Starting phenix.real_space_refine on Wed Mar 4 23:03:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fz7_29605/03_2026/8fz7_29605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fz7_29605/03_2026/8fz7_29605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fz7_29605/03_2026/8fz7_29605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fz7_29605/03_2026/8fz7_29605.map" model { file = "/net/cci-nas-00/data/ceres_data/8fz7_29605/03_2026/8fz7_29605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fz7_29605/03_2026/8fz7_29605.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 68 5.16 5 C 10728 2.51 5 N 2897 2.21 5 O 3272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 16971 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2473 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "C" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2473 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "E" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2473 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "G" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2473 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "B" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "D" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "F" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "H" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' K': 2, 'PGW': 1, 'YQ1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.62, per 1000 atoms: 0.21 Number of scatterers: 16971 At special positions: 0 Unit cell: (150.481, 150.481, 118.003, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 68 16.00 P 4 15.00 O 3272 8.00 N 2897 7.00 C 10728 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: 1.58 Conformation dependent library (CDL) restraints added in 710.6 milliseconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 16 sheets defined 52.7% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 21 through 43 removed outlier: 3.621A pdb=" N LEU A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.502A pdb=" N ALA A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 107 removed outlier: 3.760A pdb=" N MET A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 removed outlier: 3.511A pdb=" N LEU A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.939A pdb=" N ARG A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 151 " --> pdb=" O ASN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.569A pdb=" N LYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.545A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.560A pdb=" N ARG A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 242 removed outlier: 3.502A pdb=" N ILE A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.755A pdb=" N MET A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 323 through 332 removed outlier: 3.694A pdb=" N GLU A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 43 removed outlier: 3.621A pdb=" N LEU C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.502A pdb=" N ALA C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 107 removed outlier: 3.761A pdb=" N MET C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 132 removed outlier: 3.512A pdb=" N LEU C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 156 removed outlier: 3.940A pdb=" N ARG C 149 " --> pdb=" O ASP C 145 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 151 " --> pdb=" O ASN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.569A pdb=" N LYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 removed outlier: 3.544A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.558A pdb=" N ARG C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 242 removed outlier: 3.501A pdb=" N ILE C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.754A pdb=" N MET C 250 " --> pdb=" O GLY C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 323 through 332 removed outlier: 3.693A pdb=" N GLU C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 43 removed outlier: 3.621A pdb=" N LEU E 25 " --> pdb=" O THR E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.502A pdb=" N ALA E 58 " --> pdb=" O PHE E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 107 removed outlier: 3.761A pdb=" N MET E 107 " --> pdb=" O GLN E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 132 removed outlier: 3.512A pdb=" N LEU E 131 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG E 132 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 156 removed outlier: 3.939A pdb=" N ARG E 149 " --> pdb=" O ASP E 145 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS E 151 " --> pdb=" O ASN E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.569A pdb=" N LYS E 172 " --> pdb=" O SER E 168 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.544A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.559A pdb=" N ARG E 221 " --> pdb=" O ILE E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 242 removed outlier: 3.502A pdb=" N ILE E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 256 removed outlier: 3.755A pdb=" N MET E 250 " --> pdb=" O GLY E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 284 through 289 Processing helix chain 'E' and resid 323 through 332 removed outlier: 3.693A pdb=" N GLU E 328 " --> pdb=" O PRO E 324 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG E 329 " --> pdb=" O GLU E 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 43 removed outlier: 3.621A pdb=" N LEU G 25 " --> pdb=" O THR G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 58 removed outlier: 3.501A pdb=" N ALA G 58 " --> pdb=" O PHE G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 107 removed outlier: 3.760A pdb=" N MET G 107 " --> pdb=" O GLN G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 132 removed outlier: 3.512A pdb=" N LEU G 131 " --> pdb=" O THR G 127 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG G 132 " --> pdb=" O LEU G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 156 removed outlier: 3.939A pdb=" N ARG G 149 " --> pdb=" O ASP G 145 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS G 151 " --> pdb=" O ASN G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 173 removed outlier: 3.569A pdb=" N LYS G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.546A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.559A pdb=" N ARG G 221 " --> pdb=" O ILE G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 242 removed outlier: 3.501A pdb=" N ILE G 234 " --> pdb=" O SER G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 256 removed outlier: 3.754A pdb=" N MET G 250 " --> pdb=" O GLY G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 284 through 289 Processing helix chain 'G' and resid 323 through 332 removed outlier: 3.693A pdb=" N GLU G 328 " --> pdb=" O PRO G 324 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG G 329 " --> pdb=" O GLU G 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 147 through 156 removed outlier: 4.328A pdb=" N LYS B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.612A pdb=" N LYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 230 through 242 Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 279 through 284 removed outlier: 3.747A pdb=" N ASP B 284 " --> pdb=" O VAL B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 290 Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.607A pdb=" N GLU B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 131 Processing helix chain 'D' and resid 132 through 134 No H-bonds generated for 'chain 'D' and resid 132 through 134' Processing helix chain 'D' and resid 147 through 156 removed outlier: 4.328A pdb=" N LYS D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 173 removed outlier: 3.613A pdb=" N LYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 173 " --> pdb=" O ASP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 230 through 242 Processing helix