Starting phenix.real_space_refine on Thu Dec 26 06:33:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8axk_15700/12_2024/8axk_15700.cif Found real_map, /net/cci-nas-00/data/ceres_data/8axk_15700/12_2024/8axk_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8axk_15700/12_2024/8axk_15700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8axk_15700/12_2024/8axk_15700.map" model { file = "/net/cci-nas-00/data/ceres_data/8axk_15700/12_2024/8axk_15700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8axk_15700/12_2024/8axk_15700.cif" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 26.25, per 1000 atoms: 0.59 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: 10.94 Conformation dependent library (CDL) restraints added in 5.8 seconds 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: 4.18 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: 15.87 Time building geometry restraints manager: 12.70 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: 6.350 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: 0.040 Extract box with map and model: 1.560 Check model and map are aligned: 0.300 Set scattering table: 0.450 Process input model: 92.570 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.410 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.800 ------------------------------------------------------------------------------- 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 44858 Z= 0.149 Angle : 0.465 6.197 60890 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP K 174 HIS 0.002 0.000 HIS F 11 PHE 0.018 0.001 PHE K 45 TYR 0.012 0.001 TYR 1 151 ARG 0.003 0.000 ARG o 61 *********************** 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 : 5.139 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: 0.8955 (tt) REVERT: A 97 MET cc_start: 0.8332 (tpt) cc_final: 0.8066 (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: 0.7966 (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: 0.8362 (tttt) REVERT: B 67 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8264 (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: 0.5884 (mp0) REVERT: B 133 TYR cc_start: 0.7513 (m-10) cc_final: 0.6847 (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: 0.7318 (t80) REVERT: C 117 ARG cc_start: 0.8447 (mtt180) cc_final: 0.8236 (tpt170) REVERT: C 146 GLU cc_start: 0.8544 (tp30) cc_final: 0.8003 (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: 0.9047 (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: 0.8740 (mt) REVERT: D 6 SER cc_start: 0.8595 (m) cc_final: 0.7908 (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: 0.7847 (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: 0.8635 (t) REVERT: E 36 MET cc_start: 0.8695 (mmm) cc_final: 0.7871 (mmm) REVERT: E 64 MET cc_start: 0.8617 (mmm) cc_final: 0.7565 (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: 0.8182 (m-80) REVERT: E 184 THR cc_start: 0.9250 (p) cc_final: 0.8494 (t) REVERT: F 69 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7169 (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: 0.8140 (m-40) REVERT: G 7 MET cc_start: 0.8617 (mmm) cc_final: 0.8336 (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: 0.8334 (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: 0.8281 (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: 0.6099 (m-80) REVERT: H 81 LEU cc_start: 0.8738 (mt) cc_final: 0.8337 (mt) REVERT: H 83 LYS cc_start: 0.8699 (tptt) cc_final: 0.8495 (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: 0.6274 (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: 0.7307 (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: 0.7762 (mt-10) REVERT: K 46 SER cc_start: 0.7643 (m) cc_final: 0.6954 (t) REVERT: K 51 MET cc_start: 0.7789 (mmt) cc_final: 0.6948 (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: 0.6273 (ptm-80) REVERT: K 157 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7732 (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: 0.7862 (tp) REVERT: M 72 ASN cc_start: 0.8199 (m-40) cc_final: 0.7988 (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: 0.7458 (mt) REVERT: Q 49 MET cc_start: 0.9056 (mmt) cc_final: 0.8741 (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: 0.8497 (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: 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: 0.7308 (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: 0.8899 (pt) REVERT: Z 112 SER cc_start: 0.8622 (p) cc_final: 0.8415 (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: 0.8324 (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: 0.8424 (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: 0.8679 (mtmt) REVERT: z 149 THR cc_start: 0.9162 (m) cc_final: 0.8675 (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: 0.8148 (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: 0.7939 (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: 0.9116 (mmt-90) REVERT: a 72 LYS cc_start: 0.9561 (tmtt) cc_final: 0.9275 (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: 0.9000 (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: 0.8172 (t) REVERT: k 37 LEU cc_start: 0.9087 (tp) cc_final: 0.8783 (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: 0.8571 (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: 0.8175 (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: 0.7689 (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: 0.8160 (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: 0.7238 (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: 0.7208 (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: 0.8099 (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: 0.7630 (tptt) REVERT: t0 103 LYS cc_start: 0.8791 (ttmt) cc_final: 0.8188 (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: 0.8403 (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: 0.8050 (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: 0.7458 (tpt170) REVERT: v0 103 LYS cc_start: 0.9309 (mttt) cc_final: 0.8095 (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: 0.5406 time to fit residues: 2401.8225 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 : 5.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 441 optimal weight: 4.9990 chunk 396 optimal weight: 0.7980 chunk 219 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 267 optimal weight: 0.9980 chunk 211 optimal weight: 0.7980 chunk 409 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 249 optimal weight: 0.8980 chunk 305 optimal weight: 1.9990 chunk 474 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 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 6 133 ASN 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 51 GLN ** f 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 81 ASN i 43 ASN 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: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 44858 Z= 0.230 Angle : 0.618 9.665 60890 Z= 0.311 Chirality : 0.041 0.184 7369 Planarity : 0.004 0.064 7620 Dihedral : 4.156 82.430 5953 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.42 % Allowed : 2.39 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.12), residues: 5404 helix: 3.30 (0.08), residues: 4159 sheet: 1.94 (0.32), residues: 192 loop : -2.91 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 174 HIS 0.012 0.001 HIS I 76 PHE 0.031 0.002 PHE K 45 TYR 0.033 0.002 TYR o 60 ARG 0.011 0.001 ARG F 23 *********************** 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 2383 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 2362 time to evaluate : 5.218 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: 0.8802 (p) cc_final: 0.8241 (p) REVERT: A 36 MET cc_start: 0.8933 (ttp) cc_final: 0.8694 (ttm) REVERT: A 68 ILE cc_start: 0.9520 (mt) cc_final: 0.9178 (mt) REVERT: A 69 GLU cc_start: 0.7631 (tp30) cc_final: 0.6968 (mm-30) REVERT: A 97 MET cc_start: 0.8449 (tpt) cc_final: 0.8160 (tpt) REVERT: A 101 GLN cc_start: 0.8783 (tt0) cc_final: 0.8397 (tm-30) REVERT: A 177 MET cc_start: 0.7916 (ptp) cc_final: 0.7606 (mtm) REVERT: A 205 LYS cc_start: 0.8960 (mttt) cc_final: 0.8292 (tttt) REVERT: B 116 GLN cc_start: 0.8846 (mm110) cc_final: 0.8531 (tp40) REVERT: B 120 GLU cc_start: 0.6418 (mt-10) cc_final: 0.5721 (mp0) REVERT: B 190 LYS cc_start: 0.9205 (mtmt) cc_final: 0.8867 (mtmm) REVERT: C 105 LYS cc_start: 0.9173 (tttp) cc_final: 0.8781 (mtpt) REVERT: C 117 ARG cc_start: 0.8512 (mtt180) cc_final: 0.8044 (tpt170) REVERT: C 119 GLU cc_start: 0.8249 (tt0) cc_final: 0.7738 (tp30) REVERT: C 164 VAL cc_start: 0.9533 (t) cc_final: 0.9306 (t) REVERT: C 177 MET cc_start: 0.7132 (ptp) cc_final: 0.6275 (mtt) REVERT: D 2 LEU cc_start: 0.9217 (mt) cc_final: 0.8949 (mt) REVERT: D 6 SER cc_start: 0.8891 (m) cc_final: 0.8133 (p) REVERT: D 133 TYR cc_start: 0.8524 (m-10) cc_final: 0.7934 (m-10) REVERT: E 59 MET cc_start: 0.8436 (mtp) cc_final: 0.8176 (mtm) REVERT: E 64 MET cc_start: 0.8659 (mmm) cc_final: 0.7508 (mmm) REVERT: E 179 MET cc_start: 0.8611 (mmp) cc_final: 0.8366 (mmp) REVERT: E 184 THR cc_start: 0.9202 (p) cc_final: 0.8755 (t) REVERT: E 194 PHE cc_start: 0.9063 (t80) cc_final: 0.8846 (t80) REVERT: E 198 ASP cc_start: 0.7191 (t0) cc_final: 0.6989 (t0) REVERT: F 101 SER cc_start: 0.9369 (m) cc_final: 0.9006 (t) REVERT: F 133 PHE cc_start: 0.8905 (t80) cc_final: 0.8538 (t80) REVERT: F 139 LEU cc_start: 0.9290 (tp) cc_final: 0.9078 (tp) REVERT: F 152 GLN cc_start: 0.9157 (tt0) cc_final: 0.8503 (tp-100) REVERT: F 202 VAL cc_start: 0.8931 (t) cc_final: 0.8587 (t) REVERT: G 5 VAL cc_start: 0.9259 (p) cc_final: 0.8895 (p) REVERT: G 57 SER cc_start: 0.9118 (t) cc_final: 0.8915 (p) REVERT: G 75 CYS cc_start: 0.8604 (m) cc_final: 0.8278 (m) REVERT: G 79 MET cc_start: 0.8619 (mmm) cc_final: 0.8114 (mmm) REVERT: H 47 LEU cc_start: 0.4997 (OUTLIER) cc_final: 0.4764 (mt) REVERT: H 81 LEU cc_start: 0.8719 (mt) cc_final: 0.8378 (mt) REVERT: H 83 LYS cc_start: 0.9040 (tptt) cc_final: 0.8812 (tppp) REVERT: I 5 VAL cc_start: 0.9168 (t) cc_final: 0.8642 (p) REVERT: I 9 ASN cc_start: 0.8359 (m-40) cc_final: 0.8112 (m-40) REVERT: I 21 TRP cc_start: 0.6373 (t-100) cc_final: 0.6055 (m100) REVERT: J 1 MET cc_start: 0.7681 (mmp) cc_final: 0.7346 (mmm) REVERT: J 3 ASP cc_start: 0.7448 (p0) cc_final: 0.7199 (p0) REVERT: J 57 SER cc_start: 0.8600 (t) cc_final: 0.8395 (p) REVERT: J 66 TRP cc_start: 0.9143 (t60) cc_final: 0.8661 (t-100) REVERT: K 32 VAL cc_start: 0.6886 (t) cc_final: 0.6605 (t) REVERT: K 51 MET cc_start: 0.7731 (mmt) cc_final: 0.6483 (mmt) REVERT: N 46 SER cc_start: 0.8992 (m) cc_final: 0.8737 (p) REVERT: N 58 LEU cc_start: 0.9218 (mt) cc_final: 0.8884 (mt) REVERT: P 12 ILE cc_start: 0.8459 (mt) cc_final: 0.8059 (mt) REVERT: P 44 GLN cc_start: 0.8180 (tt0) cc_final: 0.7810 (tt0) REVERT: P 56 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7341 (tm-30) REVERT: P 57 SER cc_start: 0.9263 (m) cc_final: 0.8641 (p) REVERT: Q 13 ILE cc_start: 0.7787 (mt) cc_final: 0.7536 (mt) REVERT: Q 65 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8261 (mptt) REVERT: U 43 ASN cc_start: 0.8901 (t0) cc_final: 0.8531 (t0) REVERT: U 81 ASN cc_start: 0.9085 (m-40) cc_final: 0.8874 (m-40) REVERT: V 32 LEU cc_start: 0.8676 (mt) cc_final: 0.8344 (tt) REVERT: V 64 GLN cc_start: 0.8594 (tt0) cc_final: 0.8368 (tt0) REVERT: W 39 LYS cc_start: 0.8283 (mttt) cc_final: 0.7762 (mptt) REVERT: W 43 ASN cc_start: 0.8729 (t0) cc_final: 0.8097 (t0) REVERT: W 80 GLN cc_start: 0.8678 (tp40) cc_final: 0.8470 (tp-100) REVERT: X 117 LEU cc_start: 0.7763 (pp) cc_final: 0.7196 (mt) REVERT: X 142 ARG cc_start: 0.8326 (mmt-90) cc_final: 0.7862 (mmt-90) REVERT: Y 112 SER cc_start: 0.7642 (p) cc_final: 0.7389 (m) REVERT: Y 123 ASN cc_start: 0.8700 (t0) cc_final: 0.8430 (t0) REVERT: Y 127 GLN cc_start: 0.7881 (tm-30) cc_final: 0.6804 (tm-30) REVERT: 4 150 PHE cc_start: 0.9045 (p90) cc_final: 0.8672 (p90) REVERT: 4 151 TYR cc_start: 0.8303 (t80) cc_final: 0.7802 (t80) REVERT: 6 127 GLN cc_start: 0.8987 (tp40) cc_final: 0.8321 (tp40) REVERT: 6 138 ARG cc_start: 0.8448 (mtp85) cc_final: 0.7350 (mtm110) REVERT: 6 149 THR cc_start: 0.9036 (m) cc_final: 0.8127 (p) REVERT: 8 111 ILE cc_start: 0.9294 (mt) cc_final: 0.9073 (mt) REVERT: 8 115 ILE cc_start: 0.8950 (mt) cc_final: 0.8673 (mm) REVERT: 8 144 ASN cc_start: 0.8045 (t0) cc_final: 0.7569 (t0) REVERT: x 112 SER cc_start: 0.8656 (p) cc_final: 0.8299 (m) REVERT: x 150 PHE cc_start: 0.9329 (p90) cc_final: 0.8569 (p90) REVERT: x 158 LEU cc_start: 0.8470 (tp) cc_final: 0.8152 (mm) REVERT: x 168 LEU cc_start: 0.9451 (tp) cc_final: 0.9061 (tp) REVERT: y 115 ILE cc_start: 0.9373 (mt) cc_final: 0.9141 (mt) REVERT: y 158 LEU cc_start: 0.8228 (tp) cc_final: 0.7925 (mm) REVERT: y 160 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7874 (mm-30) REVERT: z 112 SER cc_start: 0.9116 (p) cc_final: 0.8807 (m) REVERT: z 119 ASN cc_start: 0.8689 (m-40) cc_final: 0.8213 (p0) REVERT: z 139 TYR cc_start: 0.8115 (m-80) cc_final: 0.7864 (m-80) REVERT: z 149 THR cc_start: 0.9071 (m) cc_final: 0.8713 (t) REVERT: 1 127 GLN cc_start: 0.7769 (tp40) cc_final: 0.7540 (tp40) REVERT: 1 130 LYS cc_start: 0.8348 (mmtp) cc_final: 0.8113 (mmtp) REVERT: 1 133 ASN cc_start: 0.8683 (m-40) cc_final: 0.8221 (t0) REVERT: 1 148 LYS cc_start: 0.8748 (mtpt) cc_final: 0.8108 (mtpp) REVERT: 3 115 ILE cc_start: 0.8826 (mt) cc_final: 0.8177 (mt) REVERT: 5 112 SER cc_start: 0.8286 (p) cc_final: 0.8056 (m) REVERT: 7 112 SER cc_start: 0.8717 (p) cc_final: 0.8487 (m) REVERT: 7 128 TYR cc_start: 0.9082 (t80) cc_final: 0.8755 (t80) REVERT: 7 164 ASN cc_start: 0.8173 (m-40) cc_final: 0.7949 (m-40) REVERT: a 24 GLN cc_start: 0.8157 (tp40) cc_final: 0.7828 (tp40) REVERT: a 26 LEU cc_start: 0.9048 (tp) cc_final: 0.8575 (tp) REVERT: a 66 ASN cc_start: 0.9039 (m-40) cc_final: 0.8765 (m110) REVERT: a 72 LYS cc_start: 0.9556 (tmtt) cc_final: 0.9312 (tptp) REVERT: b 21 ASP cc_start: 0.8302 (m-30) cc_final: 0.8049 (m-30) REVERT: b 43 ASN cc_start: 0.8487 (t0) cc_final: 0.8209 (t0) REVERT: b 45 GLN cc_start: 0.9101 (tp40) cc_final: 0.8164 (tm-30) REVERT: b 49 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7565 (mm-30) REVERT: b 59 LEU cc_start: 0.9500 (mp) cc_final: 0.9254 (mm) REVERT: b 65 SER cc_start: 0.9278 (m) cc_final: 0.8619 (t) REVERT: b 72 LYS cc_start: 0.9000 (tptp) cc_final: 0.8735 (tptp) REVERT: c 9 ASP cc_start: 0.8589 (t0) cc_final: 0.8229 (t0) REVERT: d 50 TYR cc_start: 0.9102 (t80) cc_final: 0.8883 (t80) REVERT: d 57 TYR cc_start: 0.9083 (t80) cc_final: 0.8702 (t80) REVERT: d 71 ILE cc_start: 0.8879 (mm) cc_final: 0.8452 (mm) REVERT: d 75 ASP cc_start: 0.8525 (m-30) cc_final: 0.8166 (m-30) REVERT: f 17 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7138 (tm-30) REVERT: f 75 ASP cc_start: 0.8239 (m-30) cc_final: 0.8011 (m-30) REVERT: g 25 THR cc_start: 0.8400 (p) cc_final: 0.8123 (p) REVERT: g 54 LEU cc_start: 0.9205 (tp) cc_final: 0.8978 (tp) REVERT: g 64 GLN cc_start: 0.8650 (tt0) cc_final: 0.8428 (tm-30) REVERT: g 79 ILE cc_start: 0.9168 (mm) cc_final: 0.8961 (mm) REVERT: h 25 THR cc_start: 0.7470 (t) cc_final: 0.7048 (t) REVERT: h 29 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8201 (mt-10) REVERT: h 59 LEU cc_start: 0.9301 (mt) cc_final: 0.9025 (mt) REVERT: h 66 ASN cc_start: 0.9352 (m-40) cc_final: 0.9092 (m110) REVERT: i 25 THR cc_start: 0.8063 (p) cc_final: 0.7811 (p) REVERT: i 80 GLN cc_start: 0.8263 (tm130) cc_final: 0.8019 (tm-30) REVERT: i 81 ASN cc_start: 0.9228 (m-40) cc_final: 0.8931 (m-40) REVERT: j 14 SER cc_start: 0.9136 (m) cc_final: 0.8409 (t) REVERT: j 25 THR cc_start: 0.8275 (p) cc_final: 0.7841 (t) REVERT: j 55 SER cc_start: 0.9171 (m) cc_final: 0.8881 (p) REVERT: k 13 SER cc_start: 0.8824 (p) cc_final: 0.8544 (t) REVERT: k 37 LEU cc_start: 0.9032 (tp) cc_final: 0.8679 (tt) REVERT: k 50 TYR cc_start: 0.9266 (t80) cc_final: 0.9000 (t80) REVERT: l 20 ASP cc_start: 0.7977 (m-30) cc_final: 0.7508 (m-30) REVERT: l 25 THR cc_start: 0.8963 (p) cc_final: 0.8126 (p) REVERT: l 45 GLN cc_start: 0.8099 (tp40) cc_final: 0.7541 (tp40) REVERT: l 50 TYR cc_start: 0.9250 (t80) cc_final: 0.8837 (t80) REVERT: m 20 ASP cc_start: 0.8109 (m-30) cc_final: 0.7690 (m-30) REVERT: m 50 TYR cc_start: 0.8744 (t80) cc_final: 0.8360 (t80) REVERT: m 75 ASP cc_start: 0.8269 (m-30) cc_final: 0.7701 (m-30) REVERT: n 3 VAL cc_start: 0.8633 (t) cc_final: 0.8276 (m) REVERT: n 53 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8857 (mmtm) REVERT: n 75 ASP cc_start: 0.8447 (m-30) cc_final: 0.8162 (m-30) REVERT: n 80 GLN cc_start: 0.8698 (tm-30) cc_final: 0.7958 (tm-30) REVERT: o 14 SER cc_start: 0.8794 (t) cc_final: 0.8282 (p) REVERT: o 37 LEU cc_start: 0.9061 (tp) cc_final: 0.8844 (tt) REVERT: o 43 ASN cc_start: 0.7603 (t0) cc_final: 0.7301 (t0) REVERT: o 75 ASP cc_start: 0.8665 (m-30) cc_final: 0.8382 (t0) REVERT: p 12 LEU cc_start: 0.9316 (mt) cc_final: 0.8991 (mt) REVERT: p 14 SER cc_start: 0.8876 (m) cc_final: 0.8574 (p) REVERT: p 75 ASP cc_start: 0.8691 (m-30) cc_final: 0.8177 (m-30) REVERT: q 14 SER cc_start: 0.9305 (m) cc_final: 0.9048 (p) REVERT: q 32 LEU cc_start: 0.8110 (tp) cc_final: 0.7692 (tp) REVERT: q 36 LYS cc_start: 0.8657 (mttt) cc_final: 0.8310 (mtmt) REVERT: s 7 ASN cc_start: 0.6850 (m-40) cc_final: 0.5856 (p0) REVERT: s 23 THR cc_start: 0.8573 (m) cc_final: 0.8131 (p) REVERT: s 27 GLN cc_start: 0.8344 (mt0) cc_final: 0.7821 (tm-30) REVERT: s 65 SER cc_start: 0.8923 (t) cc_final: 0.8604 (m) REVERT: s 69 LYS cc_start: 0.8538 (tptm) cc_final: 0.7470 (ttmt) REVERT: s 75 ASP cc_start: 0.7652 (m-30) cc_final: 0.7414 (m-30) REVERT: t 47 LEU cc_start: 0.9008 (mt) cc_final: 