164 ASN ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 ASN ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 64 GLN f 40 ASN f 51 GLN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 81 ASN ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 27 GLN n 81 ASN o 24 GLN o 40 ASN p 80 GLN r 24 GLN t 24 GLN u 40 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.117698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102745 restraints weight = 90029.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105307 restraints weight = 53082.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107101 restraints weight = 35917.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.108342 restraints weight = 26658.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109283 restraints weight = 21252.165| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 44859 Z= 0.138 Angle : 0.659 11.721 60892 Z= 0.326 Chirality : 0.041 0.390 7369 Planarity : 0.004 0.078 7620 Dihedral : 4.344 87.422 5953 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.12 % Allowed : 0.70 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.86 (0.11), residues: 5404 helix: 2.96 (0.08), residues: 4151 sheet: 1.93 (0.31), residues: 160 loop : -2.73 (0.16), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 113 TYR 0.039 0.002 TYR E 158 PHE 0.032 0.002 PHE t 19 TRP 0.010 0.001 TRP c 10 HIS 0.006 0.001 HIS F 11 Details of bonding type rmsd covalent geometry : bond 0.00317 (44858) covalent geometry : angle 0.65922 (60890) SS BOND : bond 0.00017 ( 1) SS BOND : angle 0.27649 ( 2) hydrogen bonds : bond 0.03974 ( 3327) hydrogen bonds : angle 3.60828 ( 9915) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2169 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 2163 time to evaluate : 1.886 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: 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 26 CYS cc_start: 0.8691 (p) cc_final: 0.7869 (p) REVERT: A 36 MET cc_start: 0.8331 (tpp) cc_final: 0.8033 (tpp) REVERT: A 50 MET cc_start: 0.8189 (ttp) cc_final: 0.7922 (ttm) REVERT: A 68 ILE cc_start: 0.9545 (mt) cc_final: 0.9241 (mt) REVERT: A 69 GLU cc_start: 0.7845 (tp30) cc_final: 0.7244 (mm-30) REVERT: A 101 GLN cc_start: 0.8828 (tt0) cc_final: 0.8391 (tm-30) REVERT: A 152 LYS cc_start: 0.9057 (tttt) cc_final: 0.8715 (mtmt) REVERT: A 177 MET cc_start: 0.7870 (mmt) cc_final: 0.7392 (mmt) REVERT: A 205 LYS cc_start: 0.9101 (mttt) cc_final: 0.8107 (tttt) REVERT: B 65 LYS cc_start: 0.8540 (tttp) cc_final: 0.7791 (tmtt) REVERT: B 110 GLU cc_start: 0.8514 (pm20) cc_final: 0.8205 (pm20) REVERT: B 146 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7757 (mm-30) REVERT: B 177 MET cc_start: 0.8116 (mtt) cc_final: 0.7899 (mtt) REVERT: B 178 MET cc_start: 0.8190 (mtm) cc_final: 0.7983 (mtp) REVERT: B 190 LYS cc_start: 0.9080 (mtmt) cc_final: 0.8304 (mtmm) REVERT: C 72 TYR cc_start: 0.5458 (t80) cc_final: 0.5183 (m-10) REVERT: C 105 LYS cc_start: 0.8970 (tttp) cc_final: 0.8651 (mtpp) REVERT: C 117 ARG cc_start: 0.8392 (mtt180) cc_final: 0.7819 (tpt170) REVERT: C 147 ILE cc_start: 0.9225 (mt) cc_final: 0.9002 (mm) REVERT: D 1 MET cc_start: 0.1919 (ptt) cc_final: 0.1666 (ptt) REVERT: D 2 LEU cc_start: 0.9200 (mt) cc_final: 0.8929 (mt) REVERT: D 6 SER cc_start: 0.8732 (m) cc_final: 0.7848 (p) REVERT: D 105 LYS cc_start: 0.9283 (ttmt) cc_final: 0.9081 (tttm) REVERT: E 44 GLN cc_start: 0.8797 (mp10) cc_final: 0.8518 (mp10) REVERT: E 59 MET cc_start: 0.8357 (mtm) cc_final: 0.8133 (mtp) REVERT: F 104 ASP cc_start: 0.8535 (t0) cc_final: 0.8243 (t0) REVERT: F 133 PHE cc_start: 0.9071 (t80) cc_final: 0.8435 (t80) REVERT: F 152 GLN cc_start: 0.9041 (tt0) cc_final: 0.8534 (tp-100) REVERT: F 153 LEU cc_start: 0.9521 (tp) cc_final: 0.9317 (tp) REVERT: F 229 PHE cc_start: 0.8482 (t80) cc_final: 0.7998 (t80) REVERT: G 79 MET cc_start: 0.8605 (mmm) cc_final: 0.8396 (mmt) REVERT: G 83 LYS cc_start: 0.8571 (mmmm) cc_final: 0.8018 (mmmm) REVERT: H 60 LEU cc_start: 0.8912 (mm) cc_final: 0.8638 (mm) REVERT: H 