Starting phenix.real_space_refine on Thu Mar 5 23:47:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6i00_0320/03_2026/6i00_0320.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i00_0320/03_2026/6i00_0320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6i00_0320/03_2026/6i00_0320.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i00_0320/03_2026/6i00_0320.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6i00_0320/03_2026/6i00_0320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i00_0320/03_2026/6i00_0320.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 156 5.16 5 C 17100 2.51 5 N 4572 2.21 5 O 4884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26712 Number of models: 1 Model: "" Number of chains: 12 Chain: "J" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "I" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Chain: "H" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "G" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Chain: "F" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "E" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Chain: "D" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "C" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Chain: "B" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "A" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Chain: "L" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "K" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 1020 residue: pdb=" N ARG J 37 " occ=0.97 ... (9 atoms not shown) pdb=" NH2 ARG J 37 " occ=0.93 residue: pdb=" N ALA J 38 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA J 38 " occ=0.97 residue: pdb=" N VAL J 41 " occ=0.97 ... (5 atoms not shown) pdb=" CG2 VAL J 41 " occ=0.93 residue: pdb=" N GLN J 42 " occ=0.97 ... (7 atoms not shown) pdb=" NE2 GLN J 42 " occ=0.95 residue: pdb=" N ALA J 43 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA J 43 " occ=0.97 residue: pdb=" N VAL J 46 " occ=0.97 ... (5 atoms not shown) pdb=" CG2 VAL J 46 " occ=0.94 residue: pdb=" N ALA J 52 " occ=0.96 ... (3 atoms not shown) pdb=" CB ALA J 52 " occ=0.93 residue: pdb=" N LYS J 56 " occ=0.97 ... (7 atoms not shown) pdb=" NZ LYS J 56 " occ=0.94 residue: pdb=" N ALA J 57 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA J 57 " occ=0.97 residue: pdb=" N LEU J 60 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU J 60 " occ=0.80 residue: pdb=" N GLU J 63 " occ=0.97 ... (7 atoms not shown) pdb=" OE2 GLU J 63 " occ=0.80 residue: pdb=" N ALA J 64 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA J 64 " occ=0.97 ... (remaining 1008 not shown) Time building chain proxies: 5.88, per 1000 atoms: 0.22 Number of scatterers: 26712 At special positions: 0 Unit cell: (137.7, 137.7, 182.75, 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 156 16.00 O 4884 8.00 N 4572 7.00 C 17100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 840.6 milliseconds 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6312 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 32 sheets defined 22.5% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'J' and resid 55 through 66 removed outlier: 3.772A pdb=" N GLU J 66 " --> pdb=" O SER J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 108 removed outlier: 4.163A pdb=" N ARG J 100 " --> pdb=" O THR J 96 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP J 101 " --> pdb=" O ALA J 97 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASP J 102 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 127 removed outlier: 3.573A pdb=" N LYS J 127 " --> pdb=" O LEU J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 210 removed outlier: 3.631A pdb=" N ARG J 206 " --> pdb=" O MET J 202 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR J 207 " --> pdb=" O PRO J 203 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA J 208 " --> pdb=" O SER J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 213 No H-bonds generated for 'chain 'J' and resid 211 through 213' Processing helix chain 'J' and resid 225 through 239 removed outlier: 4.196A pdb=" N LEU J 229 " --> pdb=" O ARG J 225 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA J 230 " --> pdb=" O GLU J 226 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR J 233 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N HIS J 234 " --> pdb=" O ALA J 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE J 235 " --> pdb=" O SER J 231 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 60 Processing helix chain 'I' and resid 60 through 66 Processing helix chain 'I' and resid 96 through 108 removed outlier: 4.150A pdb=" N ARG I 100 " --> pdb=" O THR I 96 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP I 101 " --> pdb=" O ALA I 97 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ASP I 102 " --> pdb=" O LYS I 98 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR I 106 " --> pdb=" O ASP I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 127 removed outlier: 3.799A pdb=" N LYS I 127 " --> pdb=" O LEU I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 210 Processing helix chain 'I' and resid 211 through 213 No H-bonds generated for 'chain 'I' and resid 211 through 213' Processing helix chain 'I' and resid 226 through 239 removed outlier: 4.298A pdb=" N ALA I 230 " --> pdb=" O GLU I 226 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS I 234 " --> pdb=" O ALA I 230 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE I 235 " --> pdb=" O SER I 231 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 317 removed outlier: 3.767A pdb=" N PHE I 316 " --> pdb=" O ARG I 313 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP I 317 " --> pdb=" O ALA I 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 313 through 317' Processing helix chain 'H' and resid 55 through 66 removed outlier: 3.881A pdb=" N GLU H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 108 removed outlier: 4.102A pdb=" N ARG H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASP H 102 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 127 removed outlier: 3.551A pdb=" N LYS H 127 " --> pdb=" O LEU H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 210 removed outlier: 3.615A pdb=" N ARG H 206 " --> pdb=" O MET H 202 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR H 207 " --> pdb=" O PRO H 203 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA H 208 " --> pdb=" O SER H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 213 No H-bonds generated for 'chain 'H' and resid 211 through 213' Processing helix chain 'H' and resid 225 through 239 removed outlier: 4.179A pdb=" N LEU H 229 " --> pdb=" O ARG H 225 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA H 230 " --> pdb=" O GLU H 226 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR H 233 " --> pdb=" O LEU H 229 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS H 234 " --> pdb=" O ALA H 230 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE H 235 " --> pdb=" O SER H 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 60 Processing helix chain 'G' and resid 60 through 66 Processing helix chain 'G' and resid 96 through 108 removed outlier: 4.106A pdb=" N ARG G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP G 101 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASP G 102 " --> pdb=" O LYS G 98 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR G 106 " --> pdb=" O ASP G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 127 removed outlier: 3.586A pdb=" N GLU G 119 " --> pdb=" O GLY G 115 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG G 120 " --> pdb=" O PRO G 116 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS G 127 " --> pdb=" O LEU G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 210 Processing helix chain 'G' and resid 211 through 213 No H-bonds generated for 'chain 'G' and resid 211 through 213' Processing helix chain 'G' and resid 226 through 239 removed outlier: 4.327A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS G 234 " --> pdb=" O ALA G 230 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE G 235 " --> pdb=" O SER G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 317 removed outlier: 3.772A pdb=" N PHE G 316 " --> pdb=" O ARG G 313 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP G 317 " --> pdb=" O ALA G 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 313 through 317' Processing helix chain 'F' and resid 55 through 66 removed outlier: 3.740A pdb=" N GLU F 66 " --> pdb=" O SER F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 108 removed outlier: 4.128A pdb=" N ARG F 100 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP F 101 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ASP F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 127 removed outlier: 3.595A pdb=" N LYS F 127 " --> pdb=" O LEU F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 210 removed outlier: 3.627A pdb=" N ARG F 206 " --> pdb=" O MET F 202 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR F 207 " --> pdb=" O PRO F 203 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA F 208 " --> pdb=" O SER F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 213 No H-bonds generated for 'chain 'F' and resid 211 through 213' Processing helix chain 'F' and resid 225 through 239 removed outlier: 4.231A pdb=" N LEU F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA F 230 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR F 233 " --> pdb=" O LEU F 229 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N HIS F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'E' and resid 60 through 66 Processing helix chain 'E' and resid 96 through 108 removed outlier: 4.130A pdb=" N ARG E 100 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP E 101 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASP E 102 " --> pdb=" O LYS E 98 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 127 removed outlier: 3.930A pdb=" N LEU E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS E 127 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 210 Processing helix chain 'E' and resid 211 through 213 No H-bonds generated for 'chain 'E' and resid 211 through 213' Processing helix chain 'E' and resid 226 through 239 removed outlier: 4.281A pdb=" N ALA E 230 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 66 removed outlier: 3.804A pdb=" N GLU D 66 " --> pdb=" O SER D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 108 removed outlier: 4.055A pdb=" N ARG D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASP D 102 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 127 removed outlier: 