0.8764 (mt) REVERT: t 51 GLN cc_start: 0.8967 (tt0) cc_final: 0.7040 (mm-40) REVERT: t 69 LYS cc_start: 0.9217 (tptm) cc_final: 0.8581 (mttt) REVERT: t 72 LYS cc_start: 0.9563 (tmtt) cc_final: 0.9343 (tttm) REVERT: t 75 ASP cc_start: 0.8690 (m-30) cc_final: 0.8469 (m-30) REVERT: u 15 LEU cc_start: 0.9111 (mt) cc_final: 0.8838 (tp) REVERT: u 30 LEU cc_start: 0.8823 (tp) cc_final: 0.8487 (tt) REVERT: u 69 LYS cc_start: 0.9059 (tptm) cc_final: 0.7649 (ttmt) REVERT: u 72 LYS cc_start: 0.9097 (tmtt) cc_final: 0.8702 (tmtt) REVERT: v 27 GLN cc_start: 0.7985 (mt0) cc_final: 0.7643 (tt0) REVERT: v 32 LEU cc_start: 0.9288 (tp) cc_final: 0.8985 (tp) REVERT: v 36 LYS cc_start: 0.8973 (mttt) cc_final: 0.8616 (mttm) REVERT: v 68 VAL cc_start: 0.9417 (t) cc_final: 0.9189 (m) REVERT: v 69 LYS cc_start: 0.9037 (tptm) cc_final: 0.8244 (mttm) REVERT: w 25 THR cc_start: 0.8580 (p) cc_final: 0.8205 (p) REVERT: w 57 TYR cc_start: 0.8817 (t80) cc_final: 0.8319 (t80) REVERT: w 61 ARG cc_start: 0.8520 (mmt180) cc_final: 0.6782 (ttp-170) REVERT: w 69 LYS cc_start: 0.9218 (tppt) cc_final: 0.7743 (tppt) REVERT: w 72 LYS cc_start: 0.9166 (tmtt) cc_final: 0.8556 (tptp) REVERT: a0 103 LYS cc_start: 0.8328 (tttm) cc_final: 0.7153 (tptt) REVERT: d0 103 LYS cc_start: 0.9240 (ttmt) cc_final: 0.7913 (tptt) REVERT: e0 103 LYS cc_start: 0.8941 (ttmt) cc_final: 0.8209 (tttt) REVERT: f0 103 LYS cc_start: 0.9373 (ttmt) cc_final: 0.8327 (tptt) REVERT: g0 103 LYS cc_start: 0.8954 (mtmt) cc_final: 0.7703 (tptt) REVERT: i0 103 LYS cc_start: 0.8998 (tttt) cc_final: 0.8665 (tptt) REVERT: k0 103 LYS cc_start: 0.8760 (ttmm) cc_final: 0.8137 (tptt) REVERT: l0 103 LYS cc_start: 0.8910 (ttmt) cc_final: 0.8189 (tptt) REVERT: n0 97 SER cc_start: 0.9039 (m) cc_final: 0.8656 (p) REVERT: n0 103 LYS cc_start: 0.8977 (ttmt) cc_final: 0.8444 (ttpt) REVERT: p0 103 LYS cc_start: 0.8940 (ttpt) cc_final: 0.8181 (tptt) REVERT: q0 103 LYS cc_start: 0.9066 (ttmt) cc_final: 0.8380 (tptt) REVERT: r0 102 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8047 (mt-10) REVERT: r0 103 LYS cc_start: 0.8843 (ttmt) cc_final: 0.7606 (tptt) REVERT: t0 103 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8121 (tptt) REVERT: t0 105 ARG cc_start: 0.9178 (ttm110) cc_final: 0.8012 (tpm170) REVERT: u0 100 ARG cc_start: 0.7875 (ttm110) cc_final: 0.7386 (tpt170) REVERT: u0 103 LYS cc_start: 0.9106 (ttmt) cc_final: 0.8032 (tptt) REVERT: v0 92 THR cc_start: 0.8308 (m) cc_final: 0.8039 (m) REVERT: v0 103 LYS cc_start: 0.9303 (mttt) cc_final: 0.8025 (tptt) REVERT: w0 103 LYS cc_start: 0.8978 (ttmt) cc_final: 0.8504 (tptt) REVERT: x0 103 LYS cc_start: 0.8374 (ttmt) cc_final: 0.7710 (tptt) outliers start: 21 outliers final: 4 residues processed: 2369 average time/residue: 0.5320 time to fit residues: 2116.6935 Evaluate side-chains 1987 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1982 time to evaluate : 5.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 263 optimal weight: 2.9990 chunk 147 optimal weight: 0.0270 chunk 395 optimal weight: 0.8980 chunk 323 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 475 optimal weight: 0.9980 chunk 513 optimal weight: 0.0670 chunk 423 optimal weight: 0.8980 chunk 471 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 381 optimal weight: 0.9980 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 49 ASN E 53 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** O 44 GLN P 59 ASN R 19 GLN T 80 GLN U 80 GLN ** Z 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 127 GLN 4 137 HIS ** 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** c 64 GLN d 43 ASN ** f 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 44858 Z= 0.194 Angle : 0.605 10.620 60890 Z= 0.301 Chirality : 0.040 0.189 7369 Planarity : 0.004 0.065 7620 Dihedral : 4.218 82.619 5953 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.30 % Allowed : 2.69 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.12), residues: 5404 helix: 3.20 (0.08), residues: 4150 sheet: 1.05 (0.33), residues: 224 loop : -2.87 (0.17), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 66 HIS 0.006 0.001 HIS F 11 PHE 0.029 0.002 PHE F 28 TYR 0.027 0.002 TYR B 211 ARG 0.006 0.000 ARG C 38 *********************** 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 2315 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 2300 time to evaluate : 5.238 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: 0.8666 (p) cc_final: 0.7977 (p) REVERT: A 36 MET cc_start: 0.8889 (ttp) cc_final: 0.8478 (tpp) REVERT: A 68 ILE cc_start: 0.9539 (mt) cc_final: 0.9211 (mt) REVERT: A 69 GLU cc_start: 0.7657 (tp30) cc_final: 0.6985 (mm-30) REVERT: A 97 MET cc_start: 0.8420 (tpt) cc_final: 0.8077 (tpt) REVERT: A 101 GLN cc_start: 0.8670 (tt0) cc_final: 0.8377 (tm-30) REVERT: A 104 LYS cc_start: 0.9264 (mmmm) cc_final: 0.8997 (ttmt) REVERT: A 152 LYS cc_start: 0.9182 (tttt) cc_final: 0.8629 (ttmt) REVERT: A 158 TYR cc_start: 0.8124 (t80) cc_final: 0.7897 (t80) REVERT: A 177 MET cc_start: 0.7989 (ptp) cc_final: 0.7746 (mtt) REVERT: A 205 LYS cc_start: 0.9114 (mttt) cc_final: 0.8206 (tttt) REVERT: A 209 GLU cc_start: 0.8146 (pt0) cc_final: 0.7926 (pt0) REVERT: B 110 GLU cc_start: 0.8491 (pm20) cc_final: 0.8213 (pm20) REVERT: B 120 GLU cc_start: 0.6339 (mt-10) cc_final: 0.5678 (mp0) REVERT: B 133 TYR cc_start: 0.7009 (m-10) cc_final: 0.6784 (m-80) REVERT: C 1 MET cc_start: 0.7220 (mmm) cc_final: 0.6587 (mmm) REVERT: C 25 THR cc_start: 0.9200 (p) cc_final: 0.8852 (t) REVERT: C 29 LYS cc_start: 0.8716 (mttp) cc_final: 0.8454 (mttm) REVERT: C 105 LYS cc_start: 0.9096 (tttp) cc_final: 0.8650 (mtpt) REVERT: C 117 ARG cc_start: 0.8409 (mtt180) cc_final: 0.7894 (tpt170) REVERT: C 146 GLU cc_start: 0.8121 (tp30) cc_final: 0.7734 (tp30) REVERT: C 178 MET cc_start: 0.8271 (mmp) cc_final: 0.7977 (mmm) REVERT: D 2 LEU cc_start: 0.9206 (mt) cc_final: 0.8957 (mt) REVERT: D 6 SER cc_start: 0.8842 (m) cc_final: 0.8123 (p) REVERT: D 44 GLN cc_start: 0.8302 (pm20) cc_final: 0.8088 (pm20) REVERT: D 133 TYR cc_start: 0.8313 (m-10) cc_final: 0.7973 (m-10) REVERT: E 26 CYS cc_start: 0.8657 (p) cc_final: 0.7995 (p) REVERT: E 29 LYS cc_start: 0.9082 (tttm) cc_final: 0.8860 (ttpt) REVERT: E 36 MET cc_start: 0.8768 (tpp) cc_final: 0.8369 (tpp) REVERT: E 44 GLN cc_start: 0.8402 (mm-40) cc_final: 0.8173 (mp10) REVERT: E 59 MET cc_start: 0.8444 (mtp) cc_final: 0.8150 (mtm) REVERT: E 64 MET cc_start: 0.8671 (mmm) cc_final: 0.7661 (mmm) REVERT: E 179 MET cc_start: 0.8640 (mmp) cc_final: 0.8409 (mmp) REVERT: E 184 THR cc_start: 0.9263 (p) cc_final: 0.8804 (t) REVERT: F 101 SER cc_start: 0.9309 (m) cc_final: 0.8977 (t) REVERT: F 133 PHE cc_start: 0.8866 (t80) cc_final: 0.8460 (t80) REVERT: F 152 GLN cc_start: 0.9127 (tt0) cc_final: 0.8533 (tp40) REVERT: F 170 ASN cc_start: 0.8301 (m-40) cc_final: 0.8055 (m-40) REVERT: G 5 VAL cc_start: 0.9206 (p) cc_final: 0.8881 (p) REVERT: G 57 SER cc_start: 0.9183 (t) cc_final: 0.8928 (p) REVERT: G 75 CYS cc_start: 0.8553 (m) cc_final: 0.8273 (m) REVERT: G 79 MET cc_start: 0.8630 (mmm) cc_final: 0.7780 (mmm) REVERT: H 83 LYS cc_start: 0.9004 (tptt) cc_final: 0.8709 (tppp) REVERT: I 1 MET cc_start: 0.7408 (ptp) cc_final: 0.7168 (ptp) REVERT: I 5 VAL cc_start: 0.9102 (t) cc_final: 0.8556 (p) REVERT: I 18 PHE cc_start: 0.8275 (m-80) cc_final: 0.7716 (m-80) REVERT: I 53 LEU cc_start: 0.8044 (tp) cc_final: 0.7812 (tp) REVERT: I 60 LEU cc_start: 0.8557 (mt) cc_final: 0.8350 (mt) REVERT: J 53 LEU cc_start: 0.8918 (tp) cc_final: 0.8522 (tt) REVERT: J 57 SER cc_start: 0.8582 (t) cc_final: 0.8377 (p) REVERT: K 32 VAL cc_start: 0.6805 (t) cc_final: 0.6601 (t) REVERT: K 51 MET cc_start: 0.7682 (mmt) cc_final: 0.6630 (mmt) REVERT: K 132 LYS cc_start: 0.8585 (mmtp) cc_final: 0.8159 (mttt) REVERT: K 140 LEU cc_start: 0.9128 (tp) cc_final: 0.8864 (tt) REVERT: N 58 LEU cc_start: 0.9233 (mt) cc_final: 0.8877 (mt) REVERT: N 92 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7300 (tm-30) REVERT: P 12 ILE cc_start: 0.8622 (mt) cc_final: 0.8147 (mt) REVERT: P 56 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7175 (tm-30) REVERT: P 57 SER cc_start: 0.9159 (m) cc_final: 0.8612 (p) REVERT: Q 13 ILE cc_start: 0.7727 (mt) cc_final: 0.7473 (mt) REVERT: S 45 GLN cc_start: 0.8835 (tp40) cc_final: 0.8331 (tp-100) REVERT: U 43 ASN cc_start: 0.8678 (t0) cc_final: 0.8395 (t0) REVERT: U 46 LEU cc_start: 0.9049 (mp) cc_final: 0.8327 (tt) REVERT: V 32 LEU cc_start: 0.8631 (mt) cc_final: 0.8301 (tt) REVERT: V 64 GLN cc_start: 0.8563 (tt0) cc_final: 0.8306 (tt0) REVERT: V 73 ASP cc_start: 0.8811 (t0) cc_final: 0.8587 (t0) REVERT: W 39 LYS cc_start: 0.8287 (mttt) cc_final: 0.7752 (mptt) REVERT: W 43 ASN cc_start: 0.8623 (t0) cc_final: 0.8126 (t0) REVERT: X 142 ARG cc_start: 0.8663 (mmt-90) cc_final: 0.8159 (mmt-90) REVERT: Y 112 SER cc_start: 0.7638 (p) cc_final: 0.7362 (m) REVERT: Y 123 ASN cc_start: 0.8786 (t0) cc_final: 0.8484 (t0) REVERT: Y 127 GLN cc_start: 0.7774 (tm-30) cc_final: 0.7334 (tm-30) REVERT: Y 131 ASP cc_start: 0.7629 (m-30) cc_final: 0.7321 (m-30) REVERT: Z 158 LEU cc_start: 0.8924 (tt) cc_final: 0.8611 (mm) REVERT: Z 161 LEU cc_start: 0.8630 (tp) cc_final: 0.8385 (tp) REVERT: 0 133 ASN cc_start: 0.7912 (m-40) cc_final: 0.7670 (m-40) REVERT: 4 127 GLN cc_start: 0.7970 (tp40) cc_final: 0.7669 (tp-100) REVERT: 4 133 ASN cc_start: 0.8285 (t0) cc_final: 0.8026 (t0) REVERT: 4 150 PHE cc_start: 0.9099 (p90) cc_final: 0.8576 (p90) REVERT: 4 151 TYR cc_start: 0.8399 (t80) cc_final: 0.7593 (t80) REVERT: 4 167 THR cc_start: 0.8797 (m) cc_final: 0.8572 (t) REVERT: 6 127 GLN cc_start: 0.8962 (tp40) cc_final: 0.8351 (tp40) REVERT: 6 138 ARG cc_start: 0.8388 (mtp85) cc_final: 0.7516 (mtm110) REVERT: 6 149 THR cc_start: 0.9026 (m) cc_final: 0.8010 (p) REVERT: 8 111 ILE cc_start: 0.9294 (mt) cc_final: 0.9087 (mt) REVERT: 8 115 ILE cc_start: 0.8953 (mt) cc_final: 0.8674 (mm) REVERT: 8 144 ASN cc_start: 0.7878 (t0) cc_final: 0.7515 (t0) REVERT: x 112 SER cc_start: 0.8660 (p) cc_final: 0.8422 (m) REVERT: x 149 THR cc_start: 0.9405 (t) cc_final: 0.8913 (p) REVERT: x 150 PHE cc_start: 0.9360 (p90) cc_final: 0.8619 (p90) REVERT: x 153 SER cc_start: 0.9337 (t) cc_final: 0.9032 (p) REVERT: x 158 LEU cc_start: 0.8450 (tp) cc_final: 0.8126 (mm) REVERT: y 115 ILE cc_start: 0.9386 (mt) cc_final: 0.9146 (mt) REVERT: y 158 LEU cc_start: 0.8200 (tp) cc_final: 0.7865 (mm) REVERT: y 160 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7859 (mm-30) REVERT: y 164 ASN cc_start: 0.8601 (m-40) cc_final: 0.8308 (m-40) REVERT: z 112 SER cc_start: 0.9163 (p) cc_final: 0.8750 (m) REVERT: z 119 ASN cc_start: 0.8687 (m-40) cc_final: 0.8341 (m-40) REVERT: z 127 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7657 (tm-30) REVERT: z 149 THR cc_start: 0.9025 (m) cc_final: 0.8667 (t) REVERT: z 151 TYR cc_start: 0.8628 (t80) cc_final: 0.8379 (t80) REVERT: 1 133 ASN cc_start: 0.8650 (m-40) cc_final: 0.8263 (t0) REVERT: 1 148 LYS cc_start: 0.8375 (mtpt) cc_final: 0.8039 (mtpp) REVERT: 3 115 ILE cc_start: 0.8648 (mt) cc_final: 0.8138 (mt) REVERT: 5 112 SER cc_start: 0.8270 (p) cc_final: 0.8043 (m) REVERT: 9 135 TYR cc_start: 0.7556 (t80) cc_final: 0.7000 (t80) REVERT: a 26 LEU cc_start: 0.8970 (tp) cc_final: 0.8472 (tp) REVERT: a 66 ASN cc_start: 0.8999 (m-40) cc_final: 0.8668 (m110) REVERT: a 72 LYS cc_start: 0.9547 (tmtt) cc_final: 0.9146 (tptp) REVERT: b 43 ASN cc_start: 0.8446 (t0) cc_final: 0.8206 (t0) REVERT: b 45 GLN cc_start: 0.9070 (tp40) cc_final: 0.8150 (tm-30) REVERT: b 49 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7162 (mm-30) REVERT: b 64 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7721 (tm-30) REVERT: b 65 SER cc_start: 0.9191 (m) cc_final: 0.8597 (t) REVERT: c 9 ASP cc_start: 0.8385 (t0) cc_final: 0.7952 (t0) REVERT: c 82 PHE cc_start: 0.8772 (m-10) cc_final: 0.8525 (m-10) REVERT: d 20 ASP cc_start: 0.8140 (m-30) cc_final: 0.7851 (m-30) REVERT: d 50 TYR cc_start: 0.9035 (t80) cc_final: 0.8817 (t80) REVERT: d 57 TYR cc_start: 0.9044 (t80) cc_final: 0.8630 (t80) REVERT: d 71 ILE cc_start: 0.8790 (mm) cc_final: 0.8394 (mm) REVERT: d 75 ASP cc_start: 0.8371 (m-30) cc_final: 0.8044 (m-30) REVERT: f 17 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6686 (tm-30) REVERT: f 80 GLN cc_start: 0.8452 (tm130) cc_final: 0.8068 (tm-30) REVERT: g 25 THR cc_start: 0.8250 (p) cc_final: 0.7999 (p) REVERT: g 37 LEU cc_start: 0.8861 (tp) cc_final: 0.8559 (tp) REVERT: g 50 TYR cc_start: 0.8974 (t80) cc_final: 0.8767 (t80) REVERT: g 54 LEU cc_start: 0.9182 (tp) cc_final: 0.8970 (tp) REVERT: g 72 LYS cc_start: 0.9344 (tmtt) cc_final: 0.9108 (tptm) REVERT: g 79 ILE cc_start: 0.9193 (mm) cc_final: 0.8770 (mm) REVERT: g 80 GLN cc_start: 0.8618 (tp-100) cc_final: 0.8336 (tm-30) REVERT: h 11 THR cc_start: 0.8825 (m) cc_final: 0.7984 (m) REVERT: h 19 PHE cc_start: 0.7333 (t80) cc_final: 0.7025 (t80) REVERT: h 75 ASP cc_start: 0.8230 (t0) cc_final: 0.8017 (t0) REVERT: i 47 LEU cc_start: 0.9329 (mt) cc_final: 0.9127 (mt) REVERT: i 80 GLN cc_start: 0.8281 (tm-30) cc_final: 0.8046 (tm-30) REVERT: i 81 ASN cc_start: 0.9102 (m-40) cc_final: 0.8880 (m-40) REVERT: j 14 SER cc_start: 0.8924 (m) cc_final: 0.8255 (t) REVERT: k 13 SER cc_start: 0.8781 (p) cc_final: 0.8400 (t) REVERT: k 37 LEU cc_start: 0.9025 (tp) cc_final: 0.8714 (tt) REVERT: k 50 TYR cc_start: 0.9235 (t80) cc_final: 0.9003 (t80) REVERT: l 20 ASP cc_start: 0.7661 (m-30) cc_final: 0.7267 (m-30) REVERT: l 25 THR cc_start: 0.8926 (p) cc_final: 0.8328 (p) REVERT: l 43 ASN cc_start: 0.8552 (t0) cc_final: 0.8252 (t0) REVERT: l 45 GLN cc_start: 0.8016 (tp40) cc_final: 0.7568 (tp40) REVERT: l 50 TYR cc_start: 0.9212 (t80) cc_final: 0.8828 (t80) REVERT: m 20 ASP cc_start: 0.7972 (m-30) cc_final: 0.7615 (m-30) REVERT: m 24 GLN cc_start: 0.8839 (tp40) cc_final: 0.8396 (tp40) REVERT: m 50 TYR cc_start: 0.8759 (t80) cc_final: 0.8338 (t80) REVERT: m 75 ASP cc_start: 0.8244 (m-30) cc_final: 0.7502 (m-30) REVERT: n 3 VAL cc_start: 0.8607 (t) cc_final: 0.8303 (m) REVERT: n 29 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7179 (tm-30) REVERT: n 53 LYS cc_start: 0.8971 (mmtt) cc_final: 0.8133 (mmtm) REVERT: n 75 ASP cc_start: 0.8421 (m-30) cc_final: 0.8050 (m-30) REVERT: n 80 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8036 (tm-30) REVERT: o 14 SER cc_start: 0.8813 (t) cc_final: 0.8353 (p) REVERT: o 43 ASN cc_start: 0.7490 (t0) cc_final: 0.7238 (t0) REVERT: o 50 TYR cc_start: 0.9233 (t80) cc_final: 0.8965 (t80) REVERT: o 72 LYS cc_start: 0.9437 (tmtt) cc_final: 0.8991 (tmtt) REVERT: p 12 LEU cc_start: 0.9339 (mt) cc_final: 0.9054 (mt) REVERT: p 25 THR cc_start: 0.8389 (p) cc_final: 0.7832 (t) REVERT: p 46 LEU cc_start: 0.9327 (tp) cc_final: 0.9077 (tt) REVERT: p 75 ASP cc_start: 0.8633 (m-30) cc_final: 0.7897 (m-30) REVERT: q 14 SER cc_start: 0.9292 (m) cc_final: 0.9005 (p) REVERT: q 23 THR cc_start: 0.9189 (t) cc_final: 0.8975 (m) REVERT: q 32 LEU cc_start: 0.8123 (tp) cc_final: 0.7760 (tp) REVERT: q 36 LYS cc_start: 0.8623 (mttt) cc_final: 0.8269 (mtmt) REVERT: r 59 LEU cc_start: 0.8848 (mt) cc_final: 0.8598 (mt) REVERT: s 7 ASN cc_start: 0.6781 (m-40) cc_final: 0.5818 (p0) REVERT: s 23 THR cc_start: 0.8616 (m) cc_final: 0.8331 (m) REVERT: s 24 GLN cc_start: 0.8253 (tp40) cc_final: 0.7910 (mm-40) REVERT: s 27 GLN cc_start: 0.8435 (mt0) cc_final: 0.8000 (tm-30) REVERT: s 65 SER cc_start: 0.8936 (t) cc_final: 0.8624 (m) REVERT: s 69 LYS cc_start: 0.8537 (tptm) cc_final: 0.7475 (ttmt) REVERT: t 26 LEU cc_start: 0.7848 (mt) cc_final: 0.7504 (mt) REVERT: t 47 LEU cc_start: 0.8969 (mt) cc_final: 0.8740 (mt) REVERT: t 51 GLN cc_start: 0.8715 (tt0) cc_final: 0.6581 (mm-40) REVERT: t 69 LYS cc_start: 0.9197 (tptm) cc_final: 0.8596 (mttt) REVERT: t 72 LYS cc_start: 0.9549 (tmtt) cc_final: 0.9346 (tttm) REVERT: t 75 ASP cc_start: 0.8587 (m-30) cc_final: 0.8354 (m-30) REVERT: u 15 LEU cc_start: 0.9081 (mt) cc_final: 0.8871 (tp) REVERT: u 30 LEU cc_start: 0.8794 (tp) cc_final: 0.8475 (tt) REVERT: u 49 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7124 (tp30) REVERT: u 69 LYS cc_start: 0.9024 (tptm) cc_final: 0.7672 (ttmt) REVERT: u 72 LYS cc_start: 0.9095 (tmtt) cc_final: 0.8556 (tmtt) REVERT: u 75 ASP cc_start: 0.8992 (m-30) cc_final: 0.8295 (m-30) REVERT: v 32 LEU cc_start: 0.9262 (tp) cc_final: 0.8957 (tp) REVERT: v 36 LYS cc_start: 0.9038 (mttt) cc_final: 0.8673 (mttp) REVERT: v 69 LYS cc_start: 0.9048 (tptm) cc_final: 0.8221 (mttm) REVERT: w 25 THR cc_start: 0.8605 (p) cc_final: 0.8253 (p) REVERT: w 57 TYR cc_start: 0.8836 (t80) cc_final: 0.8336 (t80) REVERT: w 61 ARG cc_start: 0.8433 (mmt180) cc_final: 0.6891 (ttp-170) REVERT: a0 103 LYS cc_start: 0.8179 (tttm) cc_final: 0.7090 (tptt) REVERT: b0 96 VAL cc_start: 0.8222 (t) cc_final: 0.7924 (t) REVERT: d0 103 LYS cc_start: 0.9260 (ttmt) cc_final: 0.7893 (tptt) REVERT: e0 103 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8159 (tttt) REVERT: f0 103 LYS cc_start: 0.9262 (ttmt) cc_final: 0.8379 (tptt) REVERT: g0 100 ARG cc_start: 0.8529 (ttm170) cc_final: 0.8281 (ttm170) REVERT: g0 103 LYS cc_start: 0.8973 (mtmt) cc_final: 0.7658 (tptt) REVERT: i0 103 LYS cc_start: 0.8935 (tttt) cc_final: 0.8632 (tptt) REVERT: k0 103 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8136 (tptt) REVERT: l0 103 LYS cc_start: 0.8915 (ttmt) cc_final: 0.8186 (tptt) REVERT: n0 97 SER cc_start: 0.9074 (m) cc_final: 0.8613 (p) REVERT: n0 103 LYS cc_start: 0.8923 (ttmt) cc_final: 0.8377 (ttpt) REVERT: p0 103 LYS cc_start: 0.8865 (ttpt) cc_final: 0.8069 (tptt) REVERT: q0 103 LYS cc_start: 0.9058 (ttmt) cc_final: 0.8359 (tptt) REVERT: r0 102 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8120 (mt-10) REVERT: r0 103 LYS cc_start: 0.8820 (ttmt) cc_final: 0.7555 (tptt) REVERT: t0 103 LYS cc_start: 0.8873 (ttmt) cc_final: 0.8104 (tptt) REVERT: t0 105 ARG cc_start: 0.9158 (ttm110) cc_final: 0.7995 (tpm170) REVERT: u0 100 ARG cc_start: 0.7835 (ttm110) cc_final: 0.7348 (tpt170) REVERT: u0 103 LYS cc_start: 0.9092 (ttmt) cc_final: 0.8019 (tptt) REVERT: v0 92 THR cc_start: 0.7984 (m) cc_final: 0.7748 (m) REVERT: v0 103 LYS cc_start: 0.9290 (mttt) cc_final: 0.7873 (tptt) REVERT: w0 103 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8450 (tptt) REVERT: x0 103 LYS cc_start: 0.8449 (ttmt) cc_final: 0.7748 (tptt) outliers start: 15 outliers final: 1 residues processed: 2303 average time/residue: 0.5694 time to fit residues: 2227.2772 Evaluate side-chains 1967 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1966 time to evaluate : 4.