77 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7944 (tm-30) REVERT: H 81 LEU cc_start: 0.8553 (mt) cc_final: 0.8274 (mt) REVERT: I 53 LEU cc_start: 0.7902 (tp) cc_final: 0.7619 (tp) REVERT: I 60 LEU cc_start: 0.8624 (mt) cc_final: 0.8378 (mt) REVERT: I 69 GLU cc_start: 0.7805 (tp30) cc_final: 0.6914 (tp30) REVERT: K 46 SER cc_start: 0.7179 (m) cc_final: 0.6463 (t) REVERT: K 51 MET cc_start: 0.7424 (mmt) cc_final: 0.7121 (mmt) REVERT: K 132 LYS cc_start: 0.8634 (mmtp) cc_final: 0.8071 (mttt) REVERT: K 176 ARG cc_start: 0.8757 (tpt-90) cc_final: 0.8499 (tpt-90) REVERT: N 33 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8072 (mmtt) REVERT: N 58 LEU cc_start: 0.9182 (mt) cc_final: 0.8864 (mt) REVERT: N 68 THR cc_start: 0.8994 (m) cc_final: 0.8738 (t) REVERT: N 89 SER cc_start: 0.9291 (t) cc_final: 0.8926 (p) REVERT: O 41 THR cc_start: 0.8747 (t) cc_final: 0.8328 (m) REVERT: P 44 GLN cc_start: 0.8308 (tt0) cc_final: 0.7983 (tt0) REVERT: P 56 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7134 (tm-30) REVERT: P 57 SER cc_start: 0.9047 (m) cc_final: 0.8554 (p) REVERT: P 95 LEU cc_start: 0.9453 (mt) cc_final: 0.9230 (mt) REVERT: R 27 GLU cc_start: 0.6769 (tm-30) cc_final: 0.6522 (pt0) REVERT: R 47 GLN cc_start: 0.8199 (tp40) cc_final: 0.7816 (tm-30) REVERT: R 51 MET cc_start: 0.7509 (mtt) cc_final: 0.7133 (mtp) REVERT: S 25 THR cc_start: 0.7659 (t) cc_final: 0.7427 (t) REVERT: S 37 LEU cc_start: 0.9014 (tp) cc_final: 0.8334 (tp) REVERT: S 50 TYR cc_start: 0.9059 (t80) cc_final: 0.8708 (t80) REVERT: T 30 LEU cc_start: 0.9059 (tp) cc_final: 0.8793 (tp) REVERT: T 56 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8106 (mt-10) REVERT: U 81 ASN cc_start: 0.9197 (m-40) cc_final: 0.8957 (m-40) REVERT: V 32 LEU cc_start: 0.8685 (mt) cc_final: 0.8327 (tt) REVERT: V 45 GLN cc_start: 0.8862 (tp40) cc_final: 0.8159 (tp-100) REVERT: V 49 GLU cc_start: 0.8190 (mp0) cc_final: 0.7551 (mp0) REVERT: V 64 GLN cc_start: 0.8608 (tt0) cc_final: 0.8311 (tt0) REVERT: W 39 LYS cc_start: 0.8337 (mttt) cc_final: 0.7716 (mptt) REVERT: W 43 ASN cc_start: 0.8612 (t0) cc_final: 0.8119 (t0) REVERT: W 72 LYS cc_start: 0.9247 (mmmm) cc_final: 0.8616 (mmmm) REVERT: Y 112 SER cc_start: 0.8121 (p) cc_final: 0.7660 (m) REVERT: Y 123 ASN cc_start: 0.8722 (t0) cc_final: 0.8428 (t0) REVERT: Z 161 LEU cc_start: 0.8479 (tp) cc_final: 0.8276 (tp) REVERT: 0 128 TYR cc_start: 0.8224 (t80) cc_final: 0.7890 (t80) REVERT: 2 127 GLN cc_start: 0.8360 (tp40) cc_final: 0.7988 (tp40) REVERT: 4 127 GLN cc_start: 0.7944 (tp40) cc_final: 0.7690 (tp-100) REVERT: 4 131 ASP cc_start: 0.8180 (p0) cc_final: 0.7951 (p0) REVERT: 4 150 PHE cc_start: 0.9003 (p90) cc_final: 0.8590 (p90) REVERT: 6 127 GLN cc_start: 0.8911 (tp40) cc_final: 0.8235 (tp40) REVERT: 6 138 ARG cc_start: 0.8401 (mtp85) cc_final: 0.7444 (mtm110) REVERT: 6 149 THR cc_start: 0.8878 (m) cc_final: 0.8070 (p) REVERT: 8 111 ILE cc_start: 0.9341 (mt) cc_final: 0.9109 (mt) REVERT: 8 144 ASN cc_start: 0.7735 (t0) cc_final: 0.7493 (t0) REVERT: 8 150 PHE cc_start: 0.9239 (p90) cc_final: 0.8713 (p90) REVERT: x 127 GLN cc_start: 0.8907 (tp-100) cc_final: 0.8533 (tp-100) REVERT: x 150 PHE cc_start: 0.9256 (p90) cc_final: 0.8591 (p90) REVERT: x 153 SER cc_start: 0.9430 (t) cc_final: 0.9041 (p) REVERT: y 115 ILE cc_start: 0.9273 (mt) cc_final: 0.8969 (mt) REVERT: y 158 LEU cc_start: 0.8218 (tp) cc_final: 0.7827 (mm) REVERT: y 160 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7834 (mm-30) REVERT: z 127 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8203 (tm-30) REVERT: z 138 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7540 (ttm110) REVERT: z 149 THR cc_start: 0.9078 (m) cc_final: 0.8758 (t) REVERT: 1 130 LYS cc_start: 0.8391 (mmmt) cc_final: 0.8052 (mmtt) REVERT: 1 133 ASN cc_start: 0.8648 (m-40) cc_final: 0.8292 (t0) REVERT: 3 115 ILE cc_start: 0.8641 (mt) cc_final: 0.8366 (mt) REVERT: 5 115 ILE cc_start: 0.8787 (mt) cc_final: 0.8581 (mm) REVERT: 9 135 TYR cc_start: 0.7638 (t80) cc_final: 0.7150 (t80) REVERT: a 31 THR cc_start: 