3.593A pdb=" N LYS D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 210 removed outlier: 3.633A pdb=" N ARG D 206 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA D 208 " --> pdb=" O SER D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 225 through 239 removed outlier: 4.312A pdb=" N LEU D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N HIS D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 311 removed outlier: 4.059A pdb=" N ILE D 311 " --> pdb=" O LEU D 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 96 through 108 removed outlier: 4.108A pdb=" N ARG C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASP C 102 " --> pdb=" O LYS C 98 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.598A pdb=" N GLU C 119 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG C 120 " --> pdb=" O PRO C 116 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 202 through 210 Processing helix chain 'C' and resid 211 through 213 No H-bonds generated for 'chain 'C' and resid 211 through 213' Processing helix chain 'C' and resid 226 through 239 removed outlier: 4.242A pdb=" N ALA C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS C 234 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 removed outlier: 3.739A pdb=" N PHE C 316 " --> pdb=" O ARG C 313 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP C 317 " --> pdb=" O ALA C 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 313 through 317' Processing helix chain 'B' and resid 55 through 66 removed outlier: 3.779A pdb=" N GLU B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 108 removed outlier: 4.141A pdb=" N ARG B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASP B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 127 removed outlier: 3.605A pdb=" N LYS B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 210 removed outlier: 3.628A pdb=" N ARG B 206 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 225 through 239 removed outlier: 4.207A pdb=" N LEU B 229 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 60 through 66 Processing helix chain 'A' and resid 96 through 108 removed outlier: 4.226A pdb=" N ARG A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASP A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 127 removed outlier: 3.835A pdb=" N LYS A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 211 removed outlier: 3.644A pdb=" N ALA A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 239 removed outlier: 4.300A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.743A pdb=" N PHE A 316 " --> pdb=" O ARG A 313 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP A 317 " --> pdb=" O ALA A 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 317' Processing helix chain 'L' and resid 55 through 66 removed outlier: 3.782A pdb=" N GLU L 66 " --> pdb=" O SER L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 108 removed outlier: 4.120A pdb=" N ARG L 100 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP L 101 " --> pdb=" O ALA L 97 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASP L 102 " --> pdb=" O LYS L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 127 removed outlier: 3.603A pdb=" N LYS L 127 " --> pdb=" O LEU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 210 removed outlier: 3.621A pdb=" N ARG L 206 " --> pdb=" O MET L 202 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR L 207 " --> pdb=" O PRO L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 213 No H-bonds generated for 'chain 'L' and resid 211 through 213' Processing helix chain 'L' and resid 225 through 239 removed outlier: 4.197A pdb=" N LEU L 229 " --> pdb=" O ARG L 225 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA L 230 " --> pdb=" O GLU L 226 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR L 233 " --> pdb=" O LEU L 229 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N HIS L 234 " --> pdb=" O ALA L 230 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE L 235 " --> pdb=" O SER L 231 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 60 Processing helix chain 'K' and resid 60 through 66 Processing helix chain 'K' and resid 96 through 108 removed outlier: 4.228A pdb=" N ARG K 100 " --> pdb=" O THR K 96 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP K 101 " --> pdb=" O ALA K 97 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ASP K 102 " --> pdb=" O LYS K 98 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR K 106 " --> pdb=" O ASP K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 127 removed outlier: 3.837A pdb=" N LYS K 127 " --> pdb=" O LEU K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 211 removed outlier: 3.643A pdb=" N ALA K 211 " --> pdb=" O THR K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 239 removed outlier: 4.305A pdb=" N ALA K 230 " --> pdb=" O GLU K 226 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS K 234 " --> pdb=" O ALA K 230 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE K 235 " --> pdb=" O SER K 231 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 317 removed outlier: 3.747A pdb=" N PHE K 316 " --> pdb=" O ARG K 313 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP K 317 " --> pdb=" O ALA K 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 313 through 317' Processing sheet with id=AA1, first strand: chain 'J' and resid 157 through 160 removed outlier: 6.914A pdb=" N PHE J 150 " --> pdb=" O LEU J 158 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS J 160 " --> pdb=" O VAL J 148 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL J 148 " --> pdb=" O LYS J 160 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU J 71 " --> pdb=" O ARG J 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 186 through 187 removed outlier: 6.326A pdb=" N LYS J 191 " --> pdb=" O ILE J 216 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N CYS J 218 " --> pdb=" O LYS J 191 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY J 193 " --> pdb=" O CYS J 218 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR J 217 " --> pdb=" O LEU J 244 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA J 246 " --> pdb=" O TYR J 217 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA J 219 " --> pdb=" O ALA J 246 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE J 283 " --> pdb=" O LEU J 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 342 through 346 removed outlier: 8.708A pdb=" N SER K 343 " --> pdb=" O PHE I 330 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU I 332 " --> pdb=" O SER K 343 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LYS K 345 " --> pdb=" O LEU I 332 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE I 334 " --> pdb=" O LYS K 345 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 342 through 346 removed outlier: 6.819A pdb=" N SER J 343 " --> pdb=" O ILE L 334 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLU L 336 " --> pdb=" O SER J 343 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS J 345 " --> pdb=" O GLU L 336 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 157 through 160 removed outlier: 7.069A pdb=" N PHE I 150 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS I 160 " --> pdb=" O VAL I 148 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL I 148 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU I 71 " --> pdb=" O ARG I 37 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA I 304 " --> pdb=" O ALA I 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 186 through 187 removed outlier: 6.505A pdb=" N LYS I 191 " --> pdb=" O ILE I 216 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N CYS I 218 " --> pdb=" O LYS I 191 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY I 193 " --> pdb=" O CYS I 218 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA I 246 " --> pdb=" O ALA I 219 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE I 283 " --> pdb=" O LEU I 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 342 through 345 Processing sheet with id=AA8, first strand: chain 'H' and resid 157 through 160 removed outlier: 3.918A pdb=" N GLY H 159 " --> pdb=" O PHE H 150 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU H 71 " --> pdb=" O ARG H 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 186 through 187 removed outlier: 6.236A pdb=" N LYS H 191 " --> pdb=" O ILE H 216 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N CYS H 218 " --> pdb=" O LYS H 191 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY H 193 " --> pdb=" O CYS H 218 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR H 217 " --> pdb=" O LEU H 244 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA H 246 " --> pdb=" O TYR H 217 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA H 219 " --> pdb=" O ALA H 246 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE H 283 " --> pdb=" O LEU H 291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 157 through 160 removed outlier: 4.138A pdb=" N GLY G 159 " --> pdb=" O PHE G 150 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU G 71 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA G 304 " --> pdb=" O ALA G 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 186 through 187 removed outlier: 3.677A pdb=" N ALA G 246 " --> pdb=" O ALA G 219 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE G 283 " --> pdb=" O LEU G 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 342 through 345 Processing sheet with id=AB4, first strand: chain 'F' and resid 157 through 160 removed outlier: 3.880A pdb=" N GLY F 159 " --> pdb=" O PHE F 150 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU F 71 " --> pdb=" O ARG F 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 186 through 187 removed outlier: 6.252A pdb=" N LYS F 191 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N CYS F 218 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLY F 193 " --> pdb=" O CYS F 218 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TYR F 217 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ALA F 246 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA F 219 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE F 283 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 157 through 160 removed outlier: 7.016A pdb=" N PHE E 150 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS E 160 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL E 148 " --> pdb=" O LYS E 160 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E 71 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA E 304 " --> pdb=" O ALA E 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 192 through 194 removed outlier: 