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 470 optimal weight: 0.8980 chunk 357 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 52 optimal weight: 0.2980 chunk 227 optimal weight: 0.9990 chunk 319 optimal weight: 3.9990 chunk 477 optimal weight: 0.6980 chunk 505 optimal weight: 0.7980 chunk 249 optimal weight: 1.9990 chunk 452 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** 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 T 80 GLN U 80 GLN U 81 ASN V 40 ASN ** X 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 137 HIS 4 137 HIS ** 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 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 64 GLN f 40 ASN f 43 ASN h 66 ASN i 40 ASN i 43 ASN m 27 GLN n 81 ASN p 80 GLN q 81 ASN r 27 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 44858 Z= 0.208 Angle : 0.610 11.067 60890 Z= 0.303 Chirality : 0.040 0.193 7369 Planarity : 0.004 0.068 7620 Dihedral : 4.232 83.181 5953 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.20 % Allowed : 2.31 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.12), residues: 5404 helix: 3.14 (0.08), residues: 4155 sheet: 1.11 (0.32), residues: 224 loop : -2.88 (0.17), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 66 HIS 0.007 0.001 HIS F 11 PHE 0.026 0.002 PHE c 19 TYR 0.028 0.001 TYR C 211 ARG 0.004 0.000 ARGv0 100 *********************** 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 2243 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 2233 time to evaluate : 5.084 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: 0.8670 (p) cc_final: 0.7949 (p) REVERT: A 36 MET cc_start: 0.8866 (ttp) cc_final: 0.8457 (tpp) REVERT: A 48 SER cc_start: 0.8936 (t) cc_final: 0.8559 (p) REVERT: A 50 MET cc_start: 0.8167 (ttp) cc_final: 0.7876 (ttm) REVERT: A 68 ILE cc_start: 0.9547 (mt) cc_final: 0.9203 (mt) REVERT: A 69 GLU cc_start: 0.7720 (tp30) cc_final: 0.7201 (mm-30) REVERT: A 97 MET cc_start: 0.8391 (tpt) cc_final: 0.7961 (tpt) REVERT: A 101 GLN cc_start: 0.8716 (tt0) cc_final: 0.8381 (tm-30) REVERT: A 104 LYS cc_start: 0.9267 (mmmm) cc_final: 0.8906 (ttmt) REVERT: A 152 LYS cc_start: 0.9165 (tttt) cc_final: 0.8654 (ttmt) REVERT: A 177 MET cc_start: 0.7961 (ptp) cc_final: 0.7643 (mtt) REVERT: A 205 LYS cc_start: 0.9046 (mttt) cc_final: 0.8140 (tttt) REVERT: A 209 GLU cc_start: 0.8011 (pt0) cc_final: 0.7697 (pt0) REVERT: B 65 LYS cc_start: 0.8556 (tttp) cc_final: 0.7976 (tttt) REVERT: C 1 MET cc_start: 0.6917 (mmm) cc_final: 0.6703 (mmm) REVERT: C 25 THR cc_start: 0.9161 (p) cc_final: 0.8683 (t) REVERT: C 29 LYS cc_start: 0.8864 (mttp) cc_final: 0.8536 (mttm) REVERT: C 105 LYS cc_start: 0.9053 (tttp) cc_final: 0.8648 (mtpt) REVERT: C 117 ARG cc_start: 0.8332 (mtt180) cc_final: 0.7866 (tpt170) REVERT: C 119 GLU cc_start: 0.8280 (tp30) cc_final: 0.7858 (tp30) REVERT: C 178 MET cc_start: 0.8403 (mmp) cc_final: 0.8173 (mmm) REVERT: C 180 MET cc_start: 0.7677 (mmm) cc_final: 0.7221 (tpp) REVERT: D 2 LEU cc_start: 0.9202 (mt) cc_final: 0.8925 (mt) REVERT: D 6 SER cc_start: 0.8833 (m) cc_final: 0.8028 (p) REVERT: D 27 TYR cc_start: 0.9112 (t80) cc_final: 0.8816 (t80) REVERT: E 36 MET cc_start: 0.8713 (tpp) cc_final: 0.8268 (tpp) REVERT: E 44 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8210 (mp10) REVERT: E 64 MET cc_start: 0.8646 (mmm) cc_final: 0.7606 (mmm) REVERT: F 101 SER cc_start: 0.9231 (m) cc_final: 0.8944 (t) REVERT: F 104 ASP cc_start: 0.8238 (t0) cc_final: 0.7979 (t0) REVERT: F 128 LYS cc_start: 0.8688 (ttpt) cc_final: 0.8477 (ttpt) REVERT: F 133 PHE cc_start: 0.8897 (t80) cc_final: 0.8444 (t80) REVERT: F 152 GLN cc_start: 0.9101 (tt0) cc_final: 0.8548 (tp40) REVERT: F 202 VAL cc_start: 0.9097 (t) cc_final: 0.8856 (t) REVERT: G 7 MET cc_start: 0.8537 (tpp) cc_final: 0.8227 (tpp) REVERT: G 57 SER cc_start: 0.9244 (t) cc_final: 0.8946 (p) REVERT: G 73 SER cc_start: 0.8957 (p) cc_final: 0.8646 (p) REVERT: G 79 MET cc_start: 0.8539 (mmm) cc_final: 0.8011 (mmm) REVERT: H 77 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7830 (tm-30) REVERT: H 79 MET cc_start: 0.7998 (mmp) cc_final: 0.7463 (mmp) REVERT: I 1 MET cc_start: 0.7309 (ptp) cc_final: 0.7029 (ptp) REVERT: I 5 VAL cc_start: 0.8855 (t) cc_final: 0.8617 (p) REVERT: I 18 PHE cc_start: 0.8298 (m-80) cc_final: 0.7679 (m-80) REVERT: I 53 LEU cc_start: 0.7948 (tp) cc_final: 0.7619 (tp) REVERT: I 60 LEU cc_start: 0.8529 (mt) cc_final: 0.8293 (mt) REVERT: K 32 VAL cc_start: 0.6822 (t) cc_final: 0.6590 (t) REVERT: K 51 MET cc_start: 0.7572 (mmt) cc_final: 0.7192 (mmt) REVERT: K 132 LYS cc_start: 0.8621 (mmtp) cc_final: 0.8205 (mttt) REVERT: K 140 LEU cc_start: 0.9106 (tp) cc_final: 0.8871 (tt) REVERT: N 58 LEU cc_start: 0.9222 (mt) cc_final: 0.8854 (mt) REVERT: N 89 SER cc_start: 0.9266 (t) cc_final: 0.8921 (p) REVERT: N 92 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7421 (tm-30) REVERT: P 46 SER cc_start: 0.9554 (m) cc_final: 0.9308 (t) REVERT: P 54 ASN cc_start: 0.8835 (t0) cc_final: 0.8568 (t0) REVERT: P 56 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7084 (tm-30) REVERT: P 57 SER cc_start: 0.9084 (m) cc_final: 0.8537 (p) REVERT: Q 13 ILE cc_start: 0.7711 (mt) cc_final: 0.7456 (mt) REVERT: R 27 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6872 (pt0) REVERT: R 50 GLU cc_start: 0.8127 (tp30) cc_final: 0.7851 (tm-30) REVERT: S 25 THR cc_start: 0.7818 (t) cc_final: 0.7617 (t) REVERT: S 37 LEU cc_start: 0.9111 (tp) cc_final: 0.8710 (tp) REVERT: T 30 LEU cc_start: 0.9152 (tp) cc_final: 0.8888 (tp) REVERT: T 50 TYR cc_start: 0.9152 (t80) cc_final: 0.8926 (t80) REVERT: T 56 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7663 (tt0) REVERT: U 81 ASN cc_start: 0.9080 (m-40) cc_final: 0.8747 (m110) REVERT: V 32 LEU cc_start: 0.8645 (mt) cc_final: 0.8297 (tt) REVERT: V 64 GLN cc_start: 0.8545 (tt0) cc_final: 0.8332 (tt0) REVERT: V 73 ASP cc_start: 0.8849 (t0) cc_final: 0.8620 (t0) REVERT: W 34 LEU cc_start: 0.9199 (tt) cc_final: 0.8931 (tt) REVERT: W 39 LYS cc_start: 0.8249 (mttt) cc_final: 0.7663 (mptt) REVERT: W 43 ASN cc_start: 0.8682 (t0) cc_final: 0.8014 (t0) REVERT: X 142 ARG cc_start: 0.8580 (mmt-90) cc_final: 0.8137 (mmt-90) REVERT: Y 112 SER cc_start: 0.7674 (p) cc_final: 0.7326 (m) REVERT: Y 123 ASN cc_start: 0.8737 (t0) cc_final: 0.8462 (t0) REVERT: Y 127 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7613 (tm-30) REVERT: Y 131 ASP cc_start: 0.7658 (m-30) cc_final: 0.7349 (m-30) REVERT: Y 144 ASN cc_start: 0.7294 (m-40) cc_final: 0.6036 (m110) REVERT: Z 117 LEU cc_start: 0.7893 (pp) cc_final: 0.7640 (mt) REVERT: Z 133 ASN cc_start: 0.9268 (t0) cc_final: 0.8939 (t0) REVERT: Z 161 LEU cc_start: 0.8612 (tp) cc_final: 0.8373 (tp) REVERT: 2 127 GLN cc_start: 0.8043 (tp40) cc_final: 0.7753 (tp40) REVERT: 4 133 ASN cc_start: 0.8316 (t0) cc_final: 0.7954 (t0) REVERT: 4 150 PHE cc_start: 0.9083 (p90) cc_final: 0.8576 (p90) REVERT: 4 151 TYR cc_start: 0.8380 (t80) cc_final: 0.8151 (t80) REVERT: 4 167 THR cc_start: 0.8784 (m) cc_final: 0.8538 (t) REVERT: 6 127 GLN cc_start: 0.8941 (tp40) cc_final: 0.8344 (tp40) REVERT: 6 138 ARG cc_start: 0.8440 (mtp85) cc_final: 0.7620 (mtm110) REVERT: 6 149 THR cc_start: 0.8814 (m) cc_final: 0.8090 (p) REVERT: 8 111 ILE cc_start: 0.9341 (mt) cc_final: 0.9134 (mt) REVERT: 8 115 ILE cc_start: 0.8922 (mt) cc_final: 0.8631 (mm) REVERT: 8 144 ASN cc_start: 0.7950 (t0) cc_final: 0.7532 (t0) REVERT: x 112 SER cc_start: 0.8663 (p) cc_final: 0.8453 (m) REVERT: x 150 PHE cc_start: 0.9339 (p90) cc_final: 0.8608 (p90) REVERT: x 153 SER cc_start: 0.9400 (t) cc_final: 0.9163 (p) REVERT: y 115 ILE cc_start: 0.9392 (mt) cc_final: 0.9175 (mt) REVERT: y 158 LEU cc_start: 0.8224 (tp) cc_final: 0.7900 (mm) REVERT: y 160 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7774 (mm-30) REVERT: y 164 ASN cc_start: 0.8631 (m-40) cc_final: 0.8389 (m-40) REVERT: z 112 SER cc_start: 0.9145 (p) cc_final: 0.8837 (m) REVERT: z 119 ASN cc_start: 0.8832 (m-40) cc_final: 0.8490 (p0) REVERT: z 127 GLN cc_start: 0.8330 (tm-30) cc_final: 0.7760 (tm-30) REVERT: z 149 THR cc_start: 0.9011 (m) cc_final: 0.8668 (t) REVERT: 1 133 ASN cc_start: 0.8589 (m-40) cc_final: 0.8307 (t0) REVERT: 1 148 LYS cc_start: 0.8425 (mtpt) cc_final: 0.8109 (mtpp) REVERT: 1 170 ASP cc_start: 0.7224 (m-30) cc_final: 0.6181 (m-30) REVERT: 3 115 ILE cc_start: 0.8586 (mt) cc_final: 0.7980 (mt) REVERT: 5 112 SER cc_start: 0.8243 (p) cc_final: 0.8031 (m) REVERT: 9 135 TYR cc_start: 0.7578 (t80) cc_final: 0.7034 (t80) REVERT: a 26 LEU cc_start: 0.8944 (tp) cc_final: 0.8482 (tp) REVERT: a 31 THR cc_start: 0.7921 (m) cc_final: 0.7574 (m) REVERT: a 66 ASN cc_start: 0.9056 (m-40) cc_final: 0.8812 (m110) REVERT: a 72 LYS cc_start: 0.9582 (tmtt) cc_final: 0.9115 (tptp) REVERT: b 43 ASN cc_start: 0.8524 (t0) cc_final: 0.8231 (t0) REVERT: b 45 GLN cc_start: 0.8996 (tp40) cc_final: 0.7993 (tm-30) REVERT: b 49 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7272 (mm-30) REVERT: b 59 LEU cc_start: 0.9425 (mp) cc_final: 0.9115 (mm) REVERT: b 64 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7624 (tm-30) REVERT: b 65 SER cc_start: 0.9199 (m) cc_final: 0.8635 (t) REVERT: b 75 ASP cc_start: 0.8737 (t0) cc_final: 0.8294 (t0) REVERT: c 9 ASP cc_start: 0.8160 (t0) cc_final: 0.7888 (t0) REVERT: c 20 ASP cc_start: 0.8222 (t0) cc_final: 0.7953 (t0) REVERT: c 82 PHE cc_start: 0.8782 (m-10) cc_final: 0.8543 (m-10) REVERT: d 20 ASP cc_start: 0.8162 (m-30) cc_final: 0.7934 (m-30) REVERT: d 57 TYR cc_start: 0.8989 (t80) cc_final: 0.8420 (t80) REVERT: d 71 ILE cc_start: 0.8750 (mm) cc_final: 0.8363 (mm) REVERT: d 75 ASP cc_start: 0.8349 (m-30) cc_final: 0.7993 (m-30) REVERT: e 56 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8305 (tt0) REVERT: f 17 GLU cc_start: 0.7310 (tm-30) cc_final: 0.6756 (tm-30) REVERT: f 20 ASP cc_start: 0.8360 (t70) cc_final: 0.8117 (t70) REVERT: f 80 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8134 (tm-30) REVERT: g 25 THR cc_start: 0.8222 (p) cc_final: 0.7996 (p) REVERT: g 54 LEU cc_start: 0.9252 (tp) cc_final: 0.9007 (tp) REVERT: g 59 LEU cc_start: 0.9489 (mt) cc_final: 0.9275 (mt) REVERT: g 79 ILE cc_start: 0.9160 (mm) cc_final: 0.8750 (mm) REVERT: g 80 GLN cc_start: 0.8642 (tp-100) cc_final: 0.8339 (tm-30) REVERT: h 19 PHE cc_start: 0.7533 (t80) cc_final: 0.6894 (t80) REVERT: h 59 LEU cc_start: 0.9219 (mt) cc_final: 0.8973 (mt) REVERT: i 80 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8140 (tm-30) REVERT: i 81 ASN cc_start: 0.9169 (m-40) cc_final: 0.8894 (m-40) REVERT: j 14 SER cc_start: 0.8953 (m) cc_final: 0.8355 (t) REVERT: j 80 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8631 (tp40) REVERT: k 50 TYR cc_start: 0.9207 (t80) cc_final: 0.9004 (t80) REVERT: l 16 SER cc_start: 0.9086 (m) cc_final: 0.8191 (t) REVERT: l 20 ASP cc_start: 0.7534 (m-30) cc_final: 0.7177 (m-30) REVERT: l 25 THR cc_start: 0.8878 (p) cc_final: 0.8218 (p) REVERT: l 26 LEU cc_start: 0.9214 (tt) cc_final: 0.8981 (tt) REVERT: l 43 ASN cc_start: 0.8739 (t0) cc_final: 0.8524 (t0) REVERT: l 45 GLN cc_start: 0.8247 (tp40) cc_final: 0.7528 (tp40) REVERT: l 50 TYR cc_start: 0.9219 (t80) cc_final: 0.8823 (t80) REVERT: m 20 ASP cc_start: 0.8174 (m-30) cc_final: 0.7717 (m-30) REVERT: m 24 GLN cc_start: 0.9029 (tp40) cc_final: 0.8762 (tp40) REVERT: m 27 GLN cc_start: 0.7942 (pt0) cc_final: 0.7334 (pt0) REVERT: m 50 TYR cc_start: 0.8784 (t80) cc_final: 0.8422 (t80) REVERT: m 75 ASP cc_start: 0.8410 (m-30) cc_final: 0.7638 (m-30) REVERT: n 3 VAL cc_start: 0.8592 (t) cc_final: 0.8307 (m) REVERT: n 23 THR cc_start: 0.8736 (t) cc_final: 0.8522 (m) REVERT: n 29 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7185 (tm-30) REVERT: n 53 LYS cc_start: 0.9003 (mmtt) cc_final: 0.8356 (mmtm) REVERT: n 75 ASP cc_start: 0.8461 (m-30) cc_final: 0.8119 (m-30) REVERT: n 80 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8031 (tm-30) REVERT: o 14 SER cc_start: 0.8774 (t) cc_final: 0.8312 (p) REVERT: o 24 GLN cc_start: 0.8852 (tp40) cc_final: 0.8624 (mm110) REVERT: o 29 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7442 (mt-10) REVERT: o 50 TYR cc_start: 0.9222 (t80) cc_final: 0.8805 (t80) REVERT: p 12 LEU cc_start: 0.9393 (mt) cc_final: 0.9085 (mt) REVERT: p 25 THR cc_start: 0.8423 (p) cc_final: 0.7779 (t) REVERT: p 75 ASP cc_start: 0.8601 (m-30) cc_final: 0.7969 (m-30) REVERT: q 12 LEU cc_start: 0.9443 (mt) cc_final: 0.9216 (mt) REVERT: q 14 SER cc_start: 0.9328 (m) cc_final: 0.9112 (p) REVERT: q 32 LEU cc_start: 0.8154 (tp) cc_final: 0.7757 (tp) REVERT: q 36 LYS cc_start: 0.8660 (mttt) cc_final: 0.8364 (mtmt) REVERT: r 27 GLN cc_start: 0.8761 (mt0) cc_final: 0.8508 (mt0) REVERT: r 59 LEU cc_start: 0.8871 (mt) cc_final: 0.8586 (mt) REVERT: s 7 ASN cc_start: 0.6697 (m-40) cc_final: 0.5682 (p0) REVERT: s 23 THR cc_start: 0.8600 (m) cc_final: 0.8344 (m) REVERT: s 24 GLN cc_start: 0.8206 (tp40) cc_final: 0.7784 (mm-40) REVERT: s 27 GLN cc_start: 0.8453 (mt0) cc_final: 0.8004 (tm-30) REVERT: s 65 SER cc_start: 0.8962 (t) cc_final: 0.8653 (m) REVERT: s 69 LYS cc_start: 0.7823 (tptm) cc_final: 0.7407 (ttmt) REVERT: t 49 GLU cc_start: 0.7606 (tp30) cc_final: 0.7395 (tp30) REVERT: t 67 THR cc_start: 0.9502 (t) cc_final: 0.9275 (t) REVERT: t 69 LYS cc_start: 0.9209 (tptm) cc_final: 0.8556 (mttt) REVERT: t 72 LYS cc_start: 0.9536 (tmtt) cc_final: 0.9216 (tttp) REVERT: t 75 ASP cc_start: 0.8621 (m-30) cc_final: 0.8375 (m-30) REVERT: u 30 LEU cc_start: 0.8907 (tp) cc_final: 0.8601 (tt) REVERT: u 69 LYS cc_start: 0.9019 (tptm) cc_final: 0.7619 (ttmt) REVERT: u 75 ASP cc_start: 0.8963 (m-30) cc_final: 0.8178 (m-30) REVERT: v 32 LEU cc_start: 0.9307 (tp) cc_final: 0.9039 (tp) REVERT: v 36 LYS cc_start: 0.9027 (mttt) cc_final: 0.8712 (mttp) REVERT: v 53 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8525 (mmmm) REVERT: v 69 LYS cc_start: 0.9101 (tptm) cc_final: 0.8187 (mttm) REVERT: w 25 THR cc_start: 0.8624 (p) cc_final: 0.8248 (p) REVERT: w 57 TYR cc_start: 0.8825 (t80) cc_final: 0.8337 (t80) REVERT: w 61 ARG cc_start: 0.8418 (mmt180) cc_final: 0.6790 (ttp-170) REVERT: w 69 LYS cc_start: 0.9151 (tppt) cc_final: 0.7616 (tppt) REVERT: a0 103 LYS cc_start: 0.8113 (tttm) cc_final: 0.7047 (tptt) REVERT: d0 103 LYS cc_start: 0.9251 (ttmt) cc_final: 0.7926 (tptt) REVERT: e0 103 LYS cc_start: 0.8830 (ttmt) cc_final: 0.8292 (tttt) REVERT: f0 103 LYS cc_start: 0.9267 (ttmt) cc_final: 0.8381 (tptt) REVERT: g0 100 ARG cc_start: 0.8657 (ttm170) cc_final: 0.8258 (ttm170) REVERT: g0 103 LYS cc_start: 0.9011 (mtmt) cc_final: 0.7676 (tptt) REVERT: i0 103 LYS cc_start: 0.8979 (tttt) cc_final: 0.8625 (tptt) REVERT: k0 103 LYS cc_start: 0.8754 (ttmm) cc_final: 0.8176 (tptt) REVERT: l0 103 LYS cc_start: 0.8924 (ttmt) cc_final: 0.8184 (tptt) REVERT: m0 103 LYS cc_start: 0.9034 (mtpt) cc_final: 0.8185 (tptt) REVERT: n0 97 SER cc_start: 0.9086 (m) cc_final: 0.8595 (p) REVERT: n0 103 LYS cc_start: 0.9014 (ttmt) cc_final: 0.8519 (ttpt) REVERT: p0 103 LYS cc_start: 0.8859 (ttpt) cc_final: 0.8046 (tptt) REVERT: q0 103 LYS cc_start: 0.9007 (ttmt) cc_final: 0.8309 (tptt) REVERT: r0 102 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8123 (mt-10) REVERT: r0 103 LYS cc_start: 0.8824 (ttmt) cc_final: 0.7549 (tptt) REVERT: t0 103 LYS cc_start: 0.8887 (ttmt) cc_final: 0.8103 (tptt) REVERT: t0 105 ARG cc_start: 0.9166 (ttm110) cc_final: 0.7988 (tpm170) REVERT: u0 100 ARG cc_start: 0.7851 (ttm110) cc_final: 0.7352 (tpt170) REVERT: u0 103 LYS cc_start: 0.9083 (ttmt) cc_final: 0.8042 (tptt) REVERT: v0 92 THR cc_start: 0.8208 (m) cc_final: 0.7991 (m) REVERT: v0 103 LYS cc_start: 0.9284 (mttt) cc_final: 0.7824 (tptt) REVERT: w0 103 LYS cc_start: 0.8938 (ttmt) cc_final: 0.8422 (tptt) REVERT: x0 103 LYS cc_start: 0.8407 (ttmt) cc_final: 0.7758 (tptt) outliers start: 10 outliers final: 0 residues processed: 2236 average time/residue: 0.5410 time to fit residues: 2038.6395 Evaluate side-chains 1934 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1934 time to evaluate : 4.