0.7890 (m) cc_final: 0.7531 (m) REVERT: a 66 ASN cc_start: 0.9076 (m-40) cc_final: 0.8858 (m110) REVERT: b 14 SER cc_start: 0.8849 (m) cc_final: 0.8584 (p) REVERT: b 43 ASN cc_start: 0.8506 (t0) cc_final: 0.8217 (t0) REVERT: b 45 GLN cc_start: 0.8943 (tp40) cc_final: 0.7773 (tm-30) REVERT: b 49 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7234 (mm-30) REVERT: b 64 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7457 (tm-30) REVERT: b 67 THR cc_start: 0.9214 (m) cc_final: 0.8868 (p) REVERT: c 59 LEU cc_start: 0.9369 (mt) cc_final: 0.9145 (mt) REVERT: c 80 GLN cc_start: 0.8881 (tp-100) cc_final: 0.8487 (tp40) REVERT: c 82 PHE cc_start: 0.8796 (m-10) cc_final: 0.8557 (m-10) REVERT: d 57 TYR cc_start: 0.9069 (t80) cc_final: 0.8712 (t80) REVERT: d 80 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7363 (tm-30) REVERT: e 40 ASN cc_start: 0.8445 (p0) cc_final: 0.8024 (p0) REVERT: f 80 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8214 (tm-30) REVERT: f 81 ASN cc_start: 0.9392 (m-40) cc_final: 0.9173 (m-40) REVERT: g 26 LEU cc_start: 0.9136 (tt) cc_final: 0.8602 (mm) REVERT: g 27 GLN cc_start: 0.8640 (mt0) cc_final: 0.8314 (mp10) REVERT: g 54 LEU cc_start: 0.9305 (tp) cc_final: 0.9047 (tp) REVERT: g 79 ILE cc_start: 0.9247 (mm) cc_final: 0.8996 (mm) REVERT: g 80 GLN cc_start: 0.8825 (tp-100) cc_final: 0.8424 (tm-30) REVERT: g 81 ASN cc_start: 0.9261 (m110) cc_final: 0.8954 (m-40) REVERT: g 82 PHE cc_start: 0.9119 (m-10) cc_final: 0.8892 (m-80) REVERT: h 24 GLN cc_start: 0.8673 (tp40) cc_final: 0.8454 (tp40) REVERT: h 26 LEU cc_start: 0.8832 (mm) cc_final: 0.8616 (mm) REVERT: i 80 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8289 (tm-30) REVERT: i 81 ASN cc_start: 0.9348 (m-40) cc_final: 0.9065 (m-40) REVERT: j 42 SER cc_start: 0.9393 (m) cc_final: 0.8909 (p) REVERT: j 80 GLN cc_start: 0.9197 (tp-100) cc_final: 0.8895 (tp-100) REVERT: k 80 GLN cc_start: 0.8732 (tp40) cc_final: 0.8529 (tp40) REVERT: l 16 SER cc_start: 0.9113 (m) cc_final: 0.8331 (t) REVERT: l 20 ASP cc_start: 0.7586 (m-30) cc_final: 0.7097 (m-30) REVERT: l 25 THR cc_start: 0.8721 (p) cc_final: 0.8435 (p) REVERT: l 29 GLU cc_start: 0.8502 (pt0) cc_final: 0.8115 (pt0) REVERT: l 45 GLN cc_start: 0.8129 (tp40) cc_final: 0.7621 (tp40) REVERT: l 50 TYR cc_start: 0.9219 (t80) cc_final: 0.8825 (t80) REVERT: m 20 ASP cc_start: 0.8121 (m-30) cc_final: 0.7605 (m-30) REVERT: m 50 TYR cc_start: 0.8861 (t80) cc_final: 0.8542 (t80) REVERT: m 75 ASP cc_start: 0.8342 (m-30) cc_final: 0.7426 (m-30) REVERT: n 3 VAL cc_start: 0.8654 (t) cc_final: 0.8382 (m) REVERT: n 75 ASP cc_start: 0.8511 (m-30) cc_final: 0.8144 (m-30) REVERT: n 80 GLN cc_start: 0.8878 (tm-30) cc_final: 0.7998 (tm-30) REVERT: o 39 LYS cc_start: 0.7782 (mmpt) cc_final: 0.7485 (mmpt) REVERT: o 50 TYR cc_start: 0.9204 (t80) cc_final: 0.8972 (t80) REVERT: p 25 THR cc_start: 0.8164 (p) cc_final: 0.7460 (t) REVERT: p 26 LEU cc_start: 0.8104 (mm) cc_final: 0.7864 (mm) REVERT: p 75 ASP cc_start: 0.8702 (m-30) cc_final: 0.8020 (m-30) REVERT: q 14 SER cc_start: 0.9464 (m) cc_final: 0.9142 (p) REVERT: q 32 LEU cc_start: 0.8170 (tp) cc_final: 0.7810 (tp) REVERT: q 36 LYS cc_start: 0.8633 (mttt) cc_final: 0.8392 (mtmt) REVERT: r 59 LEU cc_start: 0.8807 (mt) cc_final: 0.8486 (mt) REVERT: s 7 ASN cc_start: 0.7207 (m-40) cc_final: 0.6387 (p0) REVERT: s 16 SER cc_start: 0.9184 (m) cc_final: 0.8971 (m) REVERT: s 23 THR cc_start: 0.8660 (m) cc_final: 0.8314 (m) REVERT: s 24 GLN cc_start: 0.8079 (tp40) cc_final: 0.7873 (mm-40) REVERT: s 27 GLN cc_start: 0.8427 (mt0) cc_final: 0.7827 (tm-30) REVERT: s 64 GLN cc_start: 0.8887 (tt0) cc_final: 0.8538 (tt0) REVERT: s 65 SER cc_start: 0.9031 (t) cc_final: 0.8683 (m) REVERT: s 69 LYS cc_start: 0.8635 (tptm) cc_final: 0.7376 (ttmt) REVERT: t 51 GLN cc_start: 0.8712 (tt0) cc_final: 0.6723 (mm110) REVERT: t 69 LYS cc_start: 0.9324 (tptm) cc_final: 0.8529 (mttt) REVERT: t 72 LYS cc_start: 0.9446 (tmtt) cc_final: 0.9158 (tttp) REVERT: u 30 LEU cc_start: 0.8873 (tp) cc_final: 0.8671 (tt) REVERT: u 46 