6.362A pdb=" N GLY E 193 " --> pdb=" O CYS E 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR E 217 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ALA E 246 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA E 219 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE E 283 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 342 through 345 Processing sheet with id=AB9, first strand: chain 'D' and resid 157 through 160 removed outlier: 6.875A pdb=" N PHE D 150 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS D 160 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL D 148 " --> pdb=" O LYS D 160 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 147 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 136 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU D 71 " --> pdb=" O ARG D 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 186 through 187 removed outlier: 6.226A pdb=" N LYS D 191 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N CYS D 218 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY D 193 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR D 217 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ALA D 246 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ALA D 219 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL D 243 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE D 283 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 157 through 162 removed outlier: 6.977A pdb=" N PHE C 150 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS C 160 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL C 148 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ARG C 162 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N CYS C 146 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C 71 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 304 " --> pdb=" O ALA C 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 186 through 187 removed outlier: 3.669A pdb=" N ALA C 246 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE C 283 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 342 through 345 Processing sheet with id=AC5, first strand: chain 'B' and resid 157 through 160 removed outlier: 3.849A pdb=" N GLY B 159 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 132 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 71 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 137 through 139 Processing sheet with id=AC7, first strand: chain 'B' and resid 186 through 187 removed outlier: 6.222A pdb=" N LYS B 191 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N CYS B 218 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY B 193 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR B 217 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ALA B 246 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA B 219 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE B 283 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 157 through 160 removed outlier: 4.049A pdb=" N GLY A 159 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 71 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 304 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 186 through 187 removed outlier: 6.458A pdb=" N LYS A 191 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N CYS A 218 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLY A 193 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR A 217 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ALA A 246 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA A 219 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE A 283 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 157 through 160 removed outlier: 3.851A pdb=" N GLY L 159 " --> pdb=" O PHE L 150 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU L 132 " --> pdb=" O PHE L 151 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU L 71 " --> pdb=" O ARG L 37 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 137 through 139 Processing sheet with id=AD3, first strand: chain 'L' and resid 186 through 187 removed outlier: 6.213A pdb=" N LYS L 191 " --> pdb=" O ILE L 216 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N CYS L 218 " --> pdb=" O LYS L 191 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY L 193 " --> pdb=" O CYS L 218 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR L 217 " --> pdb=" O LEU L 244 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ALA L 246 " --> pdb=" O TYR L 217 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ALA L 219 " --> pdb=" O ALA L 246 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE L 283 " --> pdb=" O LEU L 291 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 157 through 160 removed outlier: 4.048A pdb=" N GLY K 159 " --> pdb=" O PHE K 150 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU K 71 " --> pdb=" O ARG K 37 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA K 304 " --> pdb=" O ALA K 38 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 186 through 187 removed outlier: 6.476A pdb=" N LYS K 191 " --> pdb=" O ILE K 216 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N CYS K 218 " --> pdb=" O LYS K 191 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY K 193 " --> pdb=" O CYS K 218 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR K 217 " --> pdb=" O LEU K 244 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ALA K 246 " --> pdb=" O TYR K 217 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ALA K 219 " --> pdb=" O ALA K 246 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE K 283 " --> pdb=" O LEU K 291 " (cutoff:3.500A) 668 hydrogen bonds defined for protein. 1896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.54 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 8246 1.34 - 1.48: 7520 1.48 - 1.62: 11318 1.62 - 1.77: 0 1.77 - 1.91: 228 Bond restraints: 27312 Sorted by residual: bond pdb=" C ARG D 251 " pdb=" O ARG D 251 " ideal model delta sigma weight residual 1.231 1.537 -0.306 2.00e-02 2.50e+03 2.34e+02 bond pdb=" C ARG B 251 " pdb=" O ARG B 251 " ideal model delta sigma weight residual 1.231 1.490 -0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C ARG H 251 " pdb=" O ARG H 251 " ideal model delta sigma weight residual 1.231 1.435 -0.204 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C ARG L 251 " pdb=" O ARG L 251 " ideal model delta sigma weight residual 1.231 1.355 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" C ARG J 251 " pdb=" O ARG J 251 " ideal model delta sigma weight residual 1.231 1.336 -0.105 2.00e-02 2.50e+03 2.76e+01 ... (remaining 27307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 34998 3.16 - 6.32: 1824 6.32 - 9.47: 126 9.47 - 12.63: 15 12.63 - 15.79: 9 Bond angle restraints: 36972 Sorted by residual: angle pdb=" CA ARG B 251 " pdb=" C ARG B 251 " pdb=" O ARG B 251 " ideal model delta sigma weight residual 120.80 136.59 -15.79 1.70e+00 3.46e-01 8.63e+01 angle pdb=" OG1 THR D 207 " pdb=" CB THR D 207 " pdb=" CG2 THR D 207 " ideal model delta sigma weight residual 109.30 96.13 13.17 2.00e+00 2.50e-01 4.33e+01 angle pdb=" OG1 THR F 207 " pdb=" CB THR F 207 " pdb=" CG2 THR F 207 " ideal model delta sigma weight residual 109.30 96.31 12.99 2.00e+00 2.50e-01 4.22e+01 angle pdb=" CB ARG J 326 " pdb=" CG ARG J 326 " pdb=" CD ARG J 326 " ideal model delta sigma weight residual 111.30 126.23 -14.93 2.30e+00 1.89e-01 4.21e+01 angle pdb=" OG1 THR H 207 " pdb=" CB THR H 207 " pdb=" CG2 THR H 207 " ideal model delta sigma weight residual 109.30 96.43 12.87 2.00e+00 2.50e-01 4.14e+01 ... (remaining 36967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.98: 13033 9.98 - 19.96: 2277 19.96 - 29.94: 566 29.94 - 39.92: 253 39.92 - 49.89: 83 Dihedral angle restraints: 16212 sinusoidal: 6324 harmonic: 9888 Sorted by residual: dihedral pdb=" CA VAL K 320 " pdb=" C VAL K 320 " pdb=" N VAL K 321 " pdb=" CA VAL K 321 " ideal model delta harmonic sigma weight residual -180.00 -130.11 -49.89 0 5.00e+00 4.00e-02 9.96e+01 dihedral pdb=" CA VAL E 320 " pdb=" C VAL E 320 " pdb=" N VAL E 321 " pdb=" CA VAL E 321 " ideal model delta harmonic sigma weight residual -180.00 -130.67 -49.33 0 5.00e+00 4.00e-02 9.73e+01 dihedral pdb=" CA VAL A 320 " pdb=" C VAL A 320 " pdb=" N VAL A 321 " pdb=" CA VAL A 321 " ideal model delta harmonic sigma weight residual -180.00 -130.85 -49.15 0 5.00e+00 4.00e-02 9.66e+01 ... (remaining 16209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2807 0.106 - 0.212: 1062 0.212 - 0.318: 200 0.318 - 0.424: 31 0.424 - 0.530: 16 Chirality restraints: 4116 Sorted by residual: chirality pdb=" CA PHE G 318 " pdb=" N PHE G 318 " pdb=" C PHE G 318 " pdb=" CB PHE G 318 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" CA PHE C 318 " pdb=" N PHE C 318 " pdb=" C PHE C 318 " pdb=" CB PHE C 318 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" CA PHE I 318 " pdb=" N PHE I 318 " pdb=" C PHE I 318 " pdb=" CB PHE I 318 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.15e+00 ... (remaining 4113 not shown) Planarity restraints: 4740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 217 " -0.018 2.00e-02 2.50e+03 3.88e-02 3.01e+01 pdb=" CG TYR J 217 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR J 217 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR J 217 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR J 217 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR J 217 " 0.044 2.00e-02 2.50e+03 pdb=" CZ TYR J 217 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR J 217 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 326 " 0.491 9.50e-02 1.11e+02 2.20e-01 2.97e+01 pdb=" NE ARG A 326 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 326 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 326 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 326 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 201 " -0.487 9.50e-02 1.11e+02 2.18e-01 2.93e+01 pdb=" NE ARG I 201 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG I 201 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG I 201 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG I 201 " -0.017 2.00e-02 2.50e+03 ... (remaining 4737 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 7014 2.81 - 3.33: 21592 3.33 - 3.85: 40260 3.85 - 4.38: 47971 4.38 - 4.90: 84769 Nonbonded interactions: 201606 Sorted by model distance: nonbonded pdb=" OG1 THR I 187 " pdb=" O GLY I 190 " model vdw 2.285 3.040 nonbonded pdb=" OG1 THR E 187 " pdb=" O GLY E 190 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR C 187 " pdb=" O GLY C 190 " model vdw 2.295 3.040 nonbonded pdb=" OG1 THR G 187 " pdb=" O GLY G 