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 421 optimal weight: 3.9990 chunk 286 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 376 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 431 optimal weight: 0.8980 chunk 349 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 258 optimal weight: 6.9990 chunk 453 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 49 ASN ** 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 R 44 GLN T 80 GLN U 80 GLN V 66 ASN W 81 ASN 0 164 ASN 4 127 GLN ** 4 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 24 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: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 44858 Z= 0.268 Angle : 0.643 10.155 60890 Z= 0.322 Chirality : 0.041 0.209 7369 Planarity : 0.004 0.072 7620 Dihedral : 4.306 84.430 5953 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.12 % Allowed : 1.90 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.12), residues: 5404 helix: 3.01 (0.08), residues: 4154 sheet: 1.16 (0.31), residues: 224 loop : -2.91 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 66 HIS 0.007 0.001 HIS F 11 PHE 0.026 0.002 PHE o 19 TYR 0.035 0.002 TYR K 171 ARG 0.020 0.001 ARG K 55 *********************** 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 2204 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 2198 time to evaluate : 4.673 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: 0.8760 (p) cc_final: 0.8056 (p) REVERT: A 36 MET cc_start: 0.8778 (ttp) cc_final: 0.8390 (tpp) REVERT: A 48 SER cc_start: 0.8935 (t) cc_final: 0.8712 (p) REVERT: A 50 MET cc_start: 0.8298 (ttp) cc_final: 0.7989 (ttm) REVERT: A 68 ILE cc_start: 0.9527 (mt) cc_final: 0.9230 (mt) REVERT: A 69 GLU cc_start: 0.7824 (tp30) cc_final: 0.7219 (mm-30) REVERT: A 101 GLN cc_start: 0.8721 (tt0) cc_final: 0.8397 (tm-30) REVERT: A 104 LYS cc_start: 0.9317 (mmmm) cc_final: 0.8984 (ttmt) REVERT: A 152 LYS cc_start: 0.9247 (tttt) cc_final: 0.8778 (ttmt) REVERT: A 177 MET cc_start: 0.7949 (ptp) cc_final: 0.7586 (mtt) REVERT: A 205 LYS cc_start: 0.9039 (mttt) cc_final: 0.8253 (tttt) REVERT: B 65 LYS cc_start: 0.8566 (tttp) cc_final: 0.8267 (tttt) REVERT: B 120 GLU cc_start: 0.6324 (mt-10) cc_final: 0.5769 (mp0) REVERT: B 146 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7864 (mm-30) REVERT: B 190 LYS cc_start: 0.9225 (mtmt) cc_final: 0.8537 (mtmm) REVERT: C 25 THR cc_start: 0.9291 (p) cc_final: 0.8804 (t) REVERT: C 29 LYS cc_start: 0.8907 (mttp) cc_final: 0.8650 (mttp) REVERT: C 59 MET cc_start: 0.8698 (mtp) cc_final: 0.8405 (mtp) REVERT: C 105 LYS cc_start: 0.8985 (tttp) cc_final: 0.8677 (mtpp) REVERT: C 117 ARG cc_start: 0.8356 (mtt180) cc_final: 0.7833 (tpt170) REVERT: D 2 LEU cc_start: 0.9239 (mt) cc_final: 0.8951 (mt) REVERT: D 6 SER cc_start: 0.8862 (m) cc_final: 0.8083 (p) REVERT: D 17 LEU cc_start: 0.9318 (tp) cc_final: 0.8895 (tt) REVERT: E 26 CYS cc_start: 0.8607 (p) cc_final: 0.7741 (p) REVERT: E 29 LYS cc_start: 0.9239 (tttm) cc_final: 0.9002 (ttpt) REVERT: E 36 MET cc_start: 0.8818 (tpp) cc_final: 0.8240 (tpp) REVERT: E 44 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8237 (mt0) REVERT: E 64 MET cc_start: 0.8655 (mmm) cc_final: 0.8020 (mmm) REVERT: E 162 VAL cc_start: 0.9384 (t) cc_final: 0.9164 (p) REVERT: F 104 ASP cc_start: 0.8293 (t0) cc_final: 0.8046 (t0) REVERT: F 128 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8491 (ttpt) REVERT: F 133 PHE cc_start: 0.8943 (t80) cc_final: 0.8527 (t80) REVERT: F 152 GLN cc_start: 0.9124 (tt0) cc_final: 0.8535 (tp40) REVERT: F 181 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8450 (mm-40) REVERT: F 202 VAL cc_start: 0.9142 (t) cc_final: 0.8923 (t) REVERT: G 57 SER cc_start: 0.9212 (t) cc_final: 0.8934 (p) REVERT: G 79 MET cc_start: 0.8638 (mmm) cc_final: 0.8129 (mmm) REVERT: H 77 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7767 (tm-30) REVERT: H 79 MET cc_start: 0.8072 (mmp) cc_final: 0.7460 (mmp) REVERT: I 5 VAL cc_start: 0.9086 (t) cc_final: 0.8539 (p) REVERT: I 6 TYR cc_start: 0.8670 (t80) cc_final: 0.8450 (t80) REVERT: I 53 LEU cc_start: 0.7967 (tp) cc_final: 0.7731 (tp) REVERT: I 60 LEU cc_start: 0.8549 (mt) cc_final: 0.8274 (mt) REVERT: K 32 VAL cc_start: 0.6826 (t) cc_final: 0.6602 (t) REVERT: K 46 SER cc_start: 0.6998 (m) cc_final: 0.6412 (t) REVERT: K 132 LYS cc_start: 0.8632 (mmtp) cc_final: 0.8208 (mttt) REVERT: K 140 LEU cc_start: 0.9128 (tp) cc_final: 0.8906 (tt) REVERT: M 73 TYR cc_start: 0.9019 (m-80) cc_final: 0.8765 (m-80) REVERT: N 58 LEU cc_start: 0.9225 (mt) cc_final: 0.8887 (mt) REVERT: N 68 THR cc_start: 0.9002 (m) cc_final: 0.8661 (t) REVERT: N 89 SER cc_start: 0.9213 (t) cc_final: 0.8194 (p) REVERT: O 41 THR cc_start: 0.8796 (t) cc_final: 0.8426 (m) REVERT: P 46 SER cc_start: 0.9572 (m) cc_final: 0.9342 (t) REVERT: P 54 ASN cc_start: 0.8885 (t0) cc_final: 0.8648 (t0) REVERT: P 56 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7181 (tm-30) REVERT: P 57 SER cc_start: 0.9076 (m) cc_final: 0.8536 (p) REVERT: R 27 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6921 (pt0) REVERT: S 37 LEU cc_start: 0.9088 (tp) cc_final: 0.8729 (tp) REVERT: U 81 ASN cc_start: 0.9200 (m-40) cc_final: 0.8991 (m-40) REVERT: V 32 LEU cc_start: 0.8684 (mt) cc_final: 0.8304 (tt) REVERT: V 64 GLN cc_start: 0.8635 (tt0) cc_final: 0.8366 (tt0) REVERT: W 39 LYS cc_start: 0.8333 (mttt) cc_final: 0.7768 (mptt) REVERT: W 43 ASN cc_start: 0.8744 (t0) cc_final: 0.8093 (t0) REVERT: X 142 ARG cc_start: 0.8609 (mmt-90) cc_final: 0.8202 (mmt-90) REVERT: Y 112 SER cc_start: 0.7928 (p) cc_final: 0.7635 (m) REVERT: Y 123 ASN cc_start: 0.8766 (t0) cc_final: 0.8490 (t0) REVERT: Y 127 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7336 (tm-30) REVERT: Y 131 ASP cc_start: 0.7759 (m-30) cc_final: 0.7380 (m-30) REVERT: Z 133 ASN cc_start: 0.9264 (t0) cc_final: 0.8963 (t0) REVERT: Z 161 LEU cc_start: 0.8641 (tp) cc_final: 0.8409 (tp) REVERT: 2 127 GLN cc_start: 0.8092 (tp40) cc_final: 0.7749 (tp40) REVERT: 4 127 GLN cc_start: 0.7795 (tp40) cc_final: 0.7478 (tp40) REVERT: 4 131 ASP cc_start: 0.8162 (p0) cc_final: 0.7715 (p0) REVERT: 4 150 PHE cc_start: 0.9061 (p90) cc_final: 0.8539 (p90) REVERT: 4 167 THR cc_start: 0.8793 (m) cc_final: 0.8534 (t) REVERT: 6 127 GLN cc_start: 0.8948 (tp40) cc_final: 0.8365 (tp40) REVERT: 6 138 ARG cc_start: 0.8461 (mtp85) cc_final: 0.7701 (mtm110) REVERT: 6 149 THR cc_start: 0.8936 (m) cc_final: 0.8194 (p) REVERT: 8 111 ILE cc_start: 0.9332 (mt) cc_final: 0.9126 (mt) REVERT: 8 115 ILE cc_start: 0.8936 (mt) cc_final: 0.8655 (mm) REVERT: 8 144 ASN cc_start: 0.7843 (t0) cc_final: 0.7528 (t0) REVERT: 8 150 PHE cc_start: 0.9292 (p90) cc_final: 0.8770 (p90) REVERT: x 112 SER cc_start: 0.8675 (p) cc_final: 0.8453 (m) REVERT: x 150 PHE cc_start: 0.9324 (p90) cc_final: 0.8660 (p90) REVERT: x 153 SER cc_start: 0.9400 (t) cc_final: 0.9169 (p) REVERT: y 115 ILE cc_start: 0.9454 (mt) cc_final: 0.9216 (mt) REVERT: y 158 LEU cc_start: 0.8253 (tp) cc_final: 0.7901 (mm) REVERT: y 160 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7781 (mm-30) REVERT: z 112 SER cc_start: 0.9205 (p) cc_final: 0.8869 (m) REVERT: z 119 ASN cc_start: 0.8858 (m-40) cc_final: 0.8528 (p0) REVERT: z 127 GLN cc_start: 0.8388 (tm-30) cc_final: 0.7749 (tm-30) REVERT: z 138 ARG cc_start: 0.8215 (ttp-170) cc_final: 0.7837 (ttp-110) REVERT: z 149 THR cc_start: 0.9095 (m) cc_final: 0.8785 (t) REVERT: 1 130 LYS cc_start: 0.8431 (mmmt) cc_final: 0.7941 (mmtt) REVERT: 1 133 ASN cc_start: 0.8671 (m-40) cc_final: 0.8269 (t0) REVERT: 3 115 ILE cc_start: 0.8625 (mt) cc_final: 0.7955 (mt) REVERT: 5 112 SER cc_start: 0.8331 (p) cc_final: 0.8096 (m) REVERT: 7 168 LEU cc_start: 0.9183 (tp) cc_final: 0.8912 (tp) REVERT: 9 135 TYR cc_start: 0.7637 (t80) cc_final: 0.7069 (t80) REVERT: a 26 LEU cc_start: 0.8895 (tp) cc_final: 0.8557 (tp) REVERT: b 14 SER cc_start: 0.8888 (m) cc_final: 0.8610 (p) REVERT: b 43 ASN cc_start: 0.8547 (t0) cc_final: 0.8261 (t0) REVERT: b 45 GLN cc_start: 0.9087 (tp40) cc_final: 0.7950 (tm-30) REVERT: b 49 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7201 (mm-30) REVERT: b 59 LEU cc_start: 0.9357 (mp) cc_final: 0.9070 (mp) REVERT: b 64 GLN cc_start: 0.8599 (tm-30) cc_final: 0.7921 (tm-30) REVERT: b 65 SER cc_start: 0.9260 (m) cc_final: 0.8842 (t) REVERT: c 9 ASP cc_start: 0.8375 (t0) cc_final: 0.7996 (t0) REVERT: c 20 ASP cc_start: 0.7989 (t0) cc_final: 0.7689 (t0) REVERT: c 59 LEU cc_start: 0.9462 (mt) cc_final: 0.9223 (mt) REVERT: c 82 PHE cc_start: 0.8782 (m-10) cc_final: 0.8534 (m-10) REVERT: d 57 TYR cc_start: 0.9015 (t80) cc_final: 0.8525 (t80) REVERT: d 75 ASP cc_start: 0.8338 (m-30) cc_final: 0.8041 (m-30) REVERT: e 40 ASN cc_start: 0.8527 (p0) cc_final: 0.8130 (p0) REVERT: e 56 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8297 (tt0) REVERT: f 20 ASP cc_start: 0.8396 (t70) cc_final: 0.8167 (t70) REVERT: f 80 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8020 (tm-30) REVERT: g 17 GLU cc_start: 0.7941 (mp0) cc_final: 0.7517 (mp0) REVERT: g 54 LEU cc_start: 0.9270 (tp) cc_final: 0.9016 (tp) REVERT: g 79 ILE cc_start: 0.9211 (mm) cc_final: 0.8846 (mm) REVERT: g 80 GLN cc_start: 0.8736 (tp-100) cc_final: 0.8356 (tm-30) REVERT: h 25 THR cc_start: 0.7359 (t) cc_final: 0.6892 (t) REVERT: h 29 GLU cc_start: 0.8555 (mp0) cc_final: 0.8240 (mp0) REVERT: i 80 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8154 (tm-30) REVERT: i 81 ASN cc_start: 0.9214 (m-40) cc_final: 0.8966 (m-40) REVERT: j 14 SER cc_start: 0.8931 (m) cc_final: 0.8614 (t) REVERT: j 80 GLN cc_start: 0.9083 (tp-100) cc_final: 0.8782 (tp-100) REVERT: k 50 TYR cc_start: 0.9259 (t80) cc_final: 0.9030 (t80) REVERT: l 16 SER cc_start: 0.9056 (m) cc_final: 0.8325 (t) REVERT: l 20 ASP cc_start: 0.7695 (m-30) cc_final: 0.7366 (m-30) REVERT: l 25 THR cc_start: 0.8756 (p) cc_final: 0.8128 (p) REVERT: l 43 ASN cc_start: 0.8808 (t0) cc_final: 0.8590 (t0) REVERT: l 45 GLN cc_start: 0.8308 (tp40) cc_final: 0.7656 (tp40) REVERT: l 50 TYR cc_start: 0.9236 (t80) cc_final: 0.8873 (t80) REVERT: m 20 ASP cc_start: 0.8241 (m-30) cc_final: 0.7854 (m-30) REVERT: m 50 TYR cc_start: 0.8839 (t80) cc_final: 0.8477 (t80) REVERT: m 75 ASP cc_start: 0.8284 (m-30) cc_final: 0.7497 (m-30) REVERT: n 3 VAL cc_start: 0.8606 (t) cc_final: 0.8310 (m) REVERT: n 23 THR cc_start: 0.8853 (t) cc_final: 0.8651 (m) REVERT: n 29 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7427 (tm-30) REVERT: n 53 LYS cc_start: 0.8896 (mmtt) cc_final: 0.8325 (mmtm) REVERT: n 75 ASP cc_start: 0.8500 (m-30) cc_final: 0.8169 (m-30) REVERT: n 80 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8030 (tm-30) REVERT: o 14 SER cc_start: 0.8791 (t) cc_final: 0.8423 (p) REVERT: o 29 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7512 (mt-10) REVERT: o 39 LYS cc_start: 0.7884 (mmpt) cc_final: 0.7359 (mmpt) REVERT: o 43 ASN cc_start: 0.7525 (t0) cc_final: 0.7207 (t0) REVERT: o 50 TYR cc_start: 0.9239 (t80) cc_final: 0.9019 (t80) REVERT: o 53 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8733 (mmpt) REVERT: o 72 LYS cc_start: 0.9462 (tmtt) cc_final: 0.9000 (tmtt) REVERT: p 25 THR cc_start: 0.8417 (p) cc_final: 0.7764 (t) REVERT: p 75 ASP cc_start: 0.8632 (m-30) cc_final: 0.8065 (m-30) REVERT: q 14 SER cc_start: 0.9400 (m) cc_final: 0.9127 (p) REVERT: q 32 LEU cc_start: 0.8294 (tp) cc_final: 0.7873 (tp) REVERT: q 36 LYS cc_start: 0.8721 (mttt) cc_final: 0.8452 (mtmt) REVERT: r 59 LEU cc_start: 0.8919 (mt) cc_final: 0.8621 (mt) REVERT: s 7 ASN cc_start: 0.6693 (m-40) cc_final: 0.5608 (p0) REVERT: s 23 THR cc_start: 0.8632 (m) cc_final: 0.8396 (m) REVERT: s 24 GLN cc_start: 0.8166 (tp40) cc_final: 0.7819 (mm-40) REVERT: s 27 GLN cc_start: 0.8508 (mt0) cc_final: 0.8025 (tm-30) REVERT: s 65 SER cc_start: 0.9140 (t) cc_final: 0.8772 (m) REVERT: s 69 LYS cc_start: 0.8593 (tptm) cc_final: 0.7437 (ttmt) REVERT: t 51 GLN cc_start: 0.8807 (tt0) cc_final: 0.6724 (mm-40) REVERT: t 52 SER cc_start: 0.8552 (m) cc_final: 0.8271 (t) REVERT: t 69 LYS cc_start: 0.9256 (tptm) cc_final: 0.8573 (mttt) REVERT: t 72 LYS cc_start: 0.9536 (tmtt) cc_final: 0.9249 (tttp) REVERT: u 30 LEU cc_start: 0.8818 (tp) cc_final: 0.8558 (tt) REVERT: u 49 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7102 (tp30) REVERT: u 69 LYS cc_start: 0.9083 (tptm) cc_final: 0.7613 (ttmt) REVERT: u 75 ASP cc_start: 0.8975 (m-30) cc_final: 0.8225 (m-30) REVERT: v 15 LEU cc_start: 0.9172 (tp) cc_final: 0.8953 (tp) REVERT: v 18 THR cc_start: 0.8165 (m) cc_final: 0.7715 (m) REVERT: v 32 LEU cc_start: 0.9292 (tp) cc_final: 0.8998 (tp) REVERT: v 36 LYS cc_start: 0.9054 (mttt) cc_final: 0.8772 (mttm) REVERT: v 53 LYS cc_start: 0.8852 (mmmt) cc_final: 0.8504 (mmmm) REVERT: v 69 LYS cc_start: 0.9124 (tptm) cc_final: 0.8258 (mttt) REVERT: w 25 THR cc_start: 0.8639 (p) cc_final: 0.8268 (p) REVERT: w 57 TYR cc_start: 0.8950 (t80) cc_final: 0.8524 (t80) REVERT: w 61 ARG cc_start: 0.8502 (mmt180) cc_final: 0.6878 (ttp-170) REVERT: w 69 LYS cc_start: 0.9139 (tppt) cc_final: 0.7688 (tppt) REVERT: a0 103 LYS cc_start: 0.8181 (tttm) cc_final: 0.7068 (tptt) REVERT: d0 103 LYS cc_start: 0.9266 (ttmt) cc_final: 0.7897 (tptt) REVERT: e0 103 LYS cc_start: 0.8777 (ttmt) cc_final: 0.8185 (tttt) REVERT: f0 103 LYS cc_start: 0.9274 (ttmt) cc_final: 0.8342 (tptt) REVERT: g0 103 LYS cc_start: 0.9092 (mtmt) cc_final: 0.7784 (tptt) REVERT: i0 103 LYS cc_start: 0.8989 (tttt) cc_final: 0.8653 (tptt) REVERT: k0 103 LYS cc_start: 0.8867 (ttmm) cc_final: 0.8109 (tptt) REVERT: l0 103 LYS cc_start: 0.8940 (ttmt) cc_final: 0.8193 (tptt) REVERT: m0 103 LYS cc_start: 0.9071 (mtpt) cc_final: 0.8190 (tptt) REVERT: n0 97 SER cc_start: 0.9118 (m) cc_final: 0.8620 (p) REVERT: n0 103 LYS cc_start: 0.9019 (ttmt) cc_final: 0.8510 (ttpt) REVERT: p0 103 LYS cc_start: 0.8855 (ttpt) cc_final: 0.8100 (tptt) REVERT: q0 103 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8385 (tptt) REVERT: r0 102 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8120 (mt-10) REVERT: r0 103 LYS cc_start: 0.8840 (ttmt) cc_final: 0.7574 (tptt) REVERT: t0 103 LYS cc_start: 0.8926 (ttmt) cc_final: 0.8127 (tptt) REVERT: t0 105 ARG cc_start: 0.9210 (ttm110) cc_final: 0.8026 (tpm170) REVERT: u0 98 SER cc_start: 0.8904 (m) cc_final: 0.7978 (p) REVERT: u0 100 ARG cc_start: 0.7868 (ttm110) cc_final: 0.7409 (tpt170) REVERT: u0 103 LYS cc_start: 0.9105 (ttmt) cc_final: 0.8049 (tptt) REVERT: v0 92 THR cc_start: 0.8489 (m) cc_final: 0.8242 (m) REVERT: v0 103 LYS cc_start: 0.9279 (mttt) cc_final: 0.7929 (tptt) REVERT: w0 103 LYS cc_start: 0.8916 (ttmt) cc_final: 0.8420 (tptt) REVERT: x0 103 LYS cc_start: 0.8430 (ttmt) cc_final: 0.7879 (tptt) outliers start: 6 outliers final: 0 residues processed: 2198 average time/residue: 0.5480 time to fit residues: 2039.8963 Evaluate side-chains 1912 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1912 time to evaluate : 5.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 170 optimal weight: 2.9990 chunk 455 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 296 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 506 optimal weight: 0.5980 chunk 420 optimal weight: 1.9990 chunk 234 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 265 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 ASN 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 4 137 HIS ** 4 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 123 ASN 9 123 ASN c 43 ASN c 64 GLN e 45 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 n 81 ASN p 80 GLN t 24 GLN u 40 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 44858 Z= 0.194 Angle : 0.625 9.599 60890 Z= 0.309 Chirality : 0.040 0.203 7369 Planarity : 0.004 0.073 7620 Dihedral : 4.322 85.025 5953 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.12 % Allowed : 1.76 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.12), residues: 5404 helix: 3.04 (0.08), residues: 4149 sheet: 1.16 (0.31), residues: 224 loop : -2.87 (0.17), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP c 10 HIS 0.006 0.001 HIS F 11 PHE 0.037 0.002 PHE u 19 TYR 0.028 0.001 TYR C 133 ARG 0.006 0.000 ARG M 85 *********************** 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 2237 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 2231 time to evaluate : 5.383 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: 0.8667 (p) cc_final: 0.7922 (p) REVERT: A 36 MET cc_start: 0.8763 (ttp) cc_final: 0.8407 (tpp) REVERT: A 50 MET cc_start: 0.8255 (ttp) cc_final: 0.7997 (ttm) REVERT: A 68 ILE cc_start: 0.9543 (mt) cc_final: 0.9191 (mt) REVERT: A 69 GLU cc_start: 0.7793 (tp30) cc_final: 0.7114 (mm-30) REVERT: A 101 GLN cc_start: 0.8702 (tt0) cc_final: 0.8386 (tm-30) REVERT: A 104 LYS cc_start: 0.9283 (mmmm) cc_final: 0.8939 (ttmt) REVERT: A 152 LYS cc_start: 0.9223 (tttt) cc_final: 0.8729 (mtmt) REVERT: A 177 MET cc_start: 0.8108 (ptp) cc_final: 0.7682 (mtt) REVERT: A 205 LYS cc_start: 0.9133 (mttt) cc_final: 0.8148 (tttt) REVERT: B 27 TYR cc_start: 0.8821 (t80) cc_final: 0.8489 (t80) REVERT: B 65 LYS cc_start: 0.8603 (tttp) cc_final: 0.8313 (tttt) REVERT: B 120 GLU cc_start: 0.6201 (mt-10) cc_final: 0.5723 (mp0) REVERT: B 146 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7598 (mm-30) REVERT: B 190 LYS cc_start: 0.9187 (mtmt) cc_final: 0.8475 (mtmm) REVERT: C 25 THR cc_start: 0.9051 (p) cc_final: 0.8732 (t) REVERT: C 105 LYS cc_start: 0.8977 (tttp) cc_final: 0.8722 (mtpp) REVERT: C 117 ARG cc_start: 0.8366 (mtt180) cc_final: 0.7844 (tpt170) REVERT: D 2 LEU cc_start: 0.9196 (mt) cc_final: 0.8930 (mt) REVERT: D 6 SER cc_start: 0.8818 (m) cc_final: 0.8022 (p) REVERT: D 17 LEU cc_start: 0.9272 (tp) cc_final: 0.8838 (tt) REVERT: E 43 LEU cc_start: 0.8917 (tp) cc_final: 0.8609 (tp) REVERT: E 44 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8207 (mt0) REVERT: E 59 MET cc_start: 0.8281 (mtm) cc_final: 0.7940 (mtm) REVERT: E 64 MET cc_start: 0.8626 (mmm) cc_final: 0.8034 (mmm) REVERT: F 58 SER cc_start: 0.8777 (m) cc_final: 0.8448 (p) REVERT: F 104 ASP cc_start: 0.8380 (t0) cc_final: 0.8039 (t0) REVERT: F 133 PHE cc_start: 0.8864 (t80) cc_final: 0.8417 (t80) REVERT: F 139 LEU cc_start: 0.9241 (tp) cc_final: 0.9039 (tp) REVERT: F 152 GLN cc_start: 0.9067 (tt0) cc_final: 0.8433 (tp-100) REVERT: F 153 LEU cc_start: 0.9489 (tp) cc_final: 0.9283 (tp) REVERT: G 57 