LEU cc_start: 0.8701 (tp) cc_final: 0.8461 (tp) REVERT: u 49 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7076 (tp30) REVERT: u 65 SER cc_start: 0.9111 (t) cc_final: 0.8872 (t) REVERT: u 69 LYS cc_start: 0.8899 (tptm) cc_final: 0.7488 (ttmt) REVERT: u 82 PHE cc_start: 0.8981 (m-80) cc_final: 0.8483 (m-80) REVERT: v 32 LEU cc_start: 0.9346 (tp) cc_final: 0.9080 (tp) REVERT: v 36 LYS cc_start: 0.8853 (mttt) cc_final: 0.8552 (mttm) REVERT: v 69 LYS cc_start: 0.9105 (tptm) cc_final: 0.8115 (mttm) REVERT: w 25 THR cc_start: 0.8612 (p) cc_final: 0.8143 (p) REVERT: w 47 LEU cc_start: 0.9083 (mm) cc_final: 0.8770 (mm) REVERT: w 57 TYR cc_start: 0.8900 (t80) cc_final: 0.8484 (t80) REVERT: w 61 ARG cc_start: 0.8305 (mmt180) cc_final: 0.6629 (ttp-170) REVERT: w 69 LYS cc_start: 0.8805 (tppt) cc_final: 0.7307 (tppt) REVERT: a0 103 LYS cc_start: 0.8041 (tttm) cc_final: 0.6949 (tptt) REVERT: d0 103 LYS cc_start: 0.9245 (ttmt) cc_final: 0.7908 (tptt) REVERT: e0 103 LYS cc_start: 0.8698 (ttmt) cc_final: 0.7844 (tttt) REVERT: f0 100 ARG cc_start: 0.8456 (ttm170) cc_final: 0.8006 (ttm170) REVERT: f0 103 LYS cc_start: 0.9178 (ttmt) cc_final: 0.8287 (tptt) REVERT: g0 103 LYS cc_start: 0.9109 (mtmt) cc_final: 0.7778 (tptt) REVERT: i0 103 LYS cc_start: 0.8892 (tttt) cc_final: 0.8566 (tptt) REVERT: j0 103 LYS cc_start: 0.8871 (mtpt) cc_final: 0.8651 (mtpt) REVERT: k0 103 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8092 (tptt) REVERT: k0 105 ARG cc_start: 0.8859 (ttm110) cc_final: 0.7277 (tmt170) REVERT: l0 103 LYS cc_start: 0.8893 (ttmt) cc_final: 0.8160 (tptt) REVERT: m0 103 LYS cc_start: 0.9073 (mtpt) cc_final: 0.8093 (tptt) REVERT: n0 97 SER cc_start: 0.9115 (m) cc_final: 0.8856 (t) REVERT: p0 103 LYS cc_start: 0.8829 (ttpt) cc_final: 0.8005 (tptt) REVERT: p0 105 ARG cc_start: 0.6966 (tmt170) cc_final: 0.6701 (tpt170) REVERT: q0 103 LYS cc_start: 0.9083 (ttmt) cc_final: 0.8262 (tptt) REVERT: r0 102 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8093 (mt-10) REVERT: r0 103 LYS cc_start: 0.8839 (ttmt) cc_final: 0.7505 (tptt) REVERT: t0 103 LYS cc_start: 0.8910 (ttmt) cc_final: 0.8047 (tptt) REVERT: t0 105 ARG cc_start: 0.9233 (ttm110) cc_final: 0.7735 (tpm170) REVERT: u0 98 SER cc_start: 0.8859 (m) cc_final: 0.7908 (p) REVERT: u0 100 ARG cc_start: 0.7799 (ttm110) cc_final: 0.7188 (tpt170) REVERT: u0 103 LYS cc_start: 0.9087 (ttmt) cc_final: 0.7909 (tptt) REVERT: v0 92 THR cc_start: 0.8443 (m) cc_final: 0.8207 (m) REVERT: v0 103 LYS cc_start: 0.9239 (mttt) cc_final: 0.7794 (tptt) REVERT: w0 103 LYS cc_start: 0.8876 (ttmt) cc_final: 0.8267 (tptt) REVERT: x0 103 LYS cc_start: 0.8429 (ttmt) cc_final: 0.7738 (tptt) outliers start: 6 outliers final: 0 residues processed: 2164 average time/residue: 0.2270 time to fit residues: 836.3630 Evaluate side-chains 1914 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1914 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 320 optimal weight: 0.0570 chunk 460 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 374 optimal weight: 0.8980 chunk 469 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 148 optimal weight: 0.2980 chunk 246 optimal weight: 4.9990 chunk 224 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 170 ASN F 247 HIS F 252 ASN ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS O 44 GLN P 59 ASN R 19 GLN U 80 GLN W 81 ASN Y 144 ASN 2 137 HIS 4 137 HIS y 123 ASN y 164 ASN ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 ASN b 40 ASN ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 40 ASN f 51 GLN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 40 ASN l 40 ASN m 27 GLN n 81 ASN o 24 GLN o 40 ASN t 24 GLN t 81 ASN u 40 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103064 restraints weight = 89913.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105652 restraints weight = 52568.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.107446 restraints weight = 35276.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108760 restraints weight = 26074.