190 " model vdw 2.310 3.040 nonbonded pdb=" OG1 THR K 187 " pdb=" O GLY K 190 " model vdw 2.319 3.040 ... (remaining 201601 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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=0.50 max=1.00 mean=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.030 Set scattering table: 0.090 Process input model: 22.290 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 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 : 0.010 0.306 27312 Z= 0.605 Angle : 1.585 15.791 36972 Z= 0.964 Chirality : 0.114 0.530 4116 Planarity : 0.016 0.220 4740 Dihedral : 11.837 49.895 9900 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.73 % Allowed : 16.23 % Favored : 83.04 % Rotamer: Outliers : 2.72 % Allowed : 7.69 % Favored : 89.59 % Cbeta Deviations : 0.79 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.33 (0.11), residues: 3420 helix: -3.58 (0.11), residues: 888 sheet: -3.23 (0.18), residues: 588 loop : -3.74 (0.11), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG D 339 TYR 0.063 0.012 TYR B 217 PHE 0.043 0.009 PHE K 318 TRP 0.054 0.013 TRP A 198 HIS 0.026 0.007 HIS F 337 Details of bonding type rmsd covalent geometry : bond 0.00983 (27312) covalent geometry : angle 1.58498 (36972) hydrogen bonds : bond 0.23827 ( 668) hydrogen bonds : angle 8.13651 ( 1896) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 671 time to evaluate : 1.029 Fit side-chains REVERT: J 58 GLU cc_start: 0.8022 (tp30) cc_final: 0.7540 (tt0) REVERT: J 169 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8889 (tp) REVERT: J 191 LYS cc_start: 0.9028 (mttt) cc_final: 0.8766 (mtpt) REVERT: J 297 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7863 (ppt170) REVERT: J 305 ASP cc_start: 0.9016 (p0) cc_final: 0.8784 (t0) REVERT: J 310 ASP cc_start: 0.9307 (t0) cc_final: 0.9010 (t0) REVERT: I 63 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7457 (tm-30) REVERT: I 295 ASN cc_start: 0.8658 (t0) cc_final: 0.8351 (t0) REVERT: I 301 LEU cc_start: 0.8494 (mt) cc_final: 0.8286 (mp) REVERT: H 58 GLU cc_start: 0.7999 (tp30) cc_final: 0.7493 (tt0) REVERT: H 63 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7979 (tp30) REVERT: H 95 ARG cc_start: 0.8036 (mpt-90) cc_final: 0.7803 (mmt90) REVERT: H 295 ASN cc_start: 0.8775 (t0) cc_final: 0.8396 (t0) REVERT: H 297 ARG cc_start: 0.8122 (mtp85) cc_final: 0.7654 (ppt170) REVERT: G 61 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7774 (tt) REVERT: G 63 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7405 (tm-30) REVERT: G 123 LEU cc_start: 0.8457 (tt) cc_final: 0.8244 (pp) REVERT: G 169 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9115 (tp) REVERT: G 295 ASN cc_start: 0.8691 (t0) cc_final: 0.8222 (t0) REVERT: G 340 LYS cc_start: 0.8578 (ttmp) cc_final: 0.8370 (ttpt) REVERT: F 89 GLU cc_start: 0.9316 (mt-10) cc_final: 0.9067 (mp0) REVERT: F 127 LYS cc_start: 0.7147 (mtmt) cc_final: 0.6851 (pttm) REVERT: F 169 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8861 (tp) REVERT: F 295 ASN cc_start: 0.8686 (t0) cc_final: 0.8472 (t0) REVERT: F 297 ARG cc_start: 0.7889 (mtp85) cc_final: 0.7508 (ptt-90) REVERT: E 55 ASP cc_start: 0.8517 (m-30) cc_final: 0.8293 (m-30) REVERT: E 192 ILE cc_start: 0.9115 (pt) cc_final: 0.8875 (mt) REVERT: E 295 ASN cc_start: 0.8697 (t0) cc_final: 0.8337 (t0) REVERT: D 58 GLU cc_start: 0.8007 (tp30) cc_final: 0.7754 (tt0) REVERT: D 63 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7832 (tp30) REVERT: D 95 ARG cc_start: 0.8039 (mpt-90) cc_final: 0.7630 (mmt90) REVERT: D 127 LYS cc_start: 0.7166 (mtmt) cc_final: 0.6867 (pttt) REVERT: D 169 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8873 (tp) REVERT: D 297 ARG cc_start: 0.7846 (mtp85) cc_final: 0.7523 (ptt-90) REVERT: C 55 ASP cc_start: 0.8669 (m-30) cc_final: 0.8424 (m-30) REVERT: C 63 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7486 (tm-30) REVERT: C 95 ARG cc_start: 0.8024 (mpt-90) cc_final: 0.6415 (mpt-90) REVERT: C 169 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9143 (tp) REVERT: C 225 ARG cc_start: 0.8209 (mpt-90) cc_final: 0.7981 (mtt-85) REVERT: C 295 ASN cc_start: 0.8713 (t0) cc_final: 0.8402 (t0) REVERT: B 58 GLU cc_start: 0.7927 (tp30) cc_final: 0.7330 (tt0) REVERT: B 169 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8981 (tp) REVERT: B 191 LYS cc_start: 0.9008 (mttt) cc_final: 0.8612 (mtpt) REVERT: B 283 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8810 (mt) REVERT: B 297 ARG cc_start: 0.7786 (mtp85) cc_final: 0.7404 (ptt90) REVERT: A 63 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7639 (tm-30) REVERT: A 95 ARG cc_start: 0.7460 (mpt-90) cc_final: 0.6558 (mtt180) REVERT: A 169 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9068 (tp) REVERT: A 197 CYS cc_start: 0.9271 (t) cc_final: 0.8961 (t) REVERT: A 289 ILE cc_start: 0.8193 (mt) cc_final: 0.7990 (pt) REVERT: A 295 ASN cc_start: 0.8687 (t0) cc_final: 0.8394 (t0) REVERT: A 299 GLU cc_start: 0.8400 (pt0) cc_final: 0.8177 (pt0) REVERT: L 58 GLU cc_start: 0.8049 (tp30) cc_final: 0.7557 (tt0) REVERT: L 89 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8802 (tt0) REVERT: L 225 ARG cc_start: 0.7722 (mpt-90) cc_final: 0.7451 (mtt-85) REVERT: L 297 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7468 (ptp90) REVERT: K 63 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7605 (tm-30) REVERT: K 169 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9221 (tp) REVERT: K 184 VAL cc_start: 0.8155 (OUTLIER) cc_final: 0.7835 (p) REVERT: K 289 ILE cc_start: 0.8180 (mt) cc_final: 0.7968 (pt) REVERT: K 295 ASN cc_start: 0.8651 (t0) cc_final: 0.8381 (t0) outliers start: 76 outliers final: 16 residues processed: 734 average time/residue: 0.1969 time to fit residues: 217.3057 Evaluate side-chains 405 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 378 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 184 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 200 ASN I 70 GLN I 200 ASN H 200 ASN G 200 ASN F 200 ASN E 200 ASN D 70 GLN D 200 ASN C 200 ASN B 200 ASN A 200 ASN L 200 ASN K 200 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.137557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.111992 restraints weight = 36158.284| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.28 r_work: 0.3038 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27312 Z= 0.150 Angle : 0.732 11.864 36972 Z= 0.376 Chirality : 0.048 0.196 4116 Planarity : 0.006 0.091 4740 Dihedral : 7.190 54.415 3848 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.58 % Favored : 88.07 % Rotamer: Outliers : 4.90 % Allowed : 10.69 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.45 (0.12), residues: 3420 helix: -2.47 (0.15), residues: 816 sheet: -2.11 (0.18), residues: 780 loop : -3.69 (0.11), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 95 TYR 0.019 0.001 TYR A 128 PHE 0.012 0.001 PHE A 318 TRP 0.008 0.001 TRP L 198 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00354 (27312) covalent geometry : angle 0.73178 (36972) hydrogen bonds : bond 0.04894 ( 668) hydrogen bonds : angle 5.86974 ( 1896) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 440 time to evaluate : 0.866 Fit side-chains REVERT: J 58 GLU cc_start: 0.7487 (tp30) cc_final: 0.7272 (tt0) REVERT: J 67 ASN cc_start: 0.8406 (p0) cc_final: 0.8180 (t0) REVERT: J 169 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8874 (tp) REVERT: J 191 LYS cc_start: 0.8910 (mttt) cc_final: 0.8504 (mtpt) REVERT: J 287 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8826 (mm) REVERT: J 295 ASN cc_start: 0.8591 (t0) cc_final: 0.8213 (t0) REVERT: I 169 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9171 (tp) REVERT: I 184 VAL cc_start: 0.7976 (OUTLIER) cc_final: 0.7674 (p) REVERT: I 301 LEU cc_start: 0.8773 (mt) cc_final: 0.8481 (mp) REVERT: H 58 GLU cc_start: 0.7487 (tp30) cc_final: 0.7234 (tt0) REVERT: H 59 ARG cc_start: 0.8299 (ttp80) cc_final: 0.8083 (ptp90) REVERT: H 295 ASN cc_start: 0.8752 (t0) cc_final: 0.8543 (t0) REVERT: G 95 ARG cc_start: 0.7586 (mpt-90) cc_final: 0.6233 (mpt-90) REVERT: G 117 GLU cc_start: 0.8376 (mp0) cc_final: 0.8035 (mp0) REVERT: G 169 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9056 (tp) REVERT: G 184 VAL cc_start: 0.8149 (OUTLIER) cc_final: 0.7895 (p) REVERT: G 295 ASN cc_start: 0.8640 (t0) cc_final: 0.8403 (t0) REVERT: G 340 LYS cc_start: 0.8208 (ttmp) cc_final: 0.7996 (ttpt) REVERT: F 58 GLU cc_start: 0.7464 (tp30) cc_final: 0.7197 (tt0) REVERT: F 89 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8182 (tt0) REVERT: F 169 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8914 (tp) REVERT: F 191 LYS cc_start: 0.8958 (mttt) cc_final: 0.8716 (mttp) REVERT: F 214 ILE cc_start: 0.9602 (OUTLIER) cc_final: 0.9396 (tt) REVERT: F 227 THR cc_start: 0.8105 (OUTLIER) cc_final: 0.7809 (p) REVERT: F 283 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8824 (mt) REVERT: F 287 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8733 (mm) REVERT: E 169 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9134 (tp) REVERT: E 184 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7804 (p) REVERT: E 192 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.9020 (mt) REVERT: E 225 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7657 (mtt-85) REVERT: D 58 GLU cc_start: 0.7886 (tp30) cc_final: 0.7573 (tt0) REVERT: D 95 ARG cc_start: 0.7651 (mpt-90) cc_final: 0.7395 (mmt90) REVERT: D 169 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8897 (tp) REVERT: D 227 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7828 (p) REVERT: D 232 MET cc_start: 0.8994 (mmp) cc_final: 0.8711 (mmt) REVERT: D 283 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8801 (mt) REVERT: C 95 ARG cc_start: 0.7620 (mpt-90) cc_final: 0.6023 (mpt-90) REVERT: C 169 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8929 (tp) REVERT: C 184 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7871 (p) REVERT: B 58 GLU cc_start: 0.7534 (tp30) cc_final: 0.7151 (tt0) REVERT: B 117 GLU cc_start: 0.8363 (mp0) cc_final: 0.7830 (mp0) REVERT: B 169 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9019 (tp) REVERT: B 227 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7818 (p) REVERT: B 283 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8811 (mt) REVERT: B 287 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8705 (mm) REVERT: B 295 ASN cc_start: 0.8453 (t0) cc_final: 0.8208 (t0) REVERT: A 95 ARG cc_start: 0.7399 (mpt-90) cc_final: 0.6518 (mtt180) REVERT: A 124 MET cc_start: 0.7960 (ttm) cc_final: 0.7645 (ttm) REVERT: A 169 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9275 (tp) REVERT: A 184 VAL cc_start: 0.8133 (OUTLIER) cc_final: 0.7892 (p) REVERT: A 299 GLU cc_start: 0.8235 (pt0) cc_final: 0.8021 (pt0) REVERT: L 89 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8306 (tt0) REVERT: L 225 ARG cc_start: 0.8086 (mpt-90) cc_final: 0.7635 (mtt-85) REVERT: L 227 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7873 (p) REVERT: K 117 GLU cc_start: 0.7993 (mp0) cc_final: 0.7710 (mp0) REVERT: K 169 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9194 (tp) outliers start: 137 outliers final: 43 residues processed: 550 average time/residue: 0.1961 time to fit residues: 164.9791 Evaluate side-chains 427 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 357 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 ASN Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain L residue 214 ILE Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 317 ASP Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 333 ASN Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 333 ASN Chi-restraints excluded: chain K residue 343 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 196 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 chunk 257 optimal weight: 0.0060 chunk 171 optimal weight: 6.9990 chunk 292 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 overall best weight: 4.