SER cc_start: 0.9203 (t) cc_final: 0.8866 (p) REVERT: G 73 SER cc_start: 0.9001 (p) cc_final: 0.8718 (p) REVERT: G 79 MET cc_start: 0.8705 (mmm) cc_final: 0.8177 (mmm) REVERT: H 60 LEU cc_start: 0.8762 (mm) cc_final: 0.8555 (mm) REVERT: H 77 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7811 (tm-30) REVERT: H 79 MET cc_start: 0.8074 (mmp) cc_final: 0.7439 (mmp) REVERT: I 5 VAL cc_start: 0.9140 (t) cc_final: 0.8535 (p) REVERT: I 53 LEU cc_start: 0.7924 (tp) cc_final: 0.7705 (tp) REVERT: I 60 LEU cc_start: 0.8522 (mt) cc_final: 0.8291 (mt) REVERT: I 69 GLU cc_start: 0.7651 (tp30) cc_final: 0.6525 (tp30) REVERT: K 32 VAL cc_start: 0.6790 (t) cc_final: 0.6555 (t) REVERT: K 132 LYS cc_start: 0.8605 (mmtp) cc_final: 0.8187 (mttt) REVERT: N 33 LYS cc_start: 0.8593 (mmmm) cc_final: 0.7960 (mmtt) REVERT: N 58 LEU cc_start: 0.9166 (mt) cc_final: 0.8823 (mt) REVERT: O 41 THR cc_start: 0.8789 (t) cc_final: 0.8433 (m) REVERT: P 44 GLN cc_start: 0.8192 (tt0) cc_final: 0.7857 (tt0) REVERT: P 46 SER cc_start: 0.9542 (m) cc_final: 0.9338 (t) REVERT: P 57 SER cc_start: 0.9029 (m) cc_final: 0.8428 (p) REVERT: R 27 GLU cc_start: 0.6974 (tm-30) cc_final: 0.6753 (pt0) REVERT: R 51 MET cc_start: 0.7743 (mtt) cc_final: 0.7319 (mtp) REVERT: S 25 THR cc_start: 0.7854 (t) cc_final: 0.7632 (t) REVERT: S 37 LEU cc_start: 0.9044 (tp) cc_final: 0.8661 (tp) REVERT: T 30 LEU cc_start: 0.9173 (tp) cc_final: 0.8911 (tp) REVERT: T 50 TYR cc_start: 0.9172 (t80) cc_final: 0.8918 (t80) REVERT: U 55 SER cc_start: 0.9132 (m) cc_final: 0.8460 (m) REVERT: U 81 ASN cc_start: 0.9201 (m-40) cc_final: 0.8992 (m-40) REVERT: V 32 LEU cc_start: 0.8688 (mt) cc_final: 0.8344 (tt) REVERT: V 64 GLN cc_start: 0.8585 (tt0) cc_final: 0.8313 (tt0) REVERT: W 39 LYS cc_start: 0.8216 (mttt) cc_final: 0.7601 (mptt) REVERT: W 43 ASN cc_start: 0.8671 (t0) cc_final: 0.8216 (t0) REVERT: X 142 ARG cc_start: 0.8598 (mmt-90) cc_final: 0.8182 (mmt-90) REVERT: Y 112 SER cc_start: 0.7942 (p) cc_final: 0.7632 (m) REVERT: Y 123 ASN cc_start: 0.8743 (t0) cc_final: 0.8501 (t0) REVERT: Y 131 ASP cc_start: 0.7738 (m-30) cc_final: 0.7286 (m-30) REVERT: Z 133 ASN cc_start: 0.9162 (t0) cc_final: 0.8827 (t0) REVERT: Z 158 LEU cc_start: 0.8956 (tt) cc_final: 0.8617 (mm) REVERT: 2 127 GLN cc_start: 0.8232 (tp40) cc_final: 0.7918 (tp40) REVERT: 4 133 ASN cc_start: 0.8234 (t0) cc_final: 0.7874 (t0) REVERT: 4 150 PHE cc_start: 0.9010 (p90) cc_final: 0.8534 (p90) REVERT: 4 167 THR cc_start: 0.8756 (m) cc_final: 0.8523 (t) REVERT: 6 127 GLN cc_start: 0.8930 (tp40) cc_final: 0.8299 (tp40) REVERT: 6 138 ARG cc_start: 0.8412 (mtp85) cc_final: 0.7672 (mtm110) REVERT: 6 149 THR cc_start: 0.8922 (m) cc_final: 0.8150 (p) REVERT: 6 168 LEU cc_start: 0.8766 (tp) cc_final: 0.8409 (tp) REVERT: 8 115 ILE cc_start: 0.8935 (mt) cc_final: 0.8676 (mm) REVERT: 8 144 ASN cc_start: 0.7731 (t0) cc_final: 0.7495 (t0) REVERT: 8 150 PHE cc_start: 0.9267 (p90) cc_final: 0.8721 (p90) REVERT: x 112 SER cc_start: 0.8647 (p) cc_final: 0.8431 (m) REVERT: x 150 PHE cc_start: 0.9265 (p90) cc_final: 0.8572 (p90) REVERT: x 153 SER cc_start: 0.9390 (t) cc_final: 0.9162 (p) REVERT: x 168 LEU cc_start: 0.9360 (tp) cc_final: 0.9140 (tt) REVERT: y 118 GLU cc_start: 0.6461 (mm-30) cc_final: 0.6211 (mm-30) REVERT: y 158 LEU cc_start: 0.8228 (tp) cc_final: 0.7879 (mm) REVERT: y 160 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7763 (mm-30) REVERT: y 164 ASN cc_start: 0.8673 (m-40) cc_final: 0.8397 (m-40) REVERT: z 112 SER cc_start: 0.9199 (p) cc_final: 0.8861 (m) REVERT: z 119 ASN cc_start: 0.8660 (m-40) cc_final: 0.8419 (p0) REVERT: z 127 GLN cc_start: 0.8460 (tm-30) cc_final: 0.7944 (tm-30) REVERT: z 149 THR cc_start: 0.9085 (m) cc_final: 0.8786 (t) REVERT: 1 130 LYS cc_start: 0.8488 (mmmt) cc_final: 0.8116 (mmtt) REVERT: 1 133 ASN cc_start: 0.8610 (m-40) cc_final: 0.8326 (t0) REVERT: 3 115 ILE cc_start: 0.8426 (mt) cc_final: 0.8159 (mt) REVERT: 9 135 TYR cc_start: 0.7596 (t80) cc_final: 0.7066 (t80) REVERT: a 26 LEU cc_start: 0.8830 (tp) cc_final: 0.8503 (tp) REVERT: a 31 THR cc_start: 0.7734 (m) cc_final: 0.7304 (m) REVERT: a 66 ASN cc_start: 0.9091 (m-40) cc_final: 0.8839 (m110) REVERT: a 80 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8437 (tm-30) REVERT: b 14 SER cc_start: 0.8910 (m) cc_final: 0.8614 (p) REVERT: b 43 ASN cc_start: 0.8464 (t0) cc_final: 0.8211 (t0) REVERT: b 45 GLN cc_start: 0.9020 (tp40) cc_final: 0.8010 (tm-30) REVERT: b 49 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7156 (mm-30) REVERT: b 59 LEU cc_start: 0.9380 (mp) cc_final: 0.9114 (mp) REVERT: b 64 GLN cc_start: 0.8460 (tm-30) cc_final: 0.7708 (tm-30) REVERT: c 59 LEU cc_start: 0.9419 (mt) cc_final: 0.9210 (mt) REVERT: d 45 GLN cc_start: 0.8815 (tp40) cc_final: 0.8614 (tp-100) REVERT: d 57 TYR cc_start: 0.8972 (t80) cc_final: 0.8524 (t80) REVERT: d 71 ILE cc_start: 0.8708 (mm) cc_final: 0.8257 (mm) REVERT: d 75 ASP cc_start: 0.8252 (m-30) cc_final: 0.7981 (m-30) REVERT: e 40 ASN cc_start: 0.8380 (p0) cc_final: 0.7949 (p0) REVERT: e 56 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8160 (tt0) REVERT: f 14 SER cc_start: 0.9029 (p) cc_final: 0.8366 (t) REVERT: f 20 ASP cc_start: 0.8293 (t70) cc_final: 0.8009 (t0) REVERT: f 80 GLN cc_start: 0.8371 (tm-30) cc_final: 0.7941 (tm-30) REVERT: g 26 LEU cc_start: 0.9210 (tt) cc_final: 0.8556 (mm) REVERT: g 54 LEU cc_start: 0.9284 (tp) cc_final: 0.9076 (tp) REVERT: g 65 SER cc_start: 0.9121 (t) cc_final: 0.8918 (t) REVERT: g 79 ILE cc_start: 0.9173 (mm) cc_final: 0.8811 (mm) REVERT: g 80 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8449 (tm-30) REVERT: h 19 PHE cc_start: 0.7277 (t80) cc_final: 0.7002 (t80) REVERT: h 20 ASP cc_start: 0.7996 (t70) cc_final: 0.7767 (t70) REVERT: h 29 GLU cc_start: 0.8538 (mp0) cc_final: 0.8301 (mp0) REVERT: h 59 LEU cc_start: 0.9260 (mp) cc_final: 0.9039 (mp) REVERT: i 72 LYS cc_start: 0.8943 (ttpt) cc_final: 0.8711 (ttpt) REVERT: i 80 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8181 (tm-30) REVERT: i 81 ASN cc_start: 0.9274 (m-40) cc_final: 0.8998 (m-40) REVERT: j 14 SER cc_start: 0.8929 (m) cc_final: 0.8567 (t) REVERT: j 80 GLN cc_start: 0.9087 (tp-100) cc_final: 0.8650 (tp40) REVERT: k 37 LEU cc_start: 0.9038 (tp) cc_final: 0.8702 (tt) REVERT: k 50 TYR cc_start: 0.9243 (t80) cc_final: 0.8877 (t80) REVERT: k 64 GLN cc_start: 0.9150 (tt0) cc_final: 0.8942 (tt0) REVERT: l 16 SER cc_start: 0.9030 (m) cc_final: 0.8309 (t) REVERT: l 20 ASP cc_start: 0.7535 (m-30) cc_final: 0.7192 (m-30) REVERT: l 25 THR cc_start: 0.8813 (p) cc_final: 0.8051 (p) REVERT: l 26 LEU cc_start: 0.9176 (tt) cc_final: 0.8911 (tt) REVERT: l 45 GLN cc_start: 0.8281 (tp40) cc_final: 0.7620 (tp40) REVERT: l 50 TYR cc_start: 0.9186 (t80) cc_final: 0.8834 (t80) REVERT: m 20 ASP cc_start: 0.8060 (m-30) cc_final: 0.7571 (m-30) REVERT: m 50 TYR cc_start: 0.8794 (t80) cc_final: 0.8413 (t80) REVERT: m 75 ASP cc_start: 0.8388 (m-30) cc_final: 0.7516 (m-30) REVERT: n 3 VAL cc_start: 0.8563 (t) cc_final: 0.8298 (m) REVERT: n 29 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7341 (tm-30) REVERT: n 53 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8430 (mmtm) REVERT: n 75 ASP cc_start: 0.8481 (m-30) cc_final: 0.8153 (m-30) REVERT: n 80 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8036 (tm-30) REVERT: o 14 SER cc_start: 0.8731 (t) cc_final: 0.8321 (p) REVERT: o 29 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7590 (mt-10) REVERT: o 39 LYS cc_start: 0.7776 (mmpt) cc_final: 0.7397 (mmpt) REVERT: o 43 ASN cc_start: 0.7410 (t0) cc_final: 0.7166 (t0) REVERT: o 50 TYR cc_start: 0.9233 (t80) cc_final: 0.8951 (t80) REVERT: o 53 LYS cc_start: 0.9032 (mmtt) cc_final: 0.8711 (mmpt) REVERT: o 72 LYS cc_start: 0.9427 (tmtt) cc_final: 0.8967 (tmtt) REVERT: p 12 LEU cc_start: 0.9395 (mt) cc_final: 0.9109 (mt) REVERT: p 25 THR cc_start: 0.8329 (p) cc_final: 0.7683 (t) REVERT: p 75 ASP cc_start: 0.8605 (m-30) cc_final: 0.8124 (m-30) REVERT: q 14 SER cc_start: 0.9426 (m) cc_final: 0.9097 (p) REVERT: q 32 LEU cc_start: 0.8141 (tp) cc_final: 0.7771 (tp) REVERT: q 36 LYS cc_start: 0.8698 (mttt) cc_final: 0.8460 (mtmt) REVERT: r 25 THR cc_start: 0.8223 (p) cc_final: 0.7681 (p) REVERT: r 59 LEU cc_start: 0.8908 (mt) cc_final: 0.8606 (mt) REVERT: s 7 ASN cc_start: 0.6570 (m-40) cc_final: 0.5559 (p0) REVERT: s 23 THR cc_start: 0.8580 (m) cc_final: 0.8284 (m) REVERT: s 27 GLN cc_start: 0.8488 (mt0) cc_final: 0.7957 (tm-30) REVERT: s 65 SER cc_start: 0.9065 (t) cc_final: 0.8717 (m) REVERT: s 69 LYS cc_start: 0.8534 (tptm) cc_final: 0.7451 (ttmt) REVERT: t 51 GLN cc_start: 0.8636 (tt0) cc_final: 0.6846 (mm110) REVERT: t 52 SER cc_start: 0.8477 (m) cc_final: 0.8239 (t) REVERT: t 69 LYS cc_start: 0.9253 (tptm) cc_final: 0.8589 (mttt) REVERT: t 72 LYS cc_start: 0.9524 (tmtt) cc_final: 0.9234 (tttp) REVERT: u 30 LEU cc_start: 0.8924 (tp) cc_final: 0.8645 (tt) REVERT: u 69 LYS cc_start: 0.8903 (tptm) cc_final: 0.7609 (ttmt) REVERT: u 82 PHE cc_start: 0.8986 (m-80) cc_final: 0.8590 (m-80) REVERT: v 32 LEU cc_start: 0.9288 (tp) cc_final: 0.9034 (tp) REVERT: v 36 LYS cc_start: 0.8992 (mttt) cc_final: 0.8683 (mttm) REVERT: v 53 LYS cc_start: 0.8792 (mmmt) cc_final: 0.8522 (mmmm) REVERT: v 69 LYS cc_start: 0.9168 (tptm) cc_final: 0.8216 (mttt) REVERT: w 25 THR cc_start: 0.8597 (p) cc_final: 0.8246 (p) REVERT: w 57 TYR cc_start: 0.8925 (t80) cc_final: 0.8485 (t80) REVERT: w 61 ARG cc_start: 0.8376 (mmt180) cc_final: 0.6693 (ttp-170) REVERT: w 69 LYS cc_start: 0.9003 (tppt) cc_final: 0.7408 (tppt) REVERT: a0 103 LYS cc_start: 0.8141 (tttm) cc_final: 0.7022 (tptt) REVERT: d0 103 LYS cc_start: 0.9257 (ttmt) cc_final: 0.7924 (tptt) REVERT: e0 103 LYS cc_start: 0.8715 (ttmt) cc_final: 0.7804 (tttt) REVERT: f0 100 ARG cc_start: 0.8333 (ttm170) cc_final: 0.7865 (ttm170) REVERT: f0 103 LYS cc_start: 0.9241 (ttmt) cc_final: 0.8312 (tptt) REVERT: g0 103 LYS cc_start: 0.9113 (mtmt) cc_final: 0.7762 (tptt) REVERT: i0 103 LYS cc_start: 0.8951 (tttt) cc_final: 0.8669 (tptt) REVERT: k0 103 LYS cc_start: 0.8856 (ttmm) cc_final: 0.8100 (tptt) REVERT: l0 103 LYS cc_start: 0.8947 (ttmt) cc_final: 0.8205 (tptt) REVERT: m0 103 LYS cc_start: 0.9039 (mtpt) cc_final: 0.8145 (tptt) REVERT: n0 97 SER cc_start: 0.9037 (m) cc_final: 0.8769 (t) REVERT: p0 103 LYS cc_start: 0.8871 (ttpt) cc_final: 0.8045 (tptt) REVERT: q0 103 LYS cc_start: 0.9026 (ttmt) cc_final: 0.8305 (tptt) REVERT: r0 102 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8060 (mt-10) REVERT: r0 103 LYS cc_start: 0.8857 (ttmt) cc_final: 0.7578 (tptt) REVERT: t0 103 LYS cc_start: 0.8922 (ttmt) cc_final: 0.8101 (tptt) REVERT: t0 105 ARG cc_start: 0.9187 (ttm110) cc_final: 0.7998 (tpm170) REVERT: u0 98 SER cc_start: 0.8727 (m) cc_final: 0.7859 (p) REVERT: u0 100 ARG cc_start: 0.7820 (ttm110) cc_final: 0.7338 (tpt170) REVERT: u0 103 LYS cc_start: 0.9122 (ttmt) cc_final: 0.7985 (tptt) REVERT: v0 92 THR cc_start: 0.8464 (m) cc_final: 0.8243 (m) REVERT: v0 103 LYS cc_start: 0.9258 (mttt) cc_final: 0.7799 (tptt) REVERT: w0 103 LYS cc_start: 0.8878 (ttmt) cc_final: 0.8363 (tptt) REVERT: x0 103 LYS cc_start: 0.8474 (ttmt) cc_final: 0.7838 (tptt) outliers start: 6 outliers final: 0 residues processed: 2233 average time/residue: 0.5370 time to fit residues: 2020.2459 Evaluate side-chains 1905 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1905 time to evaluate : 5.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 487 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 288 optimal weight: 0.0570 chunk 369 optimal weight: 4.9990 chunk 286 optimal weight: 2.9990 chunk 425 optimal weight: 2.9990 chunk 282 optimal weight: 3.9990 chunk 504 optimal weight: 4.9990 chunk 315 optimal weight: 0.9980 chunk 307 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 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 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 44 GLN P 59 ASN R 19 GLN ** R 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 80 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 b 81 ASN f 51 GLN h 51 GLN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 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 u 64 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 44858 Z= 0.210 Angle : 0.640 11.293 60890 Z= 0.317 Chirality : 0.040 0.209 7369 Planarity : 0.004 0.074 7620 Dihedral : 4.317 85.842 5953 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.12 % Allowed : 0.90 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.11), residues: 5404 helix: 3.01 (0.08), residues: 4151 sheet: 1.14 (0.31), residues: 224 loop : -2.87 (0.17), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 66 HIS 0.006 0.001 HIS F 11 PHE 0.033 0.002 PHE v 19 TYR 0.025 0.002 TYR C 133 ARG 0.014 0.000 ARG D 113 *********************** 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 2190 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 2184 time to evaluate : 5.579 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: A 26 CYS cc_start: 0.8644 (p) cc_final: 0.7939 (p) REVERT: A 50 MET cc_start: 0.8230 (ttp) cc_final: 0.7933 (ttm) REVERT: A 69 GLU cc_start: 0.7957 (tp30) cc_final: 0.7391 (mm-30) REVERT: A 101 GLN cc_start: 0.8764 (tt0) cc_final: 0.8435 (tm-30) REVERT: A 152 LYS cc_start: 0.9197 (tttt) cc_final: 0.8722 (mtmt) REVERT: A 205 LYS cc_start: 0.9113 (mttt) cc_final: 0.8204 (tttt) REVERT: B 27 TYR cc_start: 0.8819 (t80) cc_final: 0.8554 (t80) REVERT: B 65 LYS cc_start: 0.8622 (tttp) cc_final: 0.8167 (tttt) REVERT: B 120 GLU cc_start: 0.6194 (mt-10) cc_final: 0.5773 (mp0) REVERT: B 137 SER cc_start: 0.9287 (m) cc_final: 0.8920 (t) REVERT: B 146 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7675 (mm-30) REVERT: B 162 VAL cc_start: 0.8947 (m) cc_final: 0.8713 (p) REVERT: B 173 LEU cc_start: 0.8854 (mp) cc_final: 0.8573 (mp) REVERT: B 190 LYS cc_start: 0.9185 (mtmt) cc_final: 0.8447 (mtmm) REVERT: C 25 THR cc_start: 0.9235 (p) cc_final: 0.8811 (t) REVERT: C 105 LYS cc_start: 0.8946 (tttp) cc_final: 0.8695 (mtpp) REVERT: C 117 ARG cc_start: 0.8374 (mtt180) cc_final: 0.7816 (tpt170) REVERT: C 210 GLN cc_start: 0.7519 (tm-30) cc_final: 0.6903 (tm-30) REVERT: D 2 LEU cc_start: 0.9180 (mt) cc_final: 0.8919 (mt) REVERT: D 6 SER cc_start: 0.8834 (m) cc_final: 0.7982 (p) REVERT: D 17 LEU cc_start: 0.9299 (tp) cc_final: 0.8872 (tt) REVERT: D 120 GLU cc_start: 0.6506 (mm-30) cc_final: 0.6296 (mm-30) REVERT: D 134 SER cc_start: 0.9031 (m) cc_final: 0.8284 (t) REVERT: E 43 LEU cc_start: 0.8882 (tp) cc_final: 0.8568 (tp) REVERT: E 44 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8179 (mt0) REVERT: E 59 MET cc_start: 0.8338 (mtm) cc_final: 0.7977 (mtm) REVERT: E 64 MET cc_start: 0.8645 (mmm) cc_final: 0.8087 (mmm) REVERT: F 104 ASP cc_start: 0.8359 (t0) cc_final: 0.8032 (t0) REVERT: F 133 PHE cc_start: 0.9017 (t80) cc_final: 0.8400 (t80) REVERT: F 152 GLN cc_start: 0.9065 (tt0) cc_final: 0.8437 (tp-100) REVERT: F 153 LEU cc_start: 0.9498 (tp) cc_final: 0.9294 (tp) REVERT: F 190 MET cc_start: 0.9072 (mtp) cc_final: 0.8742 (mtp) REVERT: G 57 SER cc_start: 0.9177 (t) cc_final: 0.8861 (p) REVERT: G 79 MET cc_start: 0.8628 (mmm) cc_final: 0.8161 (mmm) REVERT: H 60 LEU cc_start: 0.8744 (mm) cc_final: 0.8517 (mm) REVERT: H 77 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7841 (tm-30) REVERT: H 79 MET cc_start: 0.8229 (mmp) cc_final: 0.7541 (mmp) REVERT: I 5 VAL cc_start: 0.8855 (t) cc_final: 0.8641 (p) REVERT: I 60 LEU cc_start: 0.8573 (mt) cc_final: 0.8325 (mt) REVERT: I 69 GLU cc_start: 0.7636 (tp30) cc_final: 0.6528 (tp30) REVERT: K 32 VAL cc_start: 0.6915 (t) cc_final: 0.6603 (t) REVERT: K 132 LYS cc_start: 0.8592 (mmtp) cc_final: 0.8180 (mttt) REVERT: M 91 VAL cc_start: 0.9101 (t) cc_final: 0.8898 (t) REVERT: N 58 LEU cc_start: 0.9147 (mt) cc_final: 0.8808 (mt) REVERT: N 68 THR cc_start: 0.8980 (m) cc_final: 0.8719 (t) REVERT: N 92 GLU cc_start: 0.7723 (pp20) cc_final: 0.7504 (pp20) REVERT: O 41 THR cc_start: 0.8734 (t) cc_final: 0.8345 (m) REVERT: P 44 GLN cc_start: 0.8245 (tt0) cc_final: 0.7894 (tt0) REVERT: P 56 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7379 (tm-30) REVERT: P 57 SER cc_start: 0.9113 (m) cc_final: 0.8457 (p) REVERT: S 25 THR cc_start: 0.7832 (t) cc_final: 0.7606 (t) REVERT: S 37 LEU cc_start: 0.9047 (tp) cc_final: 0.8687 (tp) REVERT: T 30 LEU cc_start: 0.9183 (tp) cc_final: 0.8903 (tp) REVERT: T 50 TYR cc_start: 0.9149 (t80) cc_final: 0.8936 (t80) REVERT: U 46 LEU cc_start: 0.9009 (mp) cc_final: 0.8361 (tt) REVERT: U 55 SER cc_start: 0.9235 (m) cc_final: 0.8507 (m) REVERT: U 81 ASN cc_start: 0.9182 (m-40) cc_final: 0.8943 (m-40) REVERT: V 32 LEU cc_start: 0.8695 (mt) cc_final: 0.8358 (tt) REVERT: V 64 GLN cc_start: 0.8575 (tt0) cc_final: 0.8296 (tt0) REVERT: W 39 LYS cc_start: 0.8159 (mttt) cc_final: 0.7584 (mptt) REVERT: W 43 ASN cc_start: 0.8665 (t0) cc_final: 0.8247 (t0) REVERT: Y 112 SER cc_start: 0.8127 (p) cc_final: 0.7719 (m) REVERT: Y 123 ASN cc_start: 0.8746 (t0) cc_final: 0.8480 (t0) REVERT: Y 138 ARG cc_start: 0.8709 (mtp85) cc_final: 0.8477 (mtp85) REVERT: Z 133 ASN cc_start: 0.9132 (t0) cc_final: 0.8791 (t0) REVERT: Z 161 LEU cc_start: 0.8614 (tp) cc_final: 0.8414 (tp) REVERT: 0 164 ASN cc_start: 0.8819 (m-40) cc_final: 0.8438 (m110) REVERT: 2 127 GLN cc_start: 0.8255 (tp40) cc_final: 0.7932 (tp40) REVERT: 4 150 PHE cc_start: 0.9028 (p90) cc_final: 0.8591 (p90) REVERT: 4 167 THR cc_start: 0.8762 (m) cc_final: 0.8522 (t) REVERT: 6 127 GLN cc_start: 0.8957 (tp40) cc_final: 0.8338 (tp40) REVERT: 6 138 ARG cc_start: 0.8363 (mtp85) cc_final: 0.7673 (mtm110) REVERT: 6 149 THR cc_start: 0.8964 (m) cc_final: 0.8200 (p) REVERT: 6 168 LEU cc_start: 0.8757 (tp) cc_final: 0.8377 (tp) REVERT: 8 115 ILE cc_start: 0.8931 (mt) cc_final: 0.8644 (mm) REVERT: 8 144 ASN cc_start: 0.7746 (t0) cc_final: 0.7474 (t0) REVERT: 8 150 PHE cc_start: 0.9272 (p90) cc_final: 0.8754 (p90) REVERT: x 150 PHE cc_start: 0.9294 (p90) cc_final: 0.8553 (p90) REVERT: x 153 SER cc_start: 0.9395 (t) cc_final: 0.9163 (p) REVERT: x 168 LEU cc_start: 0.9366 (tp) cc_final: 0.9155 (tt) REVERT: y 115 ILE cc_start: 0.9358 (mt) cc_final: 0.9101 (mt) REVERT: y 158 LEU cc_start: 0.8252 (tp) cc_final: 0.7893 (mm) REVERT: y 160 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7777 (mm-30) REVERT: y 164 ASN cc_start: 0.8691 (m-40) cc_final: 0.8488 (m-40) REVERT: z 112 SER cc_start: 0.9208 (p) cc_final: 0.8867 (m) REVERT: z 127 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8076 (tm-30) REVERT: z 149 THR cc_start: 0.9038 (m) cc_final: 0.8767 (t) REVERT: 1 118 GLU cc_start: 0.7683 (pm20) cc_final: 0.7286 (pm20) REVERT: 1 130 LYS cc_start: 0.8478 (mmmt) cc_final: 0.8145 (mmtt) REVERT: 1 133 ASN cc_start: 0.8647 (m-40) cc_final: 0.8333 (t0) REVERT: 3 115 ILE cc_start: 0.8459 (mt) cc_final: 0.8127 (mt) REVERT: 7 168 LEU cc_start: 0.9108 (tp) cc_final: 0.8893 (tp) REVERT: 9 135 TYR cc_start: 0.7592 (t80) cc_final: 0.7078 (t80) REVERT: a 26 LEU cc_start: 0.8780 (tp) cc_final: 0.8467 (tp) REVERT: a 31 THR cc_start: 0.7861 (m) cc_final: 0.7471 (m) REVERT: a 80 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8338 (tm-30) REVERT: b 14 SER cc_start: 0.8792 (m) cc_final: 0.8581 (p) REVERT: b 43 ASN cc_start: 0.8476 (t0) cc_final: 0.8187 (t0) REVERT: b 45 GLN cc_start: 0.9009 (tp40) cc_final: 0.7993 (tm-30) REVERT: b 49 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7278 (mm-30) REVERT: b 59 LEU cc_start: 0.9378 (mp) cc_final: 0.9177 (mp) REVERT: b 64 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7674 (tm-30) REVERT: c 59 LEU cc_start: 0.9408 (mt) cc_final: 0.9199 (mt) REVERT: d 45 GLN cc_start: 0.8760 (tp40) cc_final: 0.8550 (tp-100) REVERT: d 57 TYR cc_start: 0.8956 (t80) cc_final: 0.8493 (t80) REVERT: d 71 ILE cc_start: 0.8638 (mm) cc_final: 0.8111 (mm) REVERT: d 75 ASP cc_start: 0.8254 (m-30) cc_final: 0.7902 (m-30) REVERT: e 40 ASN cc_start: 0.8412 (p0) cc_final: 0.7948 (p0) REVERT: e 56 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8157 (tt0) REVERT: f 14 SER cc_start: 0.9066 (p) cc_final: 0.8388 (t) REVERT: f 20 ASP cc_start: 0.8245 (t70) cc_final: 0.7976 (t0) REVERT: f 80 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8040 (tm-30) REVERT: g 17 GLU cc_start: 0.7694 (mp0) cc_final: 0.7269 (mp0) REVERT: g 26 LEU cc_start: 0.9175 (tt) cc_final: 0.8561 (mm) REVERT: g 79 ILE cc_start: 0.9187 (mm) cc_final: 0.8977 (mm) REVERT: g 80 GLN cc_start: 0.8731 (tp-100) cc_final: 0.8277 (tm-30) REVERT: g 82 PHE cc_start: 0.9083 (m-10) cc_final: 0.8869 (m-80) REVERT: h 19 PHE cc_start: 0.7004 (t80) cc_final: 0.6794 (t80) REVERT: h 59 LEU cc_start: 0.9242 (mp) cc_final: 0.9024 (mp) REVERT: i 72 LYS cc_start: 0.8936 (ttpt) cc_final: 0.8723 (ttpt) REVERT: i 80 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8180 (tm-30) REVERT: i 81 ASN cc_start: 0.9280 (m-40) cc_final: 0.9016 (m-40) REVERT: j 14 SER cc_start: 0.8844 (m) cc_final: 0.8632 (p) REVERT: j 80 GLN cc_start: 0.9130 (tp-100) cc_final: 0.8908 (tp-100) REVERT: k 37 LEU cc_start: 0.8997 (tp) cc_final: 0.8677 (tt) REVERT: k 50 TYR cc_start: 0.9248 (t80) cc_final: 0.8893 (t80) REVERT: l 16 SER cc_start: 0.9039 (m) cc_final: 0.8315 (t) REVERT: l 20 ASP cc_start: 0.7581 (m-30) cc_final: 0.7320 (m-30) REVERT: l 25 THR cc_start: 0.8846 (p) cc_final: 0.8075 (p) REVERT: l 45 GLN cc_start: 0.8114 (tp40) cc_final: 0.7755 (tp40) REVERT: l 50 TYR cc_start: 0.9178 (t80) cc_final: 0.8826 (t80) REVERT: m 20 ASP cc_start: 0.8040 (m-30) cc_final: 0.7528 (m-30) REVERT: m 50 TYR cc_start: 0.8795 (t80) cc_final: 0.8420 (t80) REVERT: m 75 ASP cc_start: 0.8335 (m-30) cc_final: 0.7503 (m-30) REVERT: n 3 VAL cc_start: 0.8580 (t) cc_final: 0.8292 (m) REVERT: n 29 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7282 (tm-30) REVERT: n 49 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6929 (tm-30) REVERT: n 53 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8435 (mmtm) REVERT: n 75 ASP cc_start: 0.8476 (m-30) cc_final: 0.8125 (m-30) REVERT: n 80 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8006 (tm-30) REVERT: o 39 LYS cc_start: 0.7875 (mmpt) cc_final: 0.7334 (mmpt) REVERT: o 50 TYR cc_start: 0.9234 (t80) cc_final: 0.8972 (t80) REVERT: o 72 LYS cc_start: 0.9428 (tmtt) cc_final: 0.9025 (tmtt) REVERT: p 25 THR cc_start: 0.8273 (p) cc_final: 0.7632 (t) REVERT: p 75 ASP cc_start: 0.8637 (m-30) cc_final: 0.8065 (m-30) REVERT: q 14 SER cc_start: 0.9485 (m) cc_final: 0.9167 (p) REVERT: q 32 LEU cc_start: 0.8237 (tp) cc_final: 0.7886 (tp) REVERT: q 36 LYS cc_start: 0.8706 (mttt) cc_final: 0.8465 (mtmt) REVERT: r 25 THR cc_start: 0.8343 (p) cc_final: 0.8023 (p) REVERT: r 29 GLU cc_start: 0.8915 (pm20) cc_final: 0.8633 (pm20) REVERT: r 59 LEU cc_start: 0.8934 (mt) cc_final: 0.8623 (mt) REVERT: s 7 ASN cc_start: 0.6819 (m-40) cc_final: 0.5918 (p0) REVERT: s 15 LEU cc_start: 0.8807 (tp) cc_final: 0.8599 (tp) REVERT: s 23 THR cc_start: 0.8539 (m) cc_final: 0.8277 (m) REVERT: s 27 GLN cc_start: 0.8380 (mt0) cc_final: 0.7910 (tm-30) REVERT: s 65 SER cc_start: 0.9065 (t) cc_final: 0.8723 (m) REVERT: s 69 LYS cc_start: 0.7813 (tptm) cc_final: 0.7385 (ttmt) REVERT: t 49 GLU cc_start: 0.7215 (tp30) cc_final: 0.6515 (tp30) REVERT: t 51 GLN cc_start: 0.8654 (tt0) cc_final: 0.6706 (mm110) REVERT: t 69 LYS cc_start: 0.9266 (tptm) cc_final: 0.8590 (mttt) REVERT: t 72 LYS cc_start: 0.9491 (tmtt) cc_final: 0.9238 (tttp) REVERT: u 30 LEU cc_start: 0.8797 (tp) cc_final: 0.8563 (tt) REVERT: u 49 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7074 (tp30) REVERT: u 65 SER cc_start: 0.9194 (t) cc_final: 0.8977 (t) REVERT: u 69 LYS cc_start: 0.8906 (tptm) cc_final: 0.7504 (ttmt) REVERT: u 82 PHE cc_start: 0.9003 (m-80) cc_final: 0.8505 (m-80) REVERT: v 25 THR cc_start: 0.8281 (p) cc_final: 0.7989 (p) REVERT: v 32 LEU cc_start: 0.9302 (tp) cc_final: 0.9045 (tp) REVERT: v 36 LYS cc_start: 0.9015 (mttt) cc_final: 0.8711 (mttm) REVERT: v 53 LYS cc_start: 0.8750 (mmmt) cc_final: 0.8456 (mmmm) REVERT: v 69 LYS cc_start: 0.9116 (tptm) cc_final: 0.8218 (mttt) REVERT: w 25 THR cc_start: 0.8540 (p) cc_final: 0.8116 (p) REVERT: w 57 TYR cc_start: 0.8935 (t80) cc_final: 0.8503 (t80) REVERT: w 61 ARG cc_start: 0.8354 (mmt180) cc_final: 0.6674 (ttp-170) REVERT: w 69 LYS cc_start: 0.8881 (tppt) cc_final: 0.7375 (tppt) REVERT: a0 103 LYS cc_start: 0.8120 (tttm) cc_final: 0.7043 (tptt) REVERT: d0 103 LYS cc_start: 0.9260 (ttmt) cc_final: 0.7924 (tptt) REVERT: e0 103 LYS cc_start: 0.8708 (ttmt) cc_final: 0.7814 (tttt) REVERT: f0 100 ARG cc_start: 0.8507 (ttm170) cc_final: 0.8049 (ttm170) REVERT: f0 103 LYS cc_start: 0.9230 (ttmt) cc_final: 0.8344 (tptt) REVERT: g0 103 LYS cc_start: 0.9102 (mtmt) cc_final: 0.7769 (tptt) REVERT: i0 103 LYS cc_start: 0.8935 (tttt) cc_final: 0.8627 (tptt) REVERT: k0 103 LYS cc_start: 0.8863 (ttmm) cc_final: 0.8103 (tptt) REVERT: l0 103 LYS cc_start: 0.8843 (ttmt) cc_final: 0.8167 (tptt) REVERT: m0 103 LYS cc_start: 0.9060 (mtpt) cc_final: 0.8166 (tptt) REVERT: n0 97 SER cc_start: 0.9021 (m) cc_final: 0.8784 (t) REVERT: n0 103 LYS cc_start: 0.8813 (ttpt) cc_final: 0.8316 (ttpt) REVERT: p0 103 LYS cc_start: 0.8840 (ttpt) cc_final: 0.8054 (tptt) REVERT: q0 103 LYS cc_start: 0.9009 (ttmt) cc_final: 0.8308 (tptt) REVERT: r0 102 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8021 (mt-10) REVERT: r0 103 LYS cc_start: 0.8859 (ttmt) cc_final: 0.7592 (tptt) REVERT: t0 103 LYS cc_start: 0.8922 (ttmt) cc_final: 0.8139 (tptt) REVERT: t0 105 ARG cc_start: 0.9218 (ttm110) cc_final: 0.7766 (tpm170) REVERT: u0 98 SER cc_start: 0.8552 (m) cc_final: 0.7757 (p) REVERT: u0 100 ARG cc_start: 0.7828 (ttm110) cc_final: 0.7348 (tpt170) REVERT: u0 103 LYS cc_start: 0.9084 (ttmt) cc_final: 0.8016 (tptt) REVERT: v0 92 THR cc_start: 0.8469 (m) cc_final: 0.8238 (m) REVERT: v0 103 LYS cc_start: 0.9256 (mttt) cc_final: 0.7829 (tptt) REVERT: w0 103 LYS cc_start: 0.8850 (ttmt) cc_final: 0.8343 (tptt) REVERT: x0 103 LYS cc_start: 0.8507 (ttmt) cc_final: 0.7923 (tptt) outliers start: 6 outliers final: 0 residues processed: 2184 average time/residue: 0.5337 time to fit residues: 1965.2229 Evaluate side-chains 1887 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1887 time to evaluate : 5.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 311 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 301 optimal weight: 0.0060 chunk 151 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 320 optimal weight: 1.9990 chunk 343 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 396 optimal weight: 0.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** D 116 GLN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS E 116 GLN ** F 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 170 ASN F 247 HIS F 252 ASN I 9 ASN J 76 HIS O 44 GLN P 59 ASN R 19 GLN U 80 GLN V 40 ASN W 81 ASN Y 144 ASN 2 137 HIS 4 137 HIS ** 4 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 64 GLN f 51 GLN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 64 GLN n 7 ASN n 81 ASN p 81 ASN t 24 GLN u 40 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 44858 Z= 0.220 Angle : 0.655 10.737 60890 Z= 0.326 Chirality : 0.041 0.203 7369 Planarity : 0.004 0.076 7620 Dihedral : 4.343 87.134 5953 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.08 % Allowed : 1.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.11), residues: 5404 helix: 2.96 (0.08), residues: 4151 sheet: 1.94 (0.32), residues: 160 loop : -2.78 (0.16), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP j 10 HIS 0.006 0.001 HIS F 11 PHE 0.029 0.002 PHE g 19 TYR 0.026 0.002 TYR i 50 ARG 0.006 0.000 ARG K 55 *********************** 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 2164 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 2160 time to evaluate : 5.257 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: 0.8683 (p) cc_final: 0.7951 (p) REVERT: A 36 MET cc_start: 0.8320 (tpp) cc_final: 0.8031 (tpp) REVERT: A 50 MET cc_start: 0.8253 (ttp) cc_final: 0.7947 (ttm) REVERT: A 68 ILE cc_start: 0.9535 (mt) cc_final: 0.9245 (mt) REVERT: A 69 GLU cc_start: 0.7814 (tp30) cc_final: 0.7198 (mm-30) REVERT: A 101 GLN cc_start: 0.8765 (tt0) cc_final: 0.8363 (tm-30) REVERT: A 152 LYS cc_start: 0.9154 (tttt) cc_final: 0.8740 (mtmt) REVERT: A 177 MET cc_start: 0.7985 (mtt) cc_final: 0.7613 (mtt) REVERT: A 205 LYS cc_start: 0.9133 (mttt) cc_final: 0.8172 (tttt) REVERT: B 65 LYS cc_start: 0.8720 (tttp) cc_final: 0.7958 (tttt) REVERT: B 162 VAL cc_start: 0.8957 (m) cc_final: 0.8732 (p) REVERT: B 190 LYS cc_start: 0.9146 (mtmt) cc_final: 0.8469 (mtmm) REVERT: C 25 THR cc_start: 0.9216 (p) cc_final: 0.8827 (t) REVERT: C 72 TYR cc_start: 0.5477 (t80) cc_final: 0.5171 (m-10) REVERT: C 105 LYS cc_start: 0.8949 (tttp) cc_final: 0.8715 (mtpp) REVERT: C 117 ARG cc_start: 0.8387 (mtt180) cc_final: 0.7813 (tpt170) REVERT: C 210 GLN cc_start: 0.7531 (tm-30) cc_final: 0.6960 (tm-30) REVERT: D 2 LEU cc_start: 0.9214 (mt) cc_final: 0.8916 (mt) REVERT: D 6 SER cc_start: 0.8799 (m) cc_final: 0.7992 (p) REVERT: D 17 LEU cc_start: 0.9296 (tp) cc_final: 0.8906 (tt) REVERT: E 64 MET cc_start: 0.8685 (mmm) cc_final: 0.8120 (mmm) REVERT: F 31 LEU cc_start: 0.8662 (mt) cc_final: 0.8452 (mm) REVERT: F 58 SER cc_start: 0.8661 (m) cc_final: 0.8412 (p) REVERT: F 104 ASP cc_start: 0.8484 (t0) cc_final: 0.8196 (t0) REVERT: F 133 PHE cc_start: 0.9054 (t80) cc_final: 0.8457 (t80) REVERT: F 152 GLN cc_start: 0.9040 (tt0) cc_final: 0.8467 (tp-100) REVERT: F 153 LEU cc_start: 0.9494 (tp) cc_final: 0.9268 (tp) REVERT: F 190 MET cc_start: 0.9078 (mtp) cc_final: 0.8793 (mtp) REVERT: G 57 SER cc_start: 0.9161 (t) cc_final: 0.8865 (p) REVERT: G 79 MET cc_start: 0.8650 (mmm) cc_final: 0.8020 (mmm) REVERT: G 83 LYS cc_start: 0.9059 (mmmm) cc_final: 0.8843 (mmmm) REVERT: H 60 LEU cc_start: 0.8809 (mm) cc_final: 0.8599 (mm) REVERT: H 77 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7838 (tm-30) REVERT: H 79 MET cc_start: 0.8089 (mmp) cc_final: 0.7432 (mmp) REVERT: H 81 LEU cc_start: 0.8510 (mt) cc_final: 0.8245 (mt) REVERT: I 5 VAL cc_start: 0.9063 (t) cc_final: 0.8558 (p) REVERT: I 9 ASN cc_start: 0.8108 (m-40) cc_final: 0.7853 (m-40) REVERT: I 53 LEU cc_start: 0.7844 (tp) cc_final: 0.7631 (tp) REVERT: I 60 LEU cc_start: 0.8585 (mt) cc_final: 0.8365 (mt) REVERT: I 69 GLU cc_start: 0.7675 (tp30) cc_final: 0.6485 (tp30) REVERT: K 132 LYS cc_start: 0.8634 (mmtp) cc_final: 0.8113 (mttt) REVERT: N 33 LYS cc_start: 0.8640 (mmmm) cc_final: 0.8003 (mmtt) REVERT: N 58 LEU cc_start: 0.9179 (mt) cc_final: 0.8831 (mt) REVERT: O 41 THR cc_start: 0.8704 (t) cc_final: 0.8369 (m) REVERT: P 54 ASN cc_start: 0.8684 (t0) cc_final: 0.8449 (t0) REVERT: P 56 GLU cc_start: 0.7828 (tm-30) cc_final: 0.6987 (tm-30) REVERT: P 57 SER cc_start: 0.9097 (m) cc_final: 0.8520 (p) REVERT: S 25 THR cc_start: 0.7851 (t) cc_final: 0.7617 (t) REVERT: S 37 LEU cc_start: 0.9043 (tp) cc_final: 0.8713 (tp) REVERT: T 30 LEU cc_start: 0.9196 (tp) cc_final: 0.8862 (tp) REVERT: T 50 TYR cc_start: 0.9158 (t80) cc_final: 0.8917 (t80) REVERT: U 55 SER cc_start: 0.9144 (m) cc_final: 0.8413 (m) REVERT: U 81 ASN cc_start: 0.9167 (m-40) cc_final: 0.8929 (m-40) REVERT: V 32 LEU cc_start: 0.8729 (mt) cc_final: 0.8335 (tt) REVERT: V 45 GLN cc_start: 0.8798 (tp40) cc_final: 0.8098 (tp40) REVERT: V 49 GLU cc_start: 0.8159 (mp0) cc_final: 0.7625 (mp0) REVERT: V 64 GLN cc_start: 0.8365 (tt0) cc_final: 0.8109 (tt0) REVERT: W 39 LYS cc_start: 0.8136 (mttt) cc_final: 0.7557 (mptt) REVERT: W 43 ASN cc_start: 0.8653 (t0) cc_final: 0.8204 (t0) REVERT: Y 112 SER cc_start: 0.8130 (p) cc_final: 0.7721 (m) REVERT: Y 123 ASN cc_start: 0.8752 (t0) cc_final: 0.8486 (t0) REVERT: 0 164 ASN cc_start: 0.8887 (m-40) cc_final: 0.8462 (m110) REVERT: 2 127 GLN cc_start: 0.8255 (tp40) cc_final: 0.7933 (tp40) REVERT: 4 150 PHE cc_start: 0.9013 (p90) cc_final: 0.8567 (p90) REVERT: 4 167 THR cc_start: 0.8745 (m) cc_final: 0.8523 (t) REVERT: 6 127 GLN cc_start: 0.8898 (tp40) cc_final: 0.8294 (tp40) REVERT: 6 138 ARG cc_start: 0.8360 (mtp85) cc_final: 0.7684 (mtm110) REVERT: 6 149 THR cc_start: 0.8944 (m) cc_final: 0.8130 (p) REVERT: 6 168 LEU cc_start: 0.8737 (tp) cc_final: 0.8282 (tp) REVERT: 8 111 ILE cc_start: 0.9289 (mt) cc_final: 0.9079 (mt) REVERT: 8 115 ILE cc_start: 0.8917 (mt) cc_final: 0.8652 (mm) REVERT: 8 144 ASN cc_start: 0.7742 (t0) cc_final: 0.7502 (t0) REVERT: 8 150 PHE cc_start: 0.9269 (p90) cc_final: 0.8744 (p90) REVERT: x 150 PHE cc_start: 0.9297 (p90) cc_final: 0.8519 (p90) REVERT: x 153 SER cc_start: 0.9564 (t) cc_final: 0.9001 (p) REVERT: x 168 LEU cc_start: 0.9366 (tp) cc_final: 0.9108 (tt) REVERT: y 115 ILE cc_start: 0.9356 (mt) cc_final: 0.9149 (mt) REVERT: y 160 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7788 (mm-30) REVERT: z 112 SER cc_start: 0.9234 (p) cc_final: 0.8884 (m) REVERT: z 127 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8182 (tm-30) REVERT: z 149 THR cc_start: 0.9038 (m) cc_final: 0.8751 (t) REVERT: 1 130 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8174 (mmtt) REVERT: 1 133 ASN cc_start: 0.8641 (m-40) cc_final: 0.8334 (t0) REVERT: 3 115 ILE cc_start: 0.8457 (mt) cc_final: 0.8152 (mt) REVERT: 7 168 LEU cc_start: 0.9063 (tp) cc_final: 0.8844 (tp) REVERT: 9 135 TYR cc_start: 0.7608 (t80) cc_final: 0.7097 (t80) REVERT: a 31 THR cc_start: 0.7975 (m) cc_final: 0.7561 (m) REVERT: a 80 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8344 (tm-30) REVERT: b 14 SER cc_start: 0.8893 (m) cc_final: 0.8604 (p) REVERT: b 43 ASN cc_start: 0.8513 (t0) cc_final: 0.8221 (t0) REVERT: b 45 GLN cc_start: 0.8989 (tp40) cc_final: 0.7920 (tm-30) REVERT: b 49 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7021 (mm-30) REVERT: b 53 LYS cc_start: 0.9342 (mmmt) cc_final: 0.9134 (mmmt) REVERT: b 64 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7894 (tm-30) REVERT: c 59 LEU cc_start: 0.9424 (mt) cc_final: 0.9210 (mt) REVERT: d 43 ASN cc_start: 0.8407 (t0) cc_final: 0.8116 (t0) REVERT: d 57 TYR cc_start: 0.8982 (t80) cc_final: 0.8489 (t80) REVERT: d 71 ILE cc_start: 0.8654 (mm) cc_final: 0.8103 (mm) REVERT: d 75 ASP cc_start: 0.8248 (m-30) cc_final: 0.7961 (m-30) REVERT: e 40 ASN cc_start: 0.8527 (p0) cc_final: 0.8093 (p0) REVERT: f 14 SER cc_start: 0.8946 (p) cc_final: 0.8313 (t) REVERT: g 17 GLU cc_start: 0.7698 (mp0) cc_final: 0.7302 (mp0) REVERT: g 26 LEU cc_start: 0.9140 (tt) cc_final: 0.8449 (mm) REVERT: g 65 SER cc_start: 0.9092 (t) cc_final: 0.8866 (t) REVERT: g 80 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8388 (tm-30) REVERT: h 19 PHE cc_start: 0.7157 (t80) cc_final: 0.6826 (t80) REVERT: h 29 GLU cc_start: 0.8602 (mp0) cc_final: 0.8262 (mp0) REVERT: i 72 LYS cc_start: 0.8873 (ttpt) cc_final: 0.8644 (ttpt) REVERT: i 80 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8249 (tm-30) REVERT: i 81 ASN cc_start: 0.9273 (m-40) cc_final: 0.9015 (m-40) REVERT: j 14 SER cc_start: 0.8848 (m) cc_final: 0.8618 (p) REVERT: j 80 GLN cc_start: 0.9181 (tp-100) cc_final: 0.8910 (tp-100) REVERT: k 50 TYR cc_start: 0.9241 (t80) cc_final: 0.9013 (t80) REVERT: k 80 GLN cc_start: 0.8688 (tp40) cc_final: 0.8410 (tp40) REVERT: l 16 SER cc_start: 0.9154 (m) cc_final: 0.8376 (t) REVERT: l 20 ASP cc_start: 0.7566 (m-30) cc_final: 0.7328 (m-30) REVERT: l 25 THR cc_start: 0.8841 (p) cc_final: 0.7998 (p) REVERT: l 26 LEU cc_start: 0.9145 (tt) cc_final: 0.8894 (tt) REVERT: l 45 GLN cc_start: 0.8190 (tp40) cc_final: 0.7700 (tp40) REVERT: l 50 TYR cc_start: 0.9187 (t80) cc_final: 0.8790 (t80) REVERT: l 80 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8066 (tm-30) REVERT: m 20 ASP cc_start: 0.8035 (m-30) cc_final: 0.7515 (m-30) REVERT: m 50 TYR cc_start: 0.8803 (t80) cc_final: 0.8493 (t80) REVERT: m 75 ASP cc_start: 0.8370 (m-30) cc_final: 0.7493 (m-30) REVERT: n 3 VAL cc_start: 0.8656 (t) cc_final: 0.8370 (m) REVERT: n 29 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7208 (tm-30) REVERT: n 49 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6970 (tm-30) REVERT: n 53 LYS cc_start: 0.9049 (mmtt) cc_final: 0.8417 (mmtm) REVERT: n 75 ASP cc_start: 0.8494 (m-30) cc_final: 0.8153 (m-30) REVERT: n 80 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8024 (tm-30) REVERT: o 14 SER cc_start: 0.8734 (t) cc_final: 0.8303 (p) REVERT: o 39 LYS cc_start: 0.7776 (mmpt) cc_final: 0.7359 (mmpt) REVERT: o 50 TYR cc_start: 0.9272 (t80) cc_final: 0.8980 (t80) REVERT: p 25 THR cc_start: 0.8274 (p) cc_final: 0.7618 (t) REVERT: p 75 ASP cc_start: 0.8623 (m-30) cc_final: 0.8092 (m-30) REVERT: q 14 SER cc_start: 0.9487 (m) cc_final: 0.9199 (p) REVERT: q 32 LEU cc_start: 0.8198 (tp) cc_final: 0.7844 (tp) REVERT: q 36 LYS cc_start: 0.8650 (mttt) cc_final: 0.8406 (mtmt) REVERT: r 59 LEU cc_start: 0.8937 (mt) cc_final: 0.8621 (mt) REVERT: s 7 ASN cc_start: 0.6898 (m-40) cc_final: 0.6017 (p0) REVERT: s 23 THR cc_start: 0.8509 (m) cc_final: 0.8261 (m) REVERT: s 27 GLN cc_start: 0.8387 (mt0) cc_final: 0.7902 (tm-30) REVERT: s 65 SER cc_start: 0.9130 (t) cc_final: 0.8746 (m) REVERT: s 69 LYS cc_start: 0.8537 (tptm) cc_final: 0.7408 (ttmt) REVERT: t 52 SER cc_start: 0.8422 (m) cc_final: 0.8204 (t) REVERT: t 69 LYS cc_start: 0.9289 (tptm) cc_final: 0.8602 (mttt) REVERT: t 72 LYS cc_start: 0.9520 (tmtt) cc_final: 0.9269 (tttp) REVERT: u 30 LEU cc_start: 0.8945 (tp) cc_final: 0.8683 (tt) REVERT: u 49 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7064 (tp30) REVERT: u 69 LYS cc_start: 0.8885 (tptm) cc_final: 0.7448 (ttmt) REVERT: u 82 PHE cc_start: 0.9026 (m-80) cc_final: 0.8526 (m-80) REVERT: v 25 THR cc_start: 0.8280 (p) cc_final: 0.8010 (p) REVERT: v 32 LEU cc_start: 0.9303 (tp) cc_final: 0.9052 (tp) REVERT: v 36 LYS cc_start: 0.9019 (mttt) cc_final: 0.8725 (mttm) REVERT: v 53 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8463 (mmmm) REVERT: v 69 LYS cc_start: 0.9135 (tptm) cc_final: 0.8208 (mttt) REVERT: w 25 THR cc_start: 0.8562 (p) cc_final: 0.8207 (p) REVERT: w 47 LEU cc_start: 0.9161 (mm) cc_final: 0.8860 (mm) REVERT: w 57 TYR cc_start: 0.8949 (t80) cc_final: 0.8522 (t80) REVERT: w 61 ARG cc_start: 0.8348 (mmt180) cc_final: 0.6690 (ttp-170) REVERT: w 69 LYS cc_start: 0.8882 (tppt) cc_final: 0.7386 (tppt) REVERT: a0 103 LYS cc_start: 0.8137 (tttm) cc_final: 0.7040 (tptt) REVERT: d0 103 LYS cc_start: 0.9261 (ttmt) cc_final: 0.7930 (tptt) REVERT: e0 103 LYS cc_start: 0.8707 (ttmt) cc_final: 0.7810 (tttt) REVERT: f0 100 ARG cc_start: 0.8505 (ttm170) cc_final: 0.8008 (ttm170) REVERT: f0 103 LYS cc_start: 0.9167 (ttmt) cc_final: 0.8325 (tptt) REVERT: g0 103 LYS cc_start: 0.9121 (mtmt) cc_final: 0.7779 (tptt) REVERT: i0 103 LYS cc_start: 0.8938 (tttt) cc_final: 0.8639 (tptt) REVERT: k0 103 LYS cc_start: 0.8880 (ttmm) cc_final: 0.8128 (tptt) REVERT: k0 105 ARG cc_start: 0.8840 (ttm110) cc_final: 0.7339 (tmt170) REVERT: l0 103 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8178 (tptt) REVERT: m0 103 LYS cc_start: 0.9070 (mtpt) cc_final: 0.8168 (tptt) REVERT: n0 97 SER cc_start: 0.9008 (m) cc_final: 0.8788 (t) REVERT: n0 103 LYS cc_start: 0.8858 (ttpt) cc_final: 0.8337 (ttpt) REVERT: p0 103 LYS cc_start: 0.8864 (ttpt) cc_final: 0.8073 (tptt) REVERT: q0 103 LYS cc_start: 0.9025 (ttmt) cc_final: 0.8319 (tptt) REVERT: r0 102 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8075 (mt-10) REVERT: r0 103 LYS cc_start: 0.8876 (ttmt) cc_final: 0.7605 (tptt) REVERT: t0 103 LYS cc_start: 0.8935 (ttmt) cc_final: 0.8139 (tptt) REVERT: t0 105 ARG cc_start: 0.9226 (ttm110) cc_final: 0.7770 (tpm170) REVERT: u0 98 SER cc_start: 0.8739 (m) cc_final: 0.7900 (p) REVERT: u0 100 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7224 (tpt170) REVERT: u0 103 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8023 (tptt) REVERT: v0 92 THR cc_start: 0.8513 (m) cc_final: 0.8257 (m) REVERT: v0 103 LYS cc_start: 0.9263 (mttt) cc_final: 0.7834 (tptt) REVERT: w0 103 LYS cc_start: 0.8862 (ttmt) cc_final: 0.8349 (tptt) REVERT: x0 103 LYS cc_start: 0.8513 (ttmt) cc_final: 0.7846 (tptt) outliers start: 4 outliers final: 1 residues processed: 2160 average time/residue: 0.5387 time to fit residues: 1965.8895 Evaluate side-chains 1882 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1881 time to evaluate : 5.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 458 optimal weight: 0.8980 chunk 482 optimal weight: 4.9990 chunk 440 optimal weight: 0.9990 chunk 469 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 368 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 424 optimal weight: 0.8980 chunk 444 optimal weight: 0.0040 chunk 468 optimal weight: 7.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 HIS ** 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** D 116 GLN D 131 ASN ** 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 S 45 GLN W 81 ASN Y 144 ASN 2 137 HIS ** 4 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 ASN d 45 GLN f 51 GLN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 81 ASN ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 7 ASN n 81 ASN o 24 GLN p 81 ASN s 64 GLN t 24 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 44858 Z= 0.203 Angle : 0.658 12.163 60890 Z= 0.326 Chirality : 0.041 0.377 7369 Planarity : 0.004 0.077 7620 Dihedral : 4.341 87.983 5953 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.06 % Allowed : 0.60 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.11), residues: 5404 helix: 2.95 (0.08), residues: 4151 sheet: 1.90 (0.32), residues: 160 loop : -2.74 (0.16), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 66 HIS 0.006 0.001 HIS F 11 PHE 0.034 0.002 PHE o 19 TYR 0.046 0.002 TYR E 158 ARG 0.010 0.000 ARG K 55 *********************** 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 2137 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 2134 time to evaluate : 5.437 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: A 26 CYS cc_start: 0.8659 (p) cc_final: 0.7909 (p) REVERT: A 36 MET cc_start: 0.8323 (tpp) cc_final: 0.8045 (tpp) REVERT: A 50 MET cc_start: 0.8226 (ttp) cc_final: 0.7887 (ttm) REVERT: A 68 ILE cc_start: 0.9523 (mt) cc_final: 0.9229 (mt) REVERT: A 69 GLU cc_start: 0.7780 (tp30) cc_final: 0.7225 (mm-30) REVERT: A 101 GLN cc_start: 0.8824 (tt0) cc_final: 0.8332 (tm-30) REVERT: A 152 LYS cc_start: 0.9132 (tttt) cc_final: 0.8756 (ttmt) REVERT: A 177 MET cc_start: 0.7937 (mtt) cc_final: 0.7507 (mtt) REVERT: A 205 LYS cc_start: 0.9147 (mttt) cc_final: 0.8197 (tttt) REVERT: B 65 LYS cc_start: 0.8519 (tttp) cc_final: 0.7794 (tmtt) REVERT: B 110 GLU cc_start: 0.8587 (pm20) cc_final: 0.8340 (pm20) REVERT: B 162 VAL cc_start: 0.8936 (m) cc_final: 0.8699 (p) REVERT: B 190 LYS cc_start: 0.9065 (mtmt) cc_final: 0.8291 (mtmm) REVERT: C 25 THR cc_start: 0.9206 (p) cc_final: 0.8759 (t) REVERT: C 72 TYR cc_start: 0.5451 (t80) cc_final: 0.5187 (m-10) REVERT: C 105 LYS cc_start: 0.8911 (tttp) cc_final: 0.8711 (mtpp) REVERT: C 117 ARG cc_start: 0.8253 (mtt180) cc_final: 0.7692 (tpt170) REVERT: C 210 GLN cc_start: 0.7454 (tm-30) cc_final: 0.6945 (tm-30) REVERT: D 2 LEU cc_start: 0.9223 (mt) cc_final: 0.8917 (mt) REVERT: D 6 SER cc_start: 0.8773 (m) cc_final: 0.7906 (p) REVERT: D 17 LEU cc_start: 0.9317 (tp) cc_final: 0.8912 (tt) REVERT: D 116 GLN cc_start: 0.8097 (tt0) cc_final: 0.7860 (tt0) REVERT: E 44 GLN cc_start: 0.8700 (mp10) cc_final: 0.8075 (mt0) REVERT: E 59 MET cc_start: 0.8403 (mtm) cc_final: 0.8159 (mtp) REVERT: E 64 MET cc_start: 0.8762 (mmm) cc_final: 0.8136 (mmm) REVERT: F 104 ASP cc_start: 0.8552 (t0) cc_final: 0.8175 (t0) REVERT: F 133 PHE cc_start: 0.9053 (t80) cc_final: 0.8424 (t80) REVERT: F 152 GLN cc_start: 0.9017 (tt0) cc_final: 0.8530 (tp-100) REVERT: F 153 LEU cc_start: 0.9502 (tp) cc_final: 0.9299 (tp) REVERT: F 229 PHE cc_start: 0.8528 (t80) cc_final: 0.8003 (t80) REVERT: G 57 SER cc_start: 0.9176 (t) cc_final: 0.8865 (p) REVERT: G 79 MET cc_start: 0.8694 (mmm) cc_final: 0.8190 (mmm) REVERT: H 77 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7834 (tm-30) REVERT: H 79 MET cc_start: 0.8265 (mmp) cc_final: 0.7550 (mmp) REVERT: I 5 VAL cc_start: 0.9086 (t) cc_final: 0.8628 (p) REVERT: I 17 ILE cc_start: 0.9068 (mm) cc_final: 0.8816 (tt) REVERT: I 60 LEU cc_start: 0.8668 (mt) cc_final: 0.8414 (mt) REVERT: I 69 GLU cc_start: 0.7688 (tp30) cc_final: 0.6818 (tp30) REVERT: J 70 VAL cc_start: 0.9663 (t) cc_final: 0.9381 (p) REVERT: K 51 MET cc_start: 0.7858 (mmt) cc_final: 0.7616 (mmt) REVERT: K 132 LYS cc_start: 0.8649 (mmtp) cc_final: 0.8072 (mttt) REVERT: N 33 LYS cc_start: 0.8637 (mmmm) cc_final: 0.8033 (mmtt) REVERT: N 58 LEU cc_start: 0.9171 (mt) cc_final: 0.8847 (mt) REVERT: O 41 THR cc_start: 0.8878 (t) cc_final: 0.8328 (m) REVERT: O 67 GLN cc_start: 0.8959 (tt0) cc_final: 0.8723 (tt0) REVERT: P 44 GLN cc_start: 0.8083 (tt0) cc_final: 0.7767 (tt0) REVERT: P 49 MET cc_start: 0.8361 (mmt) cc_final: 0.8112 (mtp) REVERT: P 56 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7410 (tm-30) REVERT: P 57 SER cc_start: 0.9136 (m) cc_final: 0.8479 (p) REVERT: S 25 THR cc_start: 0.7739 (t) cc_final: 0.7529 (t) REVERT: S 37 LEU cc_start: 0.9018 (tp) cc_final: 0.8664 (tp) REVERT: T 30 LEU cc_start: 0.9158 (tp) cc_final: 0.8862 (tp) REVERT: T 50 TYR cc_start: 0.9152 (t80) cc_final: 0.8909 (t80) REVERT: U 81 ASN cc_start: 0.9184 (m-40) cc_final: 0.8926 (m-40) REVERT: V 32 LEU cc_start: 0.8699 (mt) cc_final: 0.8311 (tt) REVERT: V 40 ASN cc_start: 0.8513 (t0) cc_final: 0.8309 (t0) REVERT: V 45 GLN cc_start: 0.8783 (tp40) cc_final: 0.7891 (tp40) REVERT: V 46 LEU cc_start: 0.8998 (mm) cc_final: 0.8783 (mm) REVERT: V 49 GLU cc_start: 0.8123 (mp0) cc_final: 0.7450 (mp0) REVERT: V 64 GLN cc_start: 0.8291 (tt0) cc_final: 0.8081 (tt0) REVERT: W 39 LYS cc_start: 0.8157 (mttt) cc_final: 0.7541 (mptt) REVERT: W 43 ASN cc_start: 0.8619 (t0) cc_final: 0.8184 (t0) REVERT: W 56 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8032 (mt-10) REVERT: Y 112 SER cc_start: 0.8126 (p) cc_final: 0.7688 (m) REVERT: Y 123 ASN cc_start: 0.8721 (t0) cc_final: 0.8444 (t0) REVERT: Z 161 LEU cc_start: 0.8596 (tp) cc_final: 0.8372 (tp) REVERT: 0 164 ASN cc_start: 0.8867 (m-40) cc_final: 0.8462 (m110) REVERT: 2 127 GLN cc_start: 0.8241 (tp40) cc_final: 0.7950 (tp40) REVERT: 4 150 PHE cc_start: 0.9002 (p90) cc_final: 0.8582 (p90) REVERT: 4 168 LEU cc_start: 0.8802 (tp) cc_final: 0.8358 (tt) REVERT: 6 127 GLN cc_start: 0.8895 (tp40) cc_final: 0.8288 (tp40) REVERT: 6 138 ARG cc_start: 0.8352 (mtp85) cc_final: 0.7672 (mtm110) REVERT: 6 149 THR cc_start: 0.8925 (m) cc_final: 0.8156 (p) REVERT: 6 168 LEU cc_start: 0.8707 (tp) cc_final: 0.8292 (tp) REVERT: 8 115 ILE cc_start: 0.8926 (mt) cc_final: 0.8658 (mm) REVERT: 8 144 ASN cc_start: 0.7729 (t0) cc_final: 0.7478 (t0) REVERT: 8 150 PHE cc_start: 0.9273 (p90) cc_final: 0.8757 (p90) REVERT: x 150 PHE cc_start: 0.9233 (p90) cc_final: 0.8566 (p90) REVERT: x 153 SER cc_start: 0.9532 (t) cc_final: 0.8958 (p) REVERT: y 115 ILE cc_start: 0.9329 (mt) cc_final: 0.8994 (mt) REVERT: y 158 LEU cc_start: 0.8283 (tp) cc_final: 0.7897 (mm) REVERT: y 160 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7770 (mm-30) REVERT: z 127 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8181 (tm-30) REVERT: z 136 ASP cc_start: 0.7537 (p0) cc_final: 0.7100 (p0) REVERT: z 149 THR cc_start: 0.9030 (m) cc_final: 0.8767 (t) REVERT: 1 130 LYS cc_start: 0.8410 (mmmt) cc_final: 0.8170 (mmtt) REVERT: 1 133 ASN cc_start: 0.8649 (m-40) cc_final: 0.8345 (t0) REVERT: 3 115 ILE cc_start: 0.8687 (mt) cc_final: 0.8246 (mt) REVERT: 9 135 TYR cc_start: 0.7594 (t80) cc_final: 0.7109 (t80) REVERT: a 31 THR cc_start: 0.7961 (m) cc_final: 0.7534 (m) REVERT: a 80 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8368 (tm-30) REVERT: b 14 SER cc_start: 0.8787 (m) cc_final: 0.8567 (p) REVERT: b 43 ASN cc_start: 0.8495 (t0) cc_final: 0.8219 (t0) REVERT: b 45 GLN cc_start: 0.8926 (tp40) cc_final: 0.7958 (tm-30) REVERT: b 49 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7197 (mm-30) REVERT: b 64 GLN cc_start: 0.8401 (tm-30) cc_final: 0.7857 (tm-30) REVERT: c 59 LEU cc_start: 0.9423 (mt) cc_final: 0.9192 (mt) REVERT: c 80 GLN cc_start: 0.8861 (tp-100) cc_final: 0.8563 (tp40) REVERT: d 57 TYR cc_start: 0.9005 (t80) cc_final: 0.8540 (t80) REVERT: d 80 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7393 (tm-30) REVERT: e 40 ASN cc_start: 0.8537 (p0) cc_final: 0.8121 (p0) REVERT: f 14 SER cc_start: 0.8975 (p) cc_final: 0.8235 (t) REVERT: g 17 GLU cc_start: 0.7734 (mp0) cc_final: 0.7299 (mp0) REVERT: g 26 LEU cc_start: 0.9112 (tt) cc_final: 0.8640 (mm) REVERT: g 30 LEU cc_start: 0.9410 (tp) cc_final: 0.9208 (tp) REVERT: g 65 SER cc_start: 0.9055 (t) cc_final: 0.8820 (t) REVERT: g 80 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8247 (tm-30) REVERT: h 11 THR cc_start: 0.8444 (m) cc_final: 0.7515 (m) REVERT: h 19 PHE cc_start: 0.7099 (t80) cc_final: 0.6820 (t80) REVERT: h 26 LEU cc_start: 0.8868 (mm) cc_final: 0.8626 (mm) REVERT: h 59 LEU cc_start: 0.9319 (mp) cc_final: 0.9053 (mp) REVERT: i 80 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8097 (tm-30) REVERT: i 81 ASN cc_start: 0.9216 (m-40) cc_final: 0.8920 (m-40) REVERT: j 15 LEU cc_start: 0.9342 (tt) cc_final: 0.9098 (tp) REVERT: j 80 GLN cc_start: 0.9162 (tp-100) cc_final: 0.8915 (tp-100) REVERT: k 50 TYR cc_start: 0.9238 (t80) cc_final: 0.9018 (t80) REVERT: k 80 GLN cc_start: 0.8707 (tp40) cc_final: 0.8455 (tp40) REVERT: l 16 SER cc_start: 0.9178 (m) cc_final: 0.8370 (t) REVERT: l 20 ASP cc_start: 0.7559 (m-30) cc_final: 0.7321 (m-30) REVERT: l 25 THR cc_start: 0.8816 (p) cc_final: 0.8293 (p) REVERT: l 45 GLN cc_start: 0.8118 (tp40) cc_final: 0.7622 (tp40) REVERT: l 50 TYR cc_start: 0.9184 (t80) cc_final: 0.8791 (t80) REVERT: m 20 ASP cc_start: 0.7875 (m-30) cc_final: 0.7325 (m-30) REVERT: m 50 TYR cc_start: 0.8809 (t80) cc_final: 0.8423 (t80) REVERT: m 75 ASP cc_start: 0.8266 (m-30) cc_final: 0.7449 (m-30) REVERT: n 3 VAL cc_start: 0.8662 (t) cc_final: 0.8375 (m) REVERT: n 29 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7157 (tm-30) REVERT: n 53 LYS cc_start: 0.9071 (mmtt) cc_final: 0.8411 (mmtm) REVERT: n 75 ASP cc_start: 0.8478 (m-30) cc_final: 0.8134 (m-30) REVERT: n 80 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8032 (tm-30) REVERT: o 39 LYS cc_start: 0.7812 (mmpt) cc_final: 0.7429 (mmpt) REVERT: o 50 TYR cc_start: 0.9206 (t80) cc_final: 0.8975 (t80) REVERT: o 75 ASP cc_start: 0.7928 (t0) cc_final: 0.7727 (t0) REVERT: p 25 THR cc_start: 0.8298 (p) cc_final: 0.7592 (t) REVERT: p 26 LEU cc_start: 0.8093 (mm) cc_final: 0.7878 (mm) REVERT: p 75 ASP cc_start: 0.8601 (m-30) cc_final: 0.8120 (m-30) REVERT: q 14 SER cc_start: 0.9482 (m) cc_final: 0.9188 (p) REVERT: q 32 LEU cc_start: 0.8223 (tp) cc_final: 0.7874 (tp) REVERT: q 36 LYS cc_start: 0.8655 (mttt) cc_final: 0.8395 (mtmt) REVERT: r 59 LEU cc_start: 0.8925 (mt) cc_final: 0.8615 (mt) REVERT: r 72 LYS cc_start: 0.9277 (tmtt) cc_final: 0.8900 (tptp) REVERT: s 7 ASN cc_start: 0.7196 (m-40) cc_final: 0.6368 (p0) REVERT: s 23 THR cc_start: 0.8652 (m) cc_final: 0.8336 (m) REVERT: s 27 GLN cc_start: 0.8359 (mt0) cc_final: 0.7868 (tm-30) REVERT: s 69 LYS cc_start: 0.8667 (tptm) cc_final: 0.7474 (ttmt) REVERT: t 51 GLN cc_start: 0.8710 (tt0) cc_final: 0.6754 (mm110) REVERT: t 69 LYS cc_start: 0.9264 (tptm) cc_final: 0.8583 (mttt) REVERT: t 72 LYS cc_start: 0.9468 (tmtt) cc_final: 0.9220 (tttp) REVERT: u 30 LEU cc_start: 0.8880 (tp) cc_final: 0.8617 (tt) REVERT: u 49 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7074 (tp30) REVERT: u 65 SER cc_start: 0.9191 (t) cc_final: 0.8925 (t) REVERT: u 69 LYS cc_start: 0.8895 (tptm) cc_final: 0.7497 (ttmt) REVERT: u 82 PHE cc_start: 0.8987 (m-80) cc_final: 0.8407 (m-80) REVERT: v 32 LEU cc_start: 0.9298 (tp) cc_final: 0.9046 (tp) REVERT: v 36 LYS cc_start: 0.8942 (mttt) cc_final: 0.8650 (mttm) REVERT: v 53 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8444 (mmmm) REVERT: v 69 LYS cc_start: 0.9094 (tptm) cc_final: 0.8206 (mttt) REVERT: w 4 THR cc_start: 0.8313 (t) cc_final: 0.7846 (m) REVERT: w 25 THR cc_start: 0.8522 (p) cc_final: 0.8118 (p) REVERT: w 47 LEU cc_start: 0.9134 (mm) cc_final: 0.8817 (mm) REVERT: w 57 TYR cc_start: 0.8939 (t80) cc_final: 0.8514 (t80) REVERT: w 61 ARG cc_start: 0.8338 (mmt180) cc_final: 0.6676 (ttp-170) REVERT: w 69 LYS cc_start: 0.8881 (tppt) cc_final: 0.7374 (tppt) REVERT: a0 103 LYS cc_start: 0.8087 (tttm) cc_final: 0.7007 (tptt) REVERT: d0 103 LYS cc_start: 0.9252 (ttmt) cc_final: 0.7929 (tptt) REVERT: e0 103 LYS cc_start: 0.8669 (ttmt) cc_final: 0.7860 (tttt) REVERT: f0 100 ARG cc_start: 0.8446 (ttm170) cc_final: 0.7927 (ttm170) REVERT: f0 103 LYS cc_start: 0.9161 (ttmt) cc_final: 0.8375 (tptt) REVERT: g0 103 LYS cc_start: 0.9081 (mtmt) cc_final: 0.7709 (tptt) REVERT: i0 103 LYS cc_start: 0.8919 (tttt) cc_final: 0.8671 (tptt) REVERT: k0 103 LYS cc_start: 0.8881 (ttmm) cc_final: 0.8111 (tptt) REVERT: k0 105 ARG cc_start: 0.8825 (ttm110) cc_final: 0.7340 (tmt170) REVERT: l0 103 LYS cc_start: 0.8878 (ttmt) cc_final: 0.8209 (tptt) REVERT: m0 103 LYS cc_start: 0.9051 (mtpt) cc_final: 0.8141 (tptt) REVERT: n0 97 SER cc_start: 0.9052 (m) cc_final: 0.8796 (t) REVERT: p0 103 LYS cc_start: 0.8861 (ttpt) cc_final: 0.8073 (tptt) REVERT: q0 103 LYS cc_start: 0.9011 (ttmt) cc_final: 0.8300 (tptt) REVERT: r0 102 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8043 (mt-10) REVERT: r0 103 LYS cc_start: 0.8873 (ttmt) cc_final: 0.7600 (tptt) REVERT: t0 103 LYS cc_start: 0.8928 (ttmt) cc_final: 0.8135 (tptt) REVERT: t0 105 ARG cc_start: 0.9221 (ttm110) cc_final: 0.7773 (tpm170) REVERT: u0 98 SER cc_start: 0.8702 (m) cc_final: 0.7867 (p) REVERT: u0 100 ARG cc_start: 0.7808 (ttm110) cc_final: 0.7212 (tpt170) REVERT: u0 103 LYS cc_start: 0.9096 (ttmt) cc_final: 0.8011 (tptt) REVERT: v0 92 THR cc_start: 0.8481 (m) cc_final: 0.8232 (m) REVERT: v0 103 LYS cc_start: 0.9252 (mttt) cc_final: 0.7822 (tptt) REVERT: w0 103 LYS cc_start: 0.8823 (ttmt) cc_final: 0.8300 (tptt) REVERT: x0 103 LYS cc_start: 0.8453 (ttmt) cc_final: 0.7819 (tptt) outliers start: 3 outliers final: 1 residues processed: 2135 average time/residue: 0.5339 time to fit residues: 1928.6289 Evaluate side-chains 1883 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1882 time to evaluate : 5.