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109698 restraints weight = 20537.726| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 44859 Z= 0.139 Angle : 0.668 10.264 60892 Z= 0.331 Chirality : 0.041 0.371 7369 Planarity : 0.004 0.079 7620 Dihedral : 4.346 88.429 5953 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.18 % Allowed : 0.30 % Favored : 99.52 % 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: 2.85 (0.11), residues: 5404 helix: 2.94 (0.08), residues: 4154 sheet: 1.90 (0.31), residues: 160 loop : -2.72 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 138 TYR 0.034 0.002 TYR k 50 PHE 0.032 0.002 PHE g 19 TRP 0.012 0.001 TRP r 10 HIS 0.011 0.001 HIS F 11 Details of bonding type rmsd covalent geometry : bond 0.00320 (44858) covalent geometry : angle 0.66794 (60890) SS BOND : bond 0.00040 ( 1) SS BOND : angle 0.31076 ( 2) hydrogen bonds : bond 0.03963 ( 3327) hydrogen bonds : angle 3.60084 ( 9915) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2166 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 2157 time to evaluate : 1.892 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 CYS cc_start: 0.8707 (p) cc_final: 0.7876 (p) REVERT: A 36 MET cc_start: 0.8339 (tpp) cc_final: 0.8089 (tpp) REVERT: A 50 MET cc_start: 0.8166 (ttp) cc_final: 0.7842 (ttm) REVERT: A 68 ILE cc_start: 0.9560 (mt) cc_final: 0.9264 (mt) REVERT: A 69 GLU cc_start: 0.7952 (tp30) cc_final: 0.7177 (mm-30) REVERT: A 101 GLN cc_start: 0.8851 (tt0) cc_final: 0.8395 (tm-30) REVERT: A 152 LYS cc_start: 0.9060 (tttt) cc_final: 0.8726 (mtmt) REVERT: A 177 MET cc_start: 0.7934 (mmt) cc_final: 0.7496 (mmt) REVERT: A 205 LYS cc_start: 0.9107 (mttt) cc_final: 0.8159 (tttt) REVERT: B 27 TYR cc_start: 0.8764 (t80) cc_final: 0.8543 (t80) REVERT: B 65 LYS cc_start: 0.8477 (tttp) cc_final: 0.8112 (tttt) REVERT: B 110 GLU cc_start: 0.8529 (pm20) cc_final: 0.8152 (pm20) REVERT: B 137 SER cc_start: 0.9170 (m) cc_final: 0.8851 (t) REVERT: B 146 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7844 (mm-30) REVERT: B 177 MET cc_start: 0.8109 (mtt) cc_final: 0.7854 (mtt) REVERT: C 72 TYR cc_start: 0.5455 (t80) cc_final: 0.5188 (m-10) REVERT: C 105 LYS cc_start: 0.8968 (tttp) cc_final: 0.8655 (mtpp) REVERT: C 117 ARG cc_start: 0.8277 (mtt180) cc_final: 0.7724 (tpt170) REVERT: D 1 MET cc_start: 0.1946 (ptt) cc_final: 0.1673 (ptt) REVERT: D 2 LEU cc_start: 0.9179 (mt) cc_final: 0.8882 (mt) REVERT: D 6 SER cc_start: 0.8705 (m) cc_final: 0.7852 (p) REVERT: D 17 LEU cc_start: 0.9334 (tp) cc_final: 0.8888 (tt) REVERT: D 105 LYS cc_start: 0.9298 (ttmt) cc_final: 0.8992 (ttmm) REVERT: D 175 LEU cc_start: 0.9097 (tp) cc_final: 0.8890 (tt) REVERT: E 44 GLN cc_start: 0.8828 (mp10) cc_final: 0.8510 (mp10) REVERT: E 59 MET cc_start: 0.8353 (mtm) cc_final: 0.8119 (mtp) REVERT: F 104 ASP cc_start: 0.8528 (t0) cc_final: 0.8230 (t0) REVERT: F 133 PHE cc_start: 0.9077 (t80) cc_final: 0.8475 (t80) REVERT: G 74 PHE cc_start: 0.9405 (t80) cc_final: 0.9069 (t80) REVERT: G 79 MET cc_start: 0.8626 (mmm) cc_final: 0.8386 (mmt) REVERT: H 60 LEU cc_start: 0.8928 (mm) cc_final: 0.8676 (mm) REVERT: I 53 LEU cc_start: 0.7851 (tp) cc_final: 0.7597 (tp) REVERT: I 60 LEU cc_start: 0.8629 (mt) cc_final: 0.8372 (mt) REVERT: I 69 GLU cc_start: 0.7828 (tp30) cc_final: 0.6905 (tp30) REVERT: K 46 SER cc_start: 0.6940 (m) cc_final: 0.6168 (t) REVERT: K 51 MET cc_start: 0.7575 (mmt) cc_final: 0.7104 (mmt) REVERT: K 132 LYS cc_start: 0.8616 (mmtp) cc_final: 0.8068 (mttt) REVERT: K 176 ARG cc_start: 0.8774 (tpt-90) cc_final: 0.8287 (tpt-90) REVERT: N 33 LYS cc_start: 0.8617 (mmmm) cc_final: 0.8042 (mmtt) REVERT: N 58 LEU cc_start: 0.9213 (mt) cc_final: 0.8873 (mt) REVERT: N 68 THR cc_start: 0.9050 (m) cc_final: 0.8718 (t) REVERT: N 89 SER cc_start: 0.9246 (t) cc_final: 0.8845 (p) REVERT: O 41 THR cc_start: 0.8874 (t) cc_final: 0.8366 (m) REVERT: P 44 GLN cc_start: 0.8350 (tt0) cc_final: 0.8049 (tt0) REVERT: P 56 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7075 (tm-30) REVERT: P 57 SER cc_start: 0.9033 (m) cc_final: 0.8379 (p) REVERT: Q 75 ILE cc_start: 0.9627 (mt) cc_final: 0.9352 (mt) REVERT: R 27 GLU cc_start: 0.6745 (tm-30) cc_final: 0.6488 (pt0) REVERT: R 92 GLU cc_start: 0.8339 (tp30) cc_final: 0.7997 (tp30) REVERT: S 37 LEU cc_start: 0.9014 (tp) cc_final: 0.8317 (tp) REVERT: S 50 TYR cc_start: 0.9067 (t80) cc_final: 0.8703 (t80) REVERT: T 30 LEU cc_start: 0.9055 (tp) cc_final: 0.8804 (tp) REVERT: U 81 ASN cc_start: 0.9166 (m-40) cc_final: 0.8906 (m-40) REVERT: V 32 LEU cc_start: 0.8716 (mt) cc_final: 0.8343 (tt) REVERT: V 45 GLN cc_start: 0.8778 (tp40) cc_final: 0.7817 (tp40) REVERT: V 46 LEU cc_start: 0.9134 (mm) cc_final: 0.8814 (mm) REVERT: V 49 GLU cc_start: 0.8176 (mp0) cc_final: 0.7583 (mp0) REVERT: V 64 GLN cc_start: 0.8410 (tt0) cc_final: 0.8164 (tt0) REVERT: W 39 LYS cc_start: 0.8403 (mttt) cc_final: 0.7703 (mptt) REVERT: W 43 ASN cc_start: 0.8521 (t0) cc_final: 0.8177 (t0) REVERT: W 72 LYS cc_start: 0.9283 (mmmm) cc_final: 0.8950 (mmmm) REVERT: Y 112 SER cc_start: 0.8089 (p) cc_final: 0.7624 (m) REVERT: Y 123 ASN cc_start: 0.8721 (t0) cc_final: 0.8393 (t0) REVERT: Z 161 LEU cc_start: 0.8465 (tp) cc_final: 0.8259 (tp) REVERT: 0 128 TYR cc_start: 0.8256 (t80) cc_final: 0.7947 (t80) REVERT: 2 127 GLN cc_start: 0.8384 (tp40) cc_final: 0.7991 (tp40) REVERT: 4 150 PHE cc_start: 0.9006 (p90) cc_final: 0.8587 (p90) REVERT: 4 168 LEU cc_start: 0.8862 (tp) cc_final: 0.8448 (tt) REVERT: 6 127 GLN cc_start: 0.8924 (tp40) cc_final: 0.8260 (tp40) REVERT: 6 138 ARG cc_start: 0.8350 (mtp85) cc_final: 0.7538 (mtm110) REVERT: 8 144 ASN cc_start: 0.7706 (t0) cc_final: 0.7482 (t0) REVERT: x 127 GLN cc_start: 0.8896 (tp-100) cc_final: 0.8544 (tp-100) REVERT: x 150 PHE cc_start: 0.9271 (p90) cc_final: 0.8528 (p90) REVERT: x 153 SER cc_start: 0.9423 (t) cc_final: 0.9017 (p) REVERT: y 115 ILE cc_start: 0.9254 (mt) cc_final: 0.8930 (mt) REVERT: y 158 LEU cc_start: 0.8210 (tp) cc_final: 0.7819 (mm) REVERT: y 160 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7826 (mm-30) REVERT: z 127 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8304 (tm-30) REVERT: z 138 ARG cc_start: 0.8214 (ttt180) cc_final: 0.7957 (ttp-110) REVERT: 1 118 GLU cc_start: 0.7486 (pm20) cc_final: 0.7174 (pm20) REVERT: 1 133 ASN cc_start: 0.8583 (m-40) cc_final: 0.8314 (t0) REVERT: 3 115 ILE cc_start: 0.8493 (mt) cc_final: 0.8060 (mt) REVERT: 9 135 TYR cc_start: 0.7650 (t80) cc_final: 0.7159 (t80) REVERT: a 26 LEU cc_start: 0.8805 (tp) cc_final: 0.8530 (tp) REVERT: a 31 THR cc_start: 0.7907 (m) cc_final: 0.7596 (m) REVERT: a 50 TYR cc_start: 0.8686 (t80) cc_final: 0.7842 (t80) REVERT: a 66 ASN cc_start: 0.9035 (m-40) cc_final: 0.8803 (m110) REVERT: b 14 SER cc_start: 0.8890 (m) cc_final: 0.8583 (p) REVERT: b 43 ASN cc_start: 0.8469 (t0) cc_final: 0.8201 (t0) REVERT: b 45 GLN cc_start: 0.8901 (tp40) cc_final: 0.7922 (tm-30) REVERT: b 59 LEU cc_start: 0.9363 (mp) cc_final: 0.9143 (mp) REVERT: b 64 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7617 (tm-30) REVERT: b 67 THR cc_start: 0.9234 (m) cc_final: 0.8874 (p) REVERT: c 59 LEU cc_start: 0.9386 (mt) cc_final: 0.9149 (mt) REVERT: c 80 GLN cc_start: 0.8865 (tp-100) cc_final: 0.8515 (tp40) REVERT: d 54 LEU cc_start: 0.9017 (tp) cc_final: 0.8803 (tp) REVERT: d 57 TYR cc_start: 0.9011 (t80) cc_final: 0.8713 (t80) REVERT: d 80 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7276 (tm-30) REVERT: e 40 ASN cc_start: 0.8301 (p0) cc_final: 0.7831 (p0) REVERT: f 14 SER cc_start: 0.8915 (p) cc_final: 0.8246 (t) REVERT: f 80 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8192 (tm-30) REVERT: g 17 GLU cc_start: 0.7713 (mp0) cc_final: 0.7222 (mp0) REVERT: g 26 LEU cc_start: 0.9069 (tt) cc_final: 0.8494 (mm) REVERT: g 27 GLN cc_start: 0.8638 (mt0) cc_final: 0.8431 (mp10) REVERT: g 54 LEU cc_start: 0.9300 (tp) cc_final: 0.9072 (tp) REVERT: g 65 SER cc_start: 0.8947 (t) cc_final: 0.8739 (t) REVERT: g 67 THR cc_start: 0.9519 (t) cc_final: 0.9229 (t) REVERT: g 80 GLN cc_start: 0.8724 (tp-100) cc_final: 0.8225 (tm-30) REVERT: g 81 ASN cc_start: 0.9245 (m110) cc_final: 