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 333 ASN H 333 ASN F 333 ASN A 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.116981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.093152 restraints weight = 38279.678| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.03 r_work: 0.2853 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27312 Z= 0.199 Angle : 0.737 9.513 36972 Z= 0.378 Chirality : 0.049 0.239 4116 Planarity : 0.005 0.065 4740 Dihedral : 6.842 52.962 3835 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.01 % Favored : 85.64 % Rotamer: Outliers : 4.61 % Allowed : 12.48 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.12), residues: 3420 helix: -1.54 (0.18), residues: 732 sheet: -1.59 (0.18), residues: 780 loop : -3.42 (0.11), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 171 TYR 0.027 0.002 TYR K 128 PHE 0.017 0.002 PHE A 318 TRP 0.004 0.001 TRP K 228 HIS 0.006 0.001 HIS G 337 Details of bonding type rmsd covalent geometry : bond 0.00493 (27312) covalent geometry : angle 0.73724 (36972) hydrogen bonds : bond 0.05018 ( 668) hydrogen bonds : angle 5.66397 ( 1896) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 380 time to evaluate : 1.039 Fit side-chains REVERT: J 58 GLU cc_start: 0.7838 (tp30) cc_final: 0.7293 (tt0) REVERT: J 169 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8948 (tp) REVERT: J 287 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8873 (mm) REVERT: J 295 ASN cc_start: 0.8573 (t0) cc_final: 0.8269 (t0) REVERT: I 95 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.6589 (mpt-90) REVERT: I 184 VAL cc_start: 0.8065 (OUTLIER) cc_final: 0.7656 (p) REVERT: H 58 GLU cc_start: 0.7902 (tp30) cc_final: 0.7339 (tt0) REVERT: H 59 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8005 (ptp90) REVERT: H 227 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7584 (p) REVERT: G 95 ARG cc_start: 0.7747 (mpt-90) cc_final: 0.6219 (mpt-90) REVERT: G 117 GLU cc_start: 0.8189 (mp0) cc_final: 0.7779 (mp0) REVERT: G 124 MET cc_start: 0.8135 (ttm) cc_final: 0.7817 (ttm) REVERT: G 169 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9004 (tp) REVERT: G 184 VAL cc_start: 0.8207 (OUTLIER) cc_final: 0.7825 (p) REVERT: G 295 ASN cc_start: 0.8679 (t0) cc_final: 0.8465 (t0) REVERT: F 58 GLU cc_start: 0.7794 (tp30) cc_final: 0.7216 (tt0) REVERT: F 89 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8105 (tt0) REVERT: F 169 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8971 (tp) REVERT: F 287 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8852 (mm) REVERT: F 297 ARG cc_start: 0.7122 (ptt-90) cc_final: 0.6666 (ppt170) REVERT: E 184 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7783 (p) REVERT: E 192 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9057 (mt) REVERT: E 225 ARG cc_start: 0.7815 (mtm-85) cc_final: 0.7592 (mtt-85) REVERT: D 58 GLU cc_start: 0.8094 (tp30) cc_final: 0.7562 (tt0) REVERT: D 95 ARG cc_start: 0.7737 (mpt-90) cc_final: 0.7308 (mmt90) REVERT: D 169 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8900 (tp) REVERT: D 227 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7701 (p) REVERT: D 297 ARG cc_start: 0.7012 (ptt-90) cc_final: 0.6768 (ppt170) REVERT: C 95 ARG cc_start: 0.7758 (mpt-90) cc_final: 0.6143 (mpt-90) REVERT: C 184 VAL cc_start: 0.8206 (OUTLIER) cc_final: 0.7933 (p) REVERT: C 345 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8241 (mtmt) REVERT: B 169 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9012 (tp) REVERT: B 209 MET cc_start: 0.9246 (mmm) cc_final: 0.9007 (mtp) REVERT: B 287 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8763 (mm) REVERT: B 295 ASN cc_start: 0.8600 (t0) cc_final: 0.8332 (t0) REVERT: A 63 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7686 (tm-30) REVERT: A 95 ARG cc_start: 0.7453 (mpt-90) cc_final: 0.6151 (mtt180) REVERT: A 169 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9180 (tp) REVERT: A 184 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.7893 (p) REVERT: L 58 GLU cc_start: 0.7951 (tp30) cc_final: 0.7567 (tt0) REVERT: L 63 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7730 (tp30) REVERT: L 89 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8150 (tt0) REVERT: L 225 ARG cc_start: 0.8035 (mpt-90) cc_final: 0.7639 (mtt-85) REVERT: L 227 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7740 (p) REVERT: K 169 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9179 (tp) outliers start: 129 outliers final: 79 residues processed: 485 average time/residue: 0.1769 time to fit residues: 133.6478 Evaluate side-chains 430 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 330 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 331 SER Chi-restraints excluded: chain J residue 333 ASN Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 289 ILE Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 299 GLU Chi-restraints excluded: chain G residue 321 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 ASN Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 317 ASP Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 331 SER Chi-restraints excluded: chain L residue 333 ASN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 124 MET Chi-restraints excluded: chain K residue 138 GLU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 345 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 328 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 156 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 259 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 211 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 333 ASN B 323 HIS L 323 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.097657 restraints weight = 37983.292| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.16 r_work: 0.2873 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27312 Z= 0.120 Angle : 0.642 9.702 36972 Z= 0.328 Chirality : 0.046 0.281 4116 Planarity : 0.005 0.058 4740 Dihedral : 6.410 52.632 3835 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.79 % Favored : 88.86 % Rotamer: Outliers : 4.51 % Allowed : 12.91 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.13), residues: 3420 helix: -1.44 (0.18), residues: 804 sheet: -1.06 (0.18), residues: 840 loop : -3.36 (0.11), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 297 TYR 0.018 0.001 TYR A 128 PHE 0.012 0.001 PHE A 318 TRP 0.006 0.001 TRP C 198 HIS 0.002 0.001 HIS G 337 Details of bonding type rmsd covalent geometry : bond 0.00283 (27312) covalent geometry : angle 0.64246 (36972) hydrogen bonds : bond 0.03640 ( 668) hydrogen bonds : angle 5.33412 ( 1896) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 382 time to evaluate : 0.919 Fit side-chains REVERT: J 58 GLU cc_start: 0.8047 (tp30) cc_final: 0.7403 (tt0) REVERT: J 89 GLU cc_start: 0.8522 (tt0) cc_final: 0.8316 (tt0) REVERT: J 144 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9215 (mt) REVERT: J 169 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8952 (tp) REVERT: J 287 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8816 (mm) REVERT: J 295 ASN cc_start: 0.8610 (t0) cc_final: 0.8368 (t0) REVERT: I 117 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: I 184 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7888 (p) REVERT: H 227 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7622 (p) REVERT: H 289 ILE cc_start: 0.8542 (mt) cc_final: 0.8294 (mm) REVERT: H 333 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8624 (p0) REVERT: G 95 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6353 (mpt-90) REVERT: G 117 GLU cc_start: 0.8107 (mp0) cc_final: 0.7865 (mp0) REVERT: G 124 MET cc_start: 0.8411 (ttm) cc_final: 0.7996 (ttm) REVERT: G 169 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8915 (tp) REVERT: G 184 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7848 (p) REVERT: F 58 GLU cc_start: 0.7676 (tp30) cc_final: 0.7211 (tt0) REVERT: F 169 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8917 (tp) REVERT: F 283 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8621 (mt) REVERT: F 287 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8784 (mm) REVERT: E 169 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9056 (tp) REVERT: E 184 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.7963 (p) REVERT: E 192 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.9079 (mt) REVERT: E 225 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7586 (mtt-85) REVERT: D 58 GLU cc_start: 0.8002 (tp30) cc_final: 0.7503 (tt0) REVERT: D 95 ARG cc_start: 0.7767 (mpt-90) cc_final: 0.7395 (mmt90) REVERT: D 169 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8787 (tp) REVERT: D 283 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8737 (mt) REVERT: C 63 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8152 (tm-30) REVERT: C 95 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.6194 (mpt-90) REVERT: C 345 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8302 (mtmt) REVERT: B 58 GLU cc_start: 0.7848 (tp30) cc_final: 0.7418 (tt0) REVERT: B 117 GLU cc_start: 0.8157 (mp0) cc_final: 0.7654 (mp0) REVERT: B 169 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8991 (tp) REVERT: B 283 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8797 (mt) REVERT: B 287 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8685 (mm) REVERT: B 295 ASN cc_start: 0.8612 (t0) cc_final: 0.8328 (t0) REVERT: A 95 ARG cc_start: 0.7503 (mpt-90) cc_final: 0.6113 (mtt180) REVERT: A 169 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9199 (tp) REVERT: L 225 ARG cc_start: 0.8051 (mpt-90) cc_final: 0.7678 (mtt-85) REVERT: L 227 THR cc_start: 0.8085 (OUTLIER) cc_final: 0.7764 (p) REVERT: K 117 GLU cc_start: 0.8218 (mp0) cc_final: 0.7886 (mp0) REVERT: K 169 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9112 (tp) outliers start: 126 outliers final: 69 residues processed: 482 average time/residue: 0.1793 time to fit residues: 135.4180 Evaluate side-chains 450 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 355 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 301 LEU Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 331 SER Chi-restraints excluded: chain J residue 333 ASN Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 289 ILE Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 333 ASN Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 299 GLU Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 321 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 ASN Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 317 ASP Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 331 SER Chi-restraints excluded: chain L residue 333 ASN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 343 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 195 optimal weight: 4.9990 chunk 318 optimal weight: 2.9990 chunk 206 optimal weight: 10.0000 chunk 328 optimal weight: 7.9990 chunk 254 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 228 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 67 ASN J 333 ASN G 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.117768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.094592 restraints weight = 38061.568| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.02 r_work: 0.2785 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 53 | |-----------------------------------------------------------------------------| r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 27312 Z= 0.190 Angle : 0.701 9.570 36972 Z= 0.358 Chirality : 0.049 0.324 4116 Planarity : 0.005 0.049 4740 Dihedral : 6.446 51.087 3833 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.86 % Favored : 85.79 % Rotamer: Outliers : 4.40 % Allowed : 14.59 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.13), residues: 3420 helix: -1.34 (0.18), residues: 804 sheet: -1.03 (0.18), residues: 876 loop : -3.40 (0.12), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 297 TYR 0.021 0.001 TYR A 128 PHE 0.018 0.002 PHE A 318 TRP 0.003 0.001 TRP C 228 HIS 0.005 0.001 HIS E 337 Details of bonding type rmsd covalent geometry : bond 0.00472 (27312) covalent geometry : angle 0.70060 (36972) hydrogen bonds : bond 0.04474 ( 668) hydrogen bonds : angle 5.46367 ( 1896) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 362 time to evaluate : 0.974 Fit side-chains REVERT: J 89 GLU cc_start: 0.8560 (tt0) cc_final: 0.8350 (tt0) REVERT: J 144 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9210 (mt) REVERT: J 169 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8996 (tp) REVERT: J 287 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8934 (mm) REVERT: J 295 ASN cc_start: 0.8560 (t0) cc_final: 0.8329 (t0) REVERT: I 95 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.6619 (mpt-90) REVERT: I 184 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.7929 (p) REVERT: I 215 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8398 (pt0) REVERT: H 58 GLU cc_start: 0.8257 (tp30) cc_final: 0.7739 (tt0) REVERT: H 227 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7617 (p) REVERT: H 289 ILE cc_start: 0.8563 (mt) cc_final: 0.8269 (mm) REVERT: H 333 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8671 (p0) REVERT: G 95 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7311 (mpt-90) REVERT: G 124 MET cc_start: 0.8413 (ttm) cc_final: 0.8082 (ttm) REVERT: G 169 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.8989 (tp) REVERT: G 184 VAL cc_start: 0.8290 (OUTLIER) cc_final: 0.7854 (p) REVERT: F 58 GLU cc_start: 0.7673 (tp30) cc_final: 0.7206 (tt0) REVERT: F 89 GLU cc_start: 0.8645 (mp0) cc_final: 0.8437 (tt0) REVERT: F 169 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8987 (tp) REVERT: F 287 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8879 (mm) REVERT: E 184 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.8006 (p) REVERT: E 192 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9092 (mt) REVERT: E 225 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7590 (mtt-85) REVERT: D 58 GLU cc_start: 0.8112 (tp30) cc_final: 0.7637 (tt0) REVERT: D 95 ARG cc_start: 0.7786 (mpt-90) cc_final: 0.7277 (mmt90) REVERT: D 98 LYS cc_start: 0.8737 (tptp) cc_final: 0.8487 (tptp) REVERT: D 169 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8948 (tp) REVERT: D 227 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7829 (p) REVERT: C 345 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8351 (mtmt) REVERT: B 169 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9047 (tp) REVERT: B 287 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8824 (mm) REVERT: B 295 ASN cc_start: 0.8599 (t0) cc_final: 0.8315 (t0) REVERT: A 63 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7946 (tm-30) REVERT: A 95 ARG cc_start: 0.7517 (mpt-90) cc_final: 0.6032 (mtt180) REVERT: A 169 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9177 (tp) REVERT: L 225 ARG cc_start: 0.8093 (mpt-90) cc_final: 0.7841 (mtt-85) REVERT: K 123 LEU cc_start: 0.8732 (pp) cc_final: 0.8495 (pt) REVERT: K 169 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9149 (tp) outliers start: 123 outliers final: 84 residues processed: 458 average time/residue: 0.1837 time to fit residues: 130.5012 Evaluate side-chains 455 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 349 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 331 SER Chi-restraints excluded: chain J residue 333 ASN Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 289 ILE Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 333 ASN Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 299 GLU Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 317 ASP Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 331 SER Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 345 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 320 optimal weight: 7.9990 chunk 270 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 228 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 278 optimal weight: 0.9980 chunk 168 optimal weight: 10.0000 chunk 195 optimal weight: 5.9990 chunk 308 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 333 ASN I 42 GLN H 67 ASN G 42 GLN K 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.113493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.089946 restraints weight = 38671.339| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.14 r_work: 0.2749 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 53 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 102 | |-----------------------------------------------------------------------------| r_final: 0.2598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27312 Z= 0.194 Angle : 0.704 10.218 36972 Z= 0.359 Chirality : 0.049 0.301 4116 Planarity : 0.005 0.048 4740 Dihedral : 6.570 50.994 3833 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.01 % Favored : 86.64 % Rotamer: Outliers : 4.90 % Allowed : 15.41 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.13), residues: 3420 helix: -1.32 (0.18), residues: 804 sheet: -0.91 (0.19), residues: 876 loop : -3.36 (0.12), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 297 TYR 0.021 0.001 TYR A 128 PHE 0.017 0.001 PHE A 318 TRP 0.004 0.001 TRP G 228 HIS 0.005 0.001 HIS E 337 Details of bonding type rmsd covalent geometry : bond 0.00482 (27312) covalent geometry : angle 0.70357 (36972) hydrogen bonds : bond 0.04435 ( 668) hydrogen bonds : angle 5.53612 ( 1896) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 352 time to evaluate : 0.839 Fit side-chains REVERT: J 58 GLU cc_start: 0.8159 (tp30) cc_final: 0.7593 (tt0) REVERT: J 89 GLU cc_start: 0.8558 (tt0) cc_final: 0.8333 (tt0) REVERT: J 144 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9400 (mt) REVERT: J 169 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9029 (tp) REVERT: J 287 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8929 (mm) REVERT: I 95 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.6794 (mpt-90) REVERT: I 117 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: I 184 VAL cc_start: 0.8265 (OUTLIER) cc_final: 0.7913 (p) REVERT: I 215 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8462 (pt0) REVERT: H 58 GLU cc_start: 0.8263 (tp30) cc_final: 0.7714 (tt0) REVERT: H 289 ILE cc_start: 0.8526 (mt) cc_final: 0.8201 (mm) REVERT: H 333 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8709 (p0) REVERT: G 95 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7368 (mpt-90) REVERT: G 124 MET cc_start: 0.8433 (ttm) cc_final: 0.8088 (ttm) REVERT: G 184 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.7888 (p) REVERT: F 58 GLU cc_start: 0.7702 (tp30) cc_final: 0.7237 (tt0) REVERT: F 89 GLU cc_start: 0.8670 (mp0) cc_final: 0.8360 (tt0) REVERT: F 169 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9024 (tp) REVERT: F 287 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8921 (mm) REVERT: E 184 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8005 (p) REVERT: E 192 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9096 (mt) REVERT: E 225 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7565 (mtt-85) REVERT: D 58 GLU cc_start: 0.8096 (tp30) cc_final: 0.7589 (tt0) REVERT: D 95 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7309 (mmt90) REVERT: D 169 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8860 (tp) REVERT: D 227 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.7794 (p) REVERT: C 345 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8371 (mtmt) REVERT: B 89 GLU cc_start: 0.8555 (mp0) cc_final: 0.8317 (mp0) REVERT: B 169 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9104 (tp) REVERT: B 287 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8833 (mm) REVERT: B 295 ASN cc_start: 0.8607 (t0) cc_final: 0.8287 (t0) REVERT: A 63 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7889 (tm-30) REVERT: A 169 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9177 (tp) REVERT: K 169 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9147 (tp) outliers start: 137 outliers final: 101 residues processed: 458 average time/residue: 0.1819 time to fit residues: 129.9271 Evaluate side-chains 458 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 335 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 331 SER Chi-restraints excluded: chain J residue 333 ASN Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 289 ILE Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 333 ASN Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 333 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 317 ASP Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 331 SER Chi-restraints excluded: chain L residue 333 ASN Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 138 GLU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 345 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 77 optimal weight: 0.0070 chunk 207 optimal weight: 9.9990 chunk 141 optimal weight: 20.0000 chunk 152 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 328 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 290 optimal weight: 6.