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 308 optimal weight: 0.0670 chunk 496 optimal weight: 0.7980 chunk 303 optimal weight: 0.9990 chunk 235 optimal weight: 0.8980 chunk 345 optimal weight: 0.7980 chunk 521 optimal weight: 0.0060 chunk 479 optimal weight: 0.8980 chunk 414 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 320 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 overall best weight: 0.4734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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 ** R 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 80 GLN U 80 GLN Y 144 ASN 2 137 HIS 4 137 HIS ** 4 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 164 ASN ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 ASN ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 64 GLN d 66 ASN f 51 GLN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 7 ASN n 81 ASN o 24 GLN t 24 GLN t 81 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 44858 Z= 0.199 Angle : 0.678 13.645 60890 Z= 0.333 Chirality : 0.041 0.358 7369 Planarity : 0.004 0.079 7620 Dihedral : 4.363 88.706 5953 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.04 % Allowed : 0.32 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.11), residues: 5404 helix: 2.95 (0.08), residues: 4149 sheet: 1.07 (0.31), residues: 224 loop : -2.75 (0.17), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 66 HIS 0.004 0.001 HIS C 106 PHE 0.031 0.002 PHE g 19 TYR 0.039 0.001 TYR i 50 ARG 0.017 0.000 ARG K 55 ********************** 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 2143 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 2141 time to evaluate : 5.460 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: A 26 CYS cc_start: 0.8612 (p) cc_final: 0.7773 (p) REVERT: A 50 MET cc_start: 0.8166 (ttp) cc_final: 0.7847 (ttm) REVERT: A 68 ILE cc_start: 0.9540 (mt) cc_final: 0.9233 (mt) REVERT: A 69 GLU cc_start: 0.7857 (tp30) cc_final: 0.7150 (mm-30) REVERT: A 101 GLN cc_start: 0.8872 (tt0) cc_final: 0.8376 (tm-30) REVERT: A 152 LYS cc_start: 0.9119 (tttt) cc_final: 0.8746 (mtmt) REVERT: A 177 MET cc_start: 0.7890 (mtt) cc_final: 0.7654 (mtt) REVERT: A 205 LYS cc_start: 0.9118 (mttt) cc_final: 0.8174 (tttt) REVERT: B 65 LYS cc_start: 0.8540 (tttp) cc_final: 0.8202 (tttt) REVERT: B 110 GLU cc_start: 0.8597 (pm20) cc_final: 0.8338 (pm20) REVERT: B 190 LYS cc_start: 0.9079 (mtmt) cc_final: 0.8228 (mtmm) REVERT: C 25 THR cc_start: 0.9120 (p) cc_final: 0.8734 (t) REVERT: C 72 TYR cc_start: 0.5450 (t80) cc_final: 0.5153 (m-10) REVERT: C 105 LYS cc_start: 0.8842 (tttp) cc_final: 0.8600 (mtpp) REVERT: C 117 ARG cc_start: 0.8243 (mtt180) cc_final: 0.7697 (tpt170) REVERT: C 177 MET cc_start: 0.7125 (ptp) cc_final: 0.6893 (mtt) REVERT: C 210 GLN cc_start: 0.7414 (tm-30) cc_final: 0.6954 (tm-30) REVERT: D 2 LEU cc_start: 0.9193 (mt) cc_final: 0.8894 (mt) REVERT: D 6 SER cc_start: 0.8751 (m) cc_final: 0.7948 (p) REVERT: D 105 LYS cc_start: 0.9144 (ttmt) cc_final: 0.8882 (ttmm) REVERT: E 44 GLN cc_start: 0.8647 (mp10) cc_final: 0.8242 (mp10) REVERT: E 64 MET cc_start: 0.8672 (mmm) cc_final: 0.8147 (mmm) REVERT: F 104 ASP cc_start: 0.8448 (t0) cc_final: 0.8129 (t0) REVERT: F 133 PHE cc_start: 0.9043 (t80) cc_final: 0.8430 (t80) REVERT: G 57 SER cc_start: 0.9158 (t) cc_final: 0.8864 (p) REVERT: G 79 MET cc_start: 0.8678 (mmm) cc_final: 0.8189 (mmm) REVERT: H 77 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7788 (tm-30) REVERT: H 79 MET cc_start: 0.8225 (mmp) cc_final: 0.7714 (mmp) REVERT: H 81 LEU cc_start: 0.8498 (mt) cc_final: 0.8294 (mt) REVERT: I 5 VAL cc_start: 0.9093 (t) cc_final: 0.8499 (p) REVERT: I 6 TYR cc_start: 0.9000 (t80) cc_final: 0.8544 (t80) REVERT: I 17 ILE cc_start: 0.9052 (mm) cc_final: 0.8839 (tt) REVERT: I 60 LEU cc_start: 0.8641 (mt) cc_final: 0.8365 (mt) REVERT: I 69 GLU cc_start: 0.7606 (tp30) cc_final: 0.6796 (tp30) REVERT: J 79 MET cc_start: 0.6559 (mtp) cc_final: 0.6227 (mtt) REVERT: K 132 LYS cc_start: 0.8537 (mmtp) cc_final: 0.7953 (mttt) REVERT: M 85 ARG cc_start: 0.7989 (ttm-80) cc_final: 0.7547 (ttm-80) REVERT: N 33 LYS cc_start: 0.8591 (mmmm) cc_final: 0.8008 (mmtt) REVERT: N 58 LEU cc_start: 0.9180 (mt) cc_final: 0.8846 (mt) REVERT: O 11 ASP cc_start: 0.7980 (m-30) cc_final: 0.7686 (m-30) REVERT: O 41 THR cc_start: 0.8875 (t) cc_final: 0.8359 (m) REVERT: P 44 GLN cc_start: 0.8178 (tt0) cc_final: 0.7915 (tt0) REVERT: P 49 MET cc_start: 0.8369 (mmt) cc_final: 0.8116 (mtp) REVERT: P 54 ASN cc_start: 0.8697 (t0) cc_final: 0.8250 (t0) REVERT: P 56 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7022 (tm-30) REVERT: P 57 SER cc_start: 0.9114 (m) cc_final: 0.8432 (p) REVERT: P 95 LEU cc_start: 0.9428 (mt) cc_final: 0.9172 (mt) REVERT: R 92 GLU cc_start: 0.8306 (tp30) cc_final: 0.7910 (tp30) REVERT: S 25 THR cc_start: 0.7655 (t) cc_final: 0.7200 (t) REVERT: S 27 GLN cc_start: 0.8017 (pm20) cc_final: 0.7741 (pm20) REVERT: S 45 GLN cc_start: 0.8113 (tp40) cc_final: 0.7193 (tm-30) REVERT: S 46 LEU cc_start: 0.8808 (mp) cc_final: 0.8461 (tt) REVERT: T 30 LEU cc_start: 0.9152 (tp) cc_final: 0.8812 (tp) REVERT: T 37 LEU cc_start: 0.8760 (tt) cc_final: 0.8525 (tp) REVERT: T 50 TYR cc_start: 0.9119 (t80) cc_final: 0.8874 (t80) REVERT: U 55 SER cc_start: 0.8996 (m) cc_final: 0.8719 (p) REVERT: U 81 ASN cc_start: 0.9148 (m-40) cc_final: 0.8876 (m-40) REVERT: V 32 LEU cc_start: 0.8711 (mt) cc_final: 0.8316 (tt) REVERT: V 45 GLN cc_start: 0.8759 (tp40) cc_final: 0.8343 (tp40) REVERT: V 64 GLN cc_start: 0.8223 (tt0) cc_final: 0.8021 (tt0) REVERT: W 39 LYS cc_start: 0.8085 (mttt) cc_final: 0.7469 (mptt) REVERT: W 43 ASN cc_start: 0.8485 (t0) cc_final: 0.8021 (t0) REVERT: W 56 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8031 (mt-10) REVERT: Y 112 SER cc_start: 0.8103 (p) cc_final: 0.7644 (m) REVERT: Y 123 ASN cc_start: 0.8695 (t0) cc_final: 0.8383 (t0) REVERT: Z 161 LEU cc_start: 0.8576 (tp) cc_final: 0.8358 (tp) REVERT: 0 149 THR cc_start: 0.9498 (m) cc_final: 0.9096 (t) REVERT: 0 164 ASN cc_start: 0.8844 (m-40) cc_final: 0.8429 (m110) REVERT: 2 127 GLN cc_start: 0.8265 (tp40) cc_final: 0.7924 (tp40) REVERT: 4 150 PHE cc_start: 0.8999 (p90) cc_final: 0.8626 (p90) REVERT: 6 127 GLN cc_start: 0.8872 (tp40) cc_final: 0.8259 (tp40) REVERT: 6 138 ARG cc_start: 0.8356 (mtp85) cc_final: 0.7676 (mtm110) REVERT: 6 149 THR cc_start: 0.8979 (m) cc_final: 0.8173 (p) REVERT: 6 170 ASP cc_start: 0.6754 (m-30) cc_final: 0.6489 (m-30) REVERT: 8 111 ILE cc_start: 0.9325 (mt) cc_final: 0.9065 (mt) REVERT: 8 144 ASN cc_start: 0.7721 (t0) cc_final: 0.7483 (t0) REVERT: 8 150 PHE cc_start: 0.9270 (p90) cc_final: 0.8754 (p90) REVERT: x 150 PHE cc_start: 0.9285 (p90) cc_final: 0.8590 (p90) REVERT: x 153 SER cc_start: 0.9428 (t) cc_final: 0.9009 (p) REVERT: y 115 ILE cc_start: 0.9316 (mt) cc_final: 0.8950 (mt) REVERT: y 158 LEU cc_start: 0.8273 (tp) cc_final: 0.7878 (mm) REVERT: y 160 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7760 (mm-30) REVERT: z 112 SER cc_start: 0.9202 (p) cc_final: 0.8863 (m) REVERT: z 127 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8221 (tm-30) REVERT: z 149 THR cc_start: 0.8976 (m) cc_final: 0.8682 (t) REVERT: 1 133 ASN cc_start: 0.8633 (m-40) cc_final: 0.8344 (t0) REVERT: 3 115 ILE cc_start: 0.8531 (mt) cc_final: 0.8098 (mt) REVERT: 7 168 LEU cc_start: 0.8971 (tp) cc_final: 0.8756 (tp) REVERT: 9 135 TYR cc_start: 0.7574 (t80) cc_final: 0.7125 (t80) REVERT: a 26 LEU cc_start: 0.8645 (tp) cc_final: 0.8369 (tp) REVERT: a 31 THR cc_start: 0.7876 (m) cc_final: 0.7493 (m) REVERT: a 80 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8307 (tm-30) REVERT: b 14 SER cc_start: 0.8746 (m) cc_final: 0.8539 (p) REVERT: b 43 ASN cc_start: 0.8450 (t0) cc_final: 0.8175 (t0) REVERT: b 45 GLN cc_start: 0.9007 (tp40) cc_final: 0.7894 (tm-30) REVERT: b 49 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7342 (mm-30) REVERT: b 64 GLN cc_start: 0.8363 (tm-30) cc_final: 0.7792 (tm-30) REVERT: c 80 GLN cc_start: 0.8846 (tp-100) cc_final: 0.8589 (tp40) REVERT: d 57 TYR cc_start: 0.8982 (t80) cc_final: 0.8505 (t80) REVERT: d 72 LYS cc_start: 0.8915 (tttm) cc_final: 0.8684 (tttm) REVERT: d 80 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7227 (tm-30) REVERT: d 81 ASN cc_start: 0.9009 (m-40) cc_final: 0.8560 (m110) REVERT: e 40 ASN cc_start: 0.8366 (p0) cc_final: 0.7900 (p0) REVERT: g 8 ASP cc_start: 0.6142 (p0) cc_final: 0.5859 (p0) REVERT: g 26 LEU cc_start: 0.9079 (tt) cc_final: 0.8563 (mm) REVERT: g 67 THR cc_start: 0.9477 (t) cc_final: 0.9186 (t) REVERT: g 80 GLN cc_start: 0.8739 (tp-100) cc_final: 0.8208 (tm-30) REVERT: h 11 THR cc_start: 0.8403 (m) cc_final: 0.7529 (m) REVERT: h 19 PHE cc_start: 0.7064 (t80) cc_final: 0.6744 (t80) REVERT: h 50 TYR cc_start: 0.9045 (t80) cc_final: 0.8574 (t80) REVERT: h 59 LEU cc_start: 0.9207 (mp) cc_final: 0.8399 (mp) REVERT: i 65 SER cc_start: 0.9123 (t) cc_final: 0.8923 (t) REVERT: i 80 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8038 (tm-30) REVERT: i 81 ASN cc_start: 0.9203 (m-40) cc_final: 0.8893 (m-40) REVERT: j 42 SER cc_start: 0.9337 (m) cc_final: 0.8866 (p) REVERT: k 37 LEU cc_start: 0.8911 (tp) cc_final: 0.8604 (tt) REVERT: k 50 TYR cc_start: 0.9236 (t80) cc_final: 0.8909 (t80) REVERT: l 16 SER cc_start: 0.9098 (m) cc_final: 0.8342 (t) REVERT: l 20 ASP cc_start: 0.7494 (m-30) cc_final: 0.7061 (m-30) REVERT: l 25 THR cc_start: 0.8575 (p) cc_final: 0.8317 (p) REVERT: l 29 GLU cc_start: 0.8418 (pt0) cc_final: 0.8032 (pt0) REVERT: l 45 GLN cc_start: 0.8062 (tp40) cc_final: 0.7592 (tp40) REVERT: l 50 TYR cc_start: 0.9135 (t80) cc_final: 0.8771 (t80) REVERT: m 20 ASP cc_start: 0.7918 (m-30) cc_final: 0.7368 (m-30) REVERT: m 50 TYR cc_start: 0.8797 (t80) cc_final: 0.8403 (t80) REVERT: m 75 ASP cc_start: 0.8282 (m-30) cc_final: 0.7502 (m-30) REVERT: n 3 VAL cc_start: 0.8651 (t) cc_final: 0.8378 (m) REVERT: n 29 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7195 (tm-30) REVERT: n 49 GLU cc_start: 0.7307 (tm-30) cc_final: 0.7021 (tm-30) REVERT: n 53 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8505 (mmtm) REVERT: n 75 ASP cc_start: 0.8444 (m-30) cc_final: 0.8113 (m-30) REVERT: n 80 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8002 (tm-30) REVERT: o 14 SER cc_start: 0.8754 (t) cc_final: 0.8339 (p) REVERT: o 39 LYS cc_start: 0.7731 (mmpt) cc_final: 0.7419 (mmpt) REVERT: o 50 TYR cc_start: 0.9216 (t80) cc_final: 0.8929 (t80) REVERT: o 53 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8686 (mmpt) REVERT: p 25 THR cc_start: 0.8235 (p) cc_final: 0.7579 (t) REVERT: p 75 ASP cc_start: 0.8563 (m-30) cc_final: 0.8114 (m-30) REVERT: q 14 SER cc_start: 0.9415 (m) cc_final: 0.9188 (p) REVERT: q 32 LEU cc_start: 0.8159 (tp) cc_final: 0.7803 (tp) REVERT: q 36 LYS cc_start: 0.8752 (mttt) cc_final: 0.8399 (mtmt) REVERT: r 25 THR cc_start: 0.8113 (p) cc_final: 0.7852 (p) REVERT: r 29 GLU cc_start: 0.8768 (pm20) cc_final: 0.8439 (pm20) REVERT: r 72 LYS cc_start: 0.9248 (tmtt) cc_final: 0.8930 (tptp) REVERT: s 7 ASN cc_start: 0.6743 (m-40) cc_final: 0.5850 (p0) REVERT: s 10 TRP cc_start: 0.8868 (p-90) cc_final: 0.8541 (p-90) REVERT: s 23 THR cc_start: 0.8584 (m) cc_final: 0.8152 (m) REVERT: s 27 GLN cc_start: 0.8366 (mt0) cc_final: 0.7917 (tm-30) REVERT: s 69 LYS cc_start: 0.8649 (tptm) cc_final: 0.7477 (ttmt) REVERT: t 51 GLN cc_start: 0.8621 (tt0) cc_final: 0.6660 (mm110) REVERT: t 69 LYS cc_start: 0.9302 (tptm) cc_final: 0.8513 (mttt) REVERT: t 72 LYS cc_start: 0.9469 (tmtt) cc_final: 0.9234 (tttp) REVERT: u 30 LEU cc_start: 0.8968 (tp) cc_final: 0.8654 (tt) REVERT: u 49 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7092 (tp30) REVERT: u 65 SER cc_start: 0.9146 (t) cc_final: 0.8856 (t) REVERT: u 69 LYS cc_start: 0.8862 (tptm) cc_final: 0.7506 (ttmt) REVERT: u 82 PHE cc_start: 0.8930 (m-80) cc_final: 0.8392 (m-80) REVERT: v 32 LEU cc_start: 0.9293 (tp) cc_final: 0.9044 (tp) REVERT: v 36 LYS cc_start: 0.8868 (mttt) cc_final: 0.8582 (mttm) REVERT: v 53 LYS cc_start: 0.8700 (mmmt) cc_final: 0.8443 (mmmm) REVERT: v 69 LYS cc_start: 0.9110 (tptm) cc_final: 0.8167 (mttm) REVERT: w 4 THR cc_start: 0.8279 (t) cc_final: 0.7740 (m) REVERT: w 25 THR cc_start: 0.8576 (p) cc_final: 0.8166 (p) REVERT: w 57 TYR cc_start: 0.8907 (t80) cc_final: 0.8504 (t80) REVERT: w 61 ARG cc_start: 0.8239 (mmt180) cc_final: 0.6665 (ttp-170) REVERT: w 69 LYS cc_start: 0.8884 (tppt) cc_final: 0.7402 (tppt) REVERT: a0 103 LYS cc_start: 0.8060 (tttm) cc_final: 0.6974 (tptt) REVERT: d0 103 LYS cc_start: 0.9246 (ttmt) cc_final: 0.7927 (tptt) REVERT: e0 103 LYS cc_start: 0.8662 (ttmt) cc_final: 0.7834 (tttt) REVERT: f0 100 ARG cc_start: 0.8411 (ttm170) cc_final: 0.7896 (ttm170) REVERT: f0 103 LYS cc_start: 0.9330 (ttmt) cc_final: 0.8350 (tptt) REVERT: g0 103 LYS cc_start: 0.9096 (mtmt) cc_final: 0.7709 (tptt) REVERT: i0 103 LYS cc_start: 0.8912 (tttt) cc_final: 0.8678 (tptt) REVERT: k0 103 LYS cc_start: 0.8872 (ttmm) cc_final: 0.8117 (tptt) REVERT: k0 105 ARG cc_start: 0.8795 (ttm110) cc_final: 0.7350 (tmt170) REVERT: l0 103 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8199 (tptt) REVERT: m0 103 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8131 (tptt) REVERT: p0 103 LYS cc_start: 0.8886 (ttpt) cc_final: 0.8096 (tptt) REVERT: q0 103 LYS cc_start: 0.8999 (ttmt) cc_final: 0.8284 (tptt) REVERT: r0 102 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8022 (mt-10) REVERT: r0 103 LYS cc_start: 0.8862 (ttmt) cc_final: 0.7585 (tptt) REVERT: t0 103 LYS cc_start: 0.8912 (ttmt) cc_final: 0.8083 (tptt) REVERT: t0 105 ARG cc_start: 0.9211 (ttm110) cc_final: 0.7765 (tpm170) REVERT: u0 98 SER cc_start: 0.8668 (m) cc_final: 0.7816 (p) REVERT: u0 100 ARG cc_start: 0.7793 (ttm110) cc_final: 0.7372 (ttt180) REVERT: u0 103 LYS cc_start: 0.9076 (ttmt) cc_final: 0.7976 (tptt) REVERT: v0 92 THR cc_start: 0.8441 (m) cc_final: 0.8226 (m) REVERT: v0 103 LYS cc_start: 0.9239 (mttt) cc_final: 0.7765 (tptt) REVERT: w0 103 LYS cc_start: 0.8854 (ttmt) cc_final: 0.8306 (tptt) REVERT: x0 103 LYS cc_start: 0.8517 (ttmt) cc_final: 0.7923 (tptt) outliers start: 2 outliers final: 0 residues processed: 2141 average time/residue: 0.5365 time to fit residues: 1941.5103 Evaluate side-chains 1888 residues out of total 5011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1888 time to evaluate : 5.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 329 optimal weight: 0.9990 chunk 441 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 382 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 415 optimal weight: 0.3980 chunk 173 optimal weight: 0.7980 chunk 426 optimal weight: 0.5980 chunk 52 optimal weight: 0.0370 chunk 76 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS B 106 HIS ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 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 J 76 HIS O 44 GLN P 59 ASN R 19 GLN Y 144 ASN 2 137 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 81 ASN ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 51 GLN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 40 ASN n 7 ASN n 81 ASN o 24 GLN p 81 ASN t 24 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.118405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103412 restraints weight = 89587.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105971 restraints weight = 52889.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107749 restraints weight = 35857.156| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 44858 Z= 0.203 Angle : 0.681 11.342 60890 Z= 0.335 Chirality : 0.041 0.355 7369 Planarity : 0.004 0.079 7620 Dihedral : 4.382 89.378 5953 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.10 % Allowed : 0.28 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.11), residues: 5404 helix: 2.93 (0.08), residues: 4149 sheet: 1.05 (0.30), residues: 224 loop : -2.76 (0.17), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 66 HIS 0.010 0.001 HIS F 11 PHE 0.033 0.002 PHE K 150 TYR 0.058 0.002 TYR B 158 ARG 0.017 0.000 ARG K 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24063.84 seconds wall clock time: 432 minutes 35.83 seconds (25955.83 seconds total)