0.8960 (m-40) REVERT: g 82 PHE cc_start: 0.9100 (m-10) cc_final: 0.8859 (m-80) REVERT: h 24 GLN cc_start: 0.8261 (tp40) cc_final: 0.7967 (tp40) REVERT: i 80 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8159 (tm-30) REVERT: i 81 ASN cc_start: 0.9293 (m-40) cc_final: 0.8999 (m-40) REVERT: j 42 SER cc_start: 0.9389 (m) cc_final: 0.8904 (p) REVERT: j 80 GLN cc_start: 0.9199 (tp-100) cc_final: 0.8926 (tp-100) REVERT: k 80 GLN cc_start: 0.8766 (tp40) cc_final: 0.8555 (tp40) REVERT: l 16 SER cc_start: 0.9102 (m) cc_final: 0.8326 (t) REVERT: l 20 ASP cc_start: 0.7604 (m-30) cc_final: 0.7054 (m-30) REVERT: l 25 THR cc_start: 0.8571 (p) cc_final: 0.8257 (p) REVERT: l 29 GLU cc_start: 0.8519 (pt0) cc_final: 0.8140 (pt0) REVERT: l 45 GLN cc_start: 0.8068 (tp40) cc_final: 0.7587 (tp40) REVERT: l 50 TYR cc_start: 0.9202 (t80) cc_final: 0.8819 (t80) REVERT: m 20 ASP cc_start: 0.8198 (m-30) cc_final: 0.7679 (m-30) REVERT: m 50 TYR cc_start: 0.8854 (t80) cc_final: 0.8480 (t80) REVERT: m 75 ASP cc_start: 0.8379 (m-30) cc_final: 0.7538 (m-30) REVERT: n 3 VAL cc_start: 0.8717 (t) cc_final: 0.8422 (m) REVERT: n 49 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7275 (tm-30) REVERT: n 75 ASP cc_start: 0.8528 (m-30) cc_final: 0.8069 (m-30) REVERT: n 80 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8051 (tm-30) REVERT: o 39 LYS cc_start: 0.7727 (mmpt) cc_final: 0.7448 (mmpt) REVERT: o 50 TYR cc_start: 0.9215 (t80) cc_final: 0.8933 (t80) REVERT: o 53 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8727 (mmpt) REVERT: p 25 THR cc_start: 0.8248 (p) cc_final: 0.7548 (t) REVERT: p 75 ASP cc_start: 0.8660 (m-30) cc_final: 0.8070 (m-30) REVERT: q 14 SER cc_start: 0.9445 (m) cc_final: 0.9127 (p) REVERT: q 32 LEU cc_start: 0.8164 (tp) cc_final: 0.7811 (tp) REVERT: q 36 LYS cc_start: 0.8728 (mttt) cc_final: 0.8427 (mtmt) REVERT: r 24 GLN cc_start: 0.8143 (mm110) cc_final: 0.7719 (mp10) REVERT: r 25 THR cc_start: 0.8147 (p) cc_final: 0.7931 (p) REVERT: r 29 GLU cc_start: 0.8808 (pm20) cc_final: 0.8517 (pm20) REVERT: s 7 ASN cc_start: 0.6803 (m-40) cc_final: 0.5886 (p0) REVERT: s 10 TRP cc_start: 0.8881 (p-90) cc_final: 0.8539 (p-90) REVERT: s 23 THR cc_start: 0.8629 (m) cc_final: 0.8326 (m) REVERT: s 24 GLN cc_start: 0.8072 (tp40) cc_final: 0.7840 (mm-40) REVERT: s 27 GLN cc_start: 0.8462 (mt0) cc_final: 0.7893 (tm-30) REVERT: s 65 SER cc_start: 0.9022 (t) cc_final: 0.8677 (m) REVERT: s 69 LYS cc_start: 0.8646 (tptm) cc_final: 0.7378 (ttmt) REVERT: t 51 GLN cc_start: 0.8766 (tt0) cc_final: 0.6780 (mm110) REVERT: t 69 LYS cc_start: 0.9317 (tptm) cc_final: 0.8412 (mttt) REVERT: t 72 LYS cc_start: 0.9486 (tmtt) cc_final: 0.9180 (tttp) REVERT: u 30 LEU cc_start: 0.8860 (tp) cc_final: 0.8578 (tt) REVERT: u 46 LEU cc_start: 0.8665 (tp) cc_final: 0.8441 (tp) REVERT: u 49 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7164 (tp30) REVERT: u 65 SER cc_start: 0.9048 (t) cc_final: 0.8837 (t) REVERT: u 69 LYS cc_start: 0.8882 (tptm) cc_final: 0.7474 (ttmt) REVERT: u 82 PHE cc_start: 0.8938 (m-80) cc_final: 0.8419 (m-80) REVERT: v 32 LEU cc_start: 0.9338 (tp) cc_final: 0.9072 (tp) REVERT: v 36 LYS cc_start: 0.8835 (mttt) cc_final: 0.8547 (mttm) REVERT: v 66 ASN cc_start: 0.8485 (m-40) cc_final: 0.8242 (t0) REVERT: v 69 LYS cc_start: 0.9075 (tptm) cc_final: 0.8152 (mttm) REVERT: w 4 THR cc_start: 0.8282 (t) cc_final: 0.7680 (m) REVERT: w 25 THR cc_start: 0.8677 (p) cc_final: 0.8196 (p) REVERT: w 57 TYR cc_start: 0.8895 (t80) cc_final: 0.8474 (t80) REVERT: w 61 ARG cc_start: 0.8270 (mmt180) cc_final: 0.6625 (ttp-170) REVERT: w 69 LYS cc_start: 0.8790 (tppt) cc_final: 0.7313 (tppt) REVERT: a0 103 LYS cc_start: 0.8018 (tttm) cc_final: 0.6937 (tptt) REVERT: d0 103 LYS cc_start: 0.9250 (ttmt) cc_final: 0.7906 (tptt) REVERT: e0 103 LYS cc_start: 0.8696 (ttmt) cc_final: 0.7826 (tttt) REVERT: f0 100 ARG cc_start: 0.8414 (ttm170) cc_final: 0.7908 (ttm170) REVERT: f0 103 LYS cc_start: 0.9188 (ttmt) cc_final: 0.8293 (tptt) REVERT: g0 103 LYS cc_start: 0.9098 (mtmt) cc_final: 0.7783 (tptt) REVERT: i0 103 LYS cc_start: 0.8892 (tttt) cc_final: 0.8587 (tptt) REVERT: k0 103 LYS cc_start: 0.8912 (ttmm) cc_final: 0.8085 (tptt) REVERT: k0 105 ARG cc_start: 0.8865 (ttm110) cc_final: 0.7269 (tmt170) REVERT: l0 103 LYS cc_start: 0.8881 (ttmt) cc_final: 0.8146 (tptt) REVERT: m0 103 LYS cc_start: 0.9069 (mtpt) cc_final: 0.8090 (tptt) REVERT: n0 97 SER cc_start: 0.9062 (m) cc_final: 0.8820 (t) REVERT: p0 103 LYS cc_start: 0.8818 (ttpt) cc_final: 0.7984 (tptt) REVERT: p0 105 ARG cc_start: 0.7046 (tmt170) cc_final: 0.6752 (tpt170) REVERT: q0 103 LYS cc_start: 0.9081 (ttmt) cc_final: 0.8255 (tptt) REVERT: r0 102 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8049 (mt-10) REVERT: r0 103 LYS cc_start: 0.8830 (ttmt) cc_final: 0.7491 (tptt) REVERT: t0 103 LYS cc_start: 0.8903 (ttmt) cc_final: 0.8023 (tptt) REVERT: t0 105 ARG cc_start: 0.9241 (ttm110) cc_final: 0.7735 (tpm170) REVERT: u0 98 SER cc_start: 0.8693 (m) cc_final: 0.7870 (p) REVERT: u0 100 ARG cc_start: 0.7752 (ttm110) cc_final: 0.7304 (ttt180) REVERT: u0 103 LYS cc_start: 0.9110 (ttmt) cc_final: 0.7927 (tptt) REVERT: v0 92 THR cc_start: 0.8537 (m) cc_final: 0.8320 (m) REVERT: v0 103 LYS cc_start: 0.9226 (mttt) cc_final: 0.7760 (tptt) REVERT: w0 103 LYS cc_start: 0.8883 (ttmt) cc_final: 0.8274 (tptt) REVERT: x0 103 LYS cc_start: 0.8447 (ttmt) cc_final: 0.7744 (tptt) outliers start: 9 outliers final: 1 residues processed: 2158 average time/residue: 0.2268 time to fit residues: 832.6830 Evaluate side-chains 1907 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1906 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 10 optimal weight: 0.8980 chunk 408 optimal weight: 2.9990 chunk 390 optimal weight: 2.9990 chunk 496 optimal weight: 2.9990 chunk 508 optimal weight: 0.5980 chunk 428 optimal weight: 1.9990 chunk 201 optimal weight: 0.6980 chunk 316 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 208 optimal weight: 3.9990 chunk 479 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 170 ASN F 247 HIS F 252 ASN ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS O 44 GLN P 59 ASN R 19 GLN ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 144 ASN 2 137 HIS 4 137 HIS ** 4 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 123 ASN y 164 ASN ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 ASN b 40 ASN ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 64 GLN f 40 ASN f 43 ASN f 51 GLN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 40 ASN m 27 GLN n 81 ASN o 24 GLN o 40 ASN s 40 ASN t 24 GLN u 40 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.117484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102518 restraints weight = 90679.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105085 restraints weight = 53463.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.106895 restraints weight = 36138.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108157 restraints weight = 26778.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.109033 restraints weight = 21273.020| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 44859 Z= 0.144 Angle : 0.677 11.216 60892 Z= 0.335 Chirality : 0.041 0.377 7369 Planarity : 0.004 0.079 7620 Dihedral : 4.366 89.790 5953 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.18 % Allowed : 0.34 % Favored : 99.48 % 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: 2.78 (0.11), residues: 5404 helix: 2.89 (0.08), residues: 4151 sheet: 1.90 (0.31), residues: 160 loop : -2.68 (0.17), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 85 TYR 0.065 0.002 TYR B 158 PHE 0.029 0.002 PHE g 19 TRP 0.015 0.001 TRP H 66 HIS 0.011 0.001 HIS F 11 Details of bonding type rmsd covalent geometry : bond 0.00335 (44858) covalent geometry : angle 0.67658 (60890) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.31453 ( 2) hydrogen bonds : bond 0.04012 ( 3327) hydrogen bonds : angle 3.64401 ( 9915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13025.85 seconds wall clock time: 223 minutes 28.14 seconds (13408.14 seconds total)