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 67 ASN J 333 ASN I 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.114754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.091586 restraints weight = 38067.265| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.11 r_work: 0.2750 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 102 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 164 | |-----------------------------------------------------------------------------| r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27312 Z= 0.162 Angle : 0.672 10.273 36972 Z= 0.343 Chirality : 0.048 0.300 4116 Planarity : 0.005 0.051 4740 Dihedral : 6.452 51.157 3833 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.81 % Favored : 86.84 % Rotamer: Outliers : 4.94 % Allowed : 15.67 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.14), residues: 3420 helix: -1.19 (0.19), residues: 804 sheet: -0.84 (0.19), residues: 876 loop : -3.30 (0.12), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 297 TYR 0.020 0.001 TYR A 128 PHE 0.016 0.001 PHE A 318 TRP 0.005 0.001 TRP G 228 HIS 0.004 0.001 HIS E 337 Details of bonding type rmsd covalent geometry : bond 0.00400 (27312) covalent geometry : angle 0.67235 (36972) hydrogen bonds : bond 0.04079 ( 668) hydrogen bonds : angle 5.45454 ( 1896) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 348 time to evaluate : 0.881 Fit side-chains REVERT: J 58 GLU cc_start: 0.8067 (tp30) cc_final: 0.7587 (tt0) REVERT: J 89 GLU cc_start: 0.8548 (tt0) cc_final: 0.8316 (tt0) REVERT: J 169 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9027 (tp) REVERT: J 287 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8916 (mm) REVERT: I 61 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8949 (tt) REVERT: I 95 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.6710 (mpt-90) REVERT: I 117 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: I 184 VAL cc_start: 0.8267 (OUTLIER) cc_final: 0.7951 (p) REVERT: I 215 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8493 (pt0) REVERT: I 276 VAL cc_start: 0.6760 (OUTLIER) cc_final: 0.6213 (t) REVERT: H 58 GLU cc_start: 0.8231 (tp30) cc_final: 0.7718 (tt0) REVERT: H 289 ILE cc_start: 0.8497 (mt) cc_final: 0.8175 (mm) REVERT: H 333 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8690 (p0) REVERT: G 95 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7347 (mpt-90) REVERT: G 124 MET cc_start: 0.8448 (ttm) cc_final: 0.8160 (ttm) REVERT: G 128 TYR cc_start: 0.6326 (OUTLIER) cc_final: 0.4256 (p90) REVERT: G 169 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8989 (tp) REVERT: G 184 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.7991 (p) REVERT: F 58 GLU cc_start: 0.7628 (tp30) cc_final: 0.7170 (tt0) REVERT: F 89 GLU cc_start: 0.8699 (mp0) cc_final: 0.8356 (tt0) REVERT: F 169 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8995 (tp) REVERT: F 287 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8879 (mm) REVERT: E 63 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8162 (tm-30) REVERT: E 184 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8007 (p) REVERT: E 192 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9100 (mt) REVERT: E 225 ARG cc_start: 0.7765 (mtm-85) cc_final: 0.7540 (mtt-85) REVERT: D 58 GLU cc_start: 0.8049 (tp30) cc_final: 0.7536 (tt0) REVERT: D 95 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7292 (mmt90) REVERT: D 169 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8848 (tp) REVERT: C 209 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8827 (mmm) REVERT: C 345 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8335 (mtmt) REVERT: B 89 GLU cc_start: 0.8538 (mp0) cc_final: 0.8250 (mp0) REVERT: B 98 LYS cc_start: 0.8726 (tptp) cc_final: 0.8501 (tptp) REVERT: B 169 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9080 (tp) REVERT: B 287 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8784 (mm) REVERT: B 295 ASN cc_start: 0.8602 (t0) cc_final: 0.8275 (t0) REVERT: A 63 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7847 (tm-30) REVERT: A 169 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9158 (tp) REVERT: K 169 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9141 (tp) outliers start: 138 outliers final: 94 residues processed: 454 average time/residue: 0.1805 time to fit residues: 127.7296 Evaluate side-chains 450 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 331 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 331 SER Chi-restraints excluded: chain J residue 333 ASN Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 289 ILE Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 333 ASN Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 128 TYR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 299 GLU Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 333 ASN Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 317 ASP Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 331 SER Chi-restraints excluded: chain L residue 333 ASN Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 345 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 66 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 290 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 3 optimal weight: 0.4980 chunk 223 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 335 optimal weight: 7.9990 chunk 40 optimal weight: 0.0000 chunk 254 optimal weight: 6.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 67 ASN J 333 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.117279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.094517 restraints weight = 38191.147| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.06 r_work: 0.2839 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 164 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 216 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27312 Z= 0.111 Angle : 0.618 10.956 36972 Z= 0.315 Chirality : 0.046 0.307 4116 Planarity : 0.004 0.047 4740 Dihedral : 6.100 57.176 3833 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.08 % Favored : 88.57 % Rotamer: Outliers : 3.93 % Allowed : 17.10 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.14), residues: 3420 helix: -1.03 (0.19), residues: 816 sheet: -0.50 (0.18), residues: 948 loop : -3.20 (0.13), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 225 TYR 0.016 0.001 TYR A 128 PHE 0.010 0.001 PHE A 318 TRP 0.005 0.001 TRP C 198 HIS 0.003 0.001 HIS L 234 Details of bonding type rmsd covalent geometry : bond 0.00264 (27312) covalent geometry : angle 0.61788 (36972) hydrogen bonds : bond 0.03254 ( 668) hydrogen bonds : angle 5.20746 ( 1896) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 365 time to evaluate : 1.006 Fit side-chains REVERT: J 58 GLU cc_start: 0.7934 (tp30) cc_final: 0.7468 (tt0) REVERT: J 169 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8951 (tp) REVERT: I 215 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8475 (pt0) REVERT: I 276 VAL cc_start: 0.6744 (OUTLIER) cc_final: 0.6229 (t) REVERT: H 58 GLU cc_start: 0.8130 (tp30) cc_final: 0.7691 (tt0) REVERT: H 289 ILE cc_start: 0.8504 (mt) cc_final: 0.8200 (mm) REVERT: G 95 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.6340 (mpt-90) REVERT: G 124 MET cc_start: 0.8418 (ttm) cc_final: 0.8140 (ttm) REVERT: G 184 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8086 (p) REVERT: F 58 GLU cc_start: 0.7428 (tp30) cc_final: 0.7096 (tt0) REVERT: F 169 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8866 (tp) REVERT: F 287 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8757 (mm) REVERT: E 184 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.8031 (p) REVERT: E 192 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8860 (mt) REVERT: D 58 GLU cc_start: 0.7904 (tp30) cc_final: 0.7438 (tt0) REVERT: D 95 ARG cc_start: 0.7796 (mpt-90) cc_final: 0.7366 (mmt90) REVERT: C 95 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6161 (mpt-90) REVERT: C 215 GLU cc_start: 0.8916 (pt0) cc_final: 0.8554 (mt-10) REVERT: C 345 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8341 (mtmt) REVERT: B 58 GLU cc_start: 0.7879 (tp30) cc_final: 0.7465 (tt0) REVERT: B 117 GLU cc_start: 0.8182 (mp0) cc_final: 0.7746 (mp0) REVERT: B 169 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8994 (tp) REVERT: B 287 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8679 (mm) REVERT: B 295 ASN cc_start: 0.8639 (t0) cc_final: 0.8309 (t0) REVERT: A 63 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7766 (tm-30) REVERT: A 169 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9103 (tp) REVERT: A 196 ILE cc_start: 0.9011 (mp) cc_final: 0.8740 (mm) REVERT: K 169 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9079 (tp) outliers start: 110 outliers final: 73 residues processed: 447 average time/residue: 0.1877 time to fit residues: 130.3779 Evaluate side-chains 428 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 340 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 331 SER Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 289 ILE Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 299 GLU Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 321 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 333 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 317 ASP Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 331 SER Chi-restraints excluded: chain L residue 333 ASN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 343 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 334 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 160 optimal weight: 5.9990 chunk 324 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 97 optimal weight: 0.0070 chunk 330 optimal weight: 8.9990 chunk 282 optimal weight: 2.9990 overall best weight: 3.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.114288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.091914 restraints weight = 38254.290| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.00 r_work: 0.2779 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 216 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 263 | |-----------------------------------------------------------------------------| r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27312 Z= 0.153 Angle : 0.661 10.315 36972 Z= 0.337 Chirality : 0.047 0.293 4116 Planarity : 0.005 0.044 4740 Dihedral : 6.155 58.333 3832 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.87 % Favored : 86.78 % Rotamer: Outliers : 3.72 % Allowed : 17.24 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.14), residues: 3420 helix: -1.05 (0.19), residues: 816 sheet: -0.49 (0.18), residues: 948 loop : -3.16 (0.13), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 225 TYR 0.019 0.001 TYR A 128 PHE 0.014 0.001 PHE E 318 TRP 0.005 0.001 TRP G 228 HIS 0.004 0.001 HIS E 337 Details of bonding type rmsd covalent geometry : bond 0.00379 (27312) covalent geometry : angle 0.66060 (36972) hydrogen bonds : bond 0.03902 ( 668) hydrogen bonds : angle 5.30876 ( 1896) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 339 time to evaluate : 0.996 Fit side-chains REVERT: J 58 GLU cc_start: 0.7897 (tp30) cc_final: 0.7489 (tt0) REVERT: J 89 GLU cc_start: 0.8642 (tt0) cc_final: 0.8349 (tt0) REVERT: J 169 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.9012 (tp) REVERT: I 215 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8447 (pt0) REVERT: I 276 VAL cc_start: 0.6835 (OUTLIER) cc_final: 0.6288 (t) REVERT: H 289 ILE cc_start: 0.8507 (mt) cc_final: 0.8196 (mm) REVERT: G 95 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7287 (mpt-90) REVERT: G 124 MET cc_start: 0.8417 (ttm) cc_final: 0.8167 (ttm) REVERT: G 128 TYR cc_start: 0.6701 (OUTLIER) cc_final: 0.4335 (p90) REVERT: G 184 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8103 (p) REVERT: F 58 GLU cc_start: 0.7386 (tp30) cc_final: 0.7032 (tt0) REVERT: F 169 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8994 (tp) REVERT: F 287 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8858 (mm) REVERT: E 184 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8050 (p) REVERT: E 192 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.8836 (mt) REVERT: E 209 MET cc_start: 0.9436 (mtm) cc_final: 0.9139 (mtt) REVERT: D 58 GLU cc_start: 0.7921 (tp30) cc_final: 0.7457 (tt0) REVERT: D 95 ARG cc_start: 0.7796 (mpt-90) cc_final: 0.7402 (mmt90) REVERT: D 169 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8785 (tp) REVERT: C 95 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.6567 (mpt-90) REVERT: C 215 GLU cc_start: 0.8958 (pt0) cc_final: 0.8611 (mt-10) REVERT: C 345 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8362 (mtmt) REVERT: B 58 GLU cc_start: 0.7878 (tp30) cc_final: 0.7656 (tt0) REVERT: B 117 GLU cc_start: 0.8193 (mp0) cc_final: 0.7784 (mp0) REVERT: B 169 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9039 (tp) REVERT: B 287 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8808 (mm) REVERT: B 295 ASN cc_start: 0.8620 (t0) cc_final: 0.8296 (t0) REVERT: B 317 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7928 (m-30) REVERT: A 169 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9101 (tp) REVERT: K 169 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9112 (tp) outliers start: 104 outliers final: 78 residues processed: 419 average time/residue: 0.1783 time to fit residues: 117.0032 Evaluate side-chains 429 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 333 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 331 SER Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 289 ILE Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 128 TYR Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 299 GLU Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 321 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 333 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 317 ASP Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 331 SER Chi-restraints excluded: chain L residue 333 ASN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 124 MET Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 345 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 146 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 186 optimal weight: 0.3980 chunk 285 optimal weight: 0.2980 chunk 323 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 277 optimal weight: 0.6980 chunk 263 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 323 HIS H 323 HIS F 323 HIS D 323 HIS B 67 ASN A 42 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.120922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.099739 restraints weight = 38010.721| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.91 r_work: 0.2934 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 263 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 305 | |-----------------------------------------------------------------------------| r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27312 Z= 0.100 Angle : 0.594 10.395 36972 Z= 0.303 Chirality : 0.044 0.251 4116 Planarity : 0.004 0.040 4740 Dihedral : 5.676 51.195 3832 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.42 % Favored : 90.23 % Rotamer: Outliers : 2.68 % Allowed : 18.31 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.14), residues: 3420 helix: -0.94 (0.19), residues: 816 sheet: -0.46 (0.19), residues: 876 loop : -2.86 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 297 TYR 0.019 0.001 TYR A 210 PHE 0.013 0.001 PHE I 185 TRP 0.009 0.001 TRP G 228 HIS 0.004 0.001 HIS L 234 Details of bonding type rmsd covalent geometry : bond 0.00234 (27312) covalent geometry : angle 0.59437 (36972) hydrogen bonds : bond 0.02757 ( 668) hydrogen bonds : angle 5.01917 ( 1896) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 374 time to evaluate : 1.015 Fit side-chains REVERT: J 58 GLU cc_start: 0.7723 (tp30) cc_final: 0.7304 (tt0) REVERT: J 89 GLU cc_start: 0.8580 (tt0) cc_final: 0.8348 (tt0) REVERT: J 169 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8844 (tp) REVERT: J 215 GLU cc_start: 0.9257 (pt0) cc_final: 0.8935 (mt-10) REVERT: J 310 ASP cc_start: 0.9278 (t0) cc_final: 0.8945 (t0) REVERT: I 276 VAL cc_start: 0.6408 (OUTLIER) cc_final: 0.5890 (t) REVERT: H 58 GLU cc_start: 0.7788 (tp30) cc_final: 0.7472 (tt0) REVERT: H 214 ILE cc_start: 0.9500 (OUTLIER) cc_final: 0.9284 (tt) REVERT: H 215 GLU cc_start: 0.9006 (pt0) cc_final: 0.8802 (mt-10) REVERT: H 289 ILE cc_start: 0.8469 (mt) cc_final: 0.8190 (mm) REVERT: G 128 TYR cc_start: 0.6602 (OUTLIER) cc_final: 0.4404 (p90) REVERT: G 184 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8341 (p) REVERT: G 345 LYS cc_start: 0.8704 (ptpp) cc_final: 0.8503 (mtmt) REVERT: F 169 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8870 (tp) REVERT: F 283 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8454 (mt) REVERT: F 287 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8694 (mm) REVERT: E 192 ILE cc_start: 0.9273 (pt) cc_final: 0.8815 (mt) REVERT: D 58 GLU cc_start: 0.7672 (tp30) cc_final: 0.7154 (tt0) REVERT: D 95 ARG cc_start: 0.7830 (mpt-90) cc_final: 0.7588 (mmt90) REVERT: D 196 ILE cc_start: 0.8894 (mm) cc_final: 0.8630 (mm) REVERT: D 215 GLU cc_start: 0.9217 (pt0) cc_final: 0.8812 (mt-10) REVERT: D 283 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8667 (mt) REVERT: C 215 GLU cc_start: 0.8960 (pt0) cc_final: 0.8628 (mt-10) REVERT: C 345 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8387 (mtmt) REVERT: B 58 GLU cc_start: 0.7598 (tp30) cc_final: 0.7379 (tt0) REVERT: B 117 GLU cc_start: 0.8097 (mp0) cc_final: 0.7729 (mp0) REVERT: B 169 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8956 (tp) REVERT: B 283 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8706 (mt) REVERT: B 287 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8610 (mm) REVERT: L 215 GLU cc_start: 0.9148 (pt0) cc_final: 0.8822 (mt-10) REVERT: K 169 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9074 (tp) outliers start: 75 outliers final: 55 residues processed: 432 average time/residue: 0.1658 time to fit residues: 114.1953 Evaluate side-chains 404 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 335 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 331 SER Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 289 ILE Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 128 TYR Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 321 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 333 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 317 ASP Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 331 SER Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 124 MET Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 321 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 320 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 296 optimal weight: 0.6980 chunk 217 optimal weight: 5.9990 chunk 199 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 333 ASN F 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.096702 restraints weight = 37968.405| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.98 r_work: 0.2856 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 305 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 335 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27312 Z= 0.112 Angle : 0.611 10.484 36972 Z= 0.311 Chirality : 0.045 0.256 4116 Planarity : 0.004 0.036 4740 Dihedral : 5.510 48.516 3829 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.76 % Favored : 88.89 % Rotamer: Outliers : 2.97 % Allowed : 18.24 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.14), residues: 3420 helix: -0.89 (0.19), residues: 816 sheet: -0.40 (0.19), residues: 876 loop : -2.82 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 297 TYR 0.014 0.001 TYR A 128 PHE 0.012 0.001 PHE K 249 TRP 0.005 0.001 TRP G 228 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00272 (27312) covalent geometry : angle 0.61097 (36972) hydrogen bonds : bond 0.03155 ( 668) hydrogen bonds : angle 5.00460 ( 1896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6595.83 seconds wall clock time: 113 minutes 22.23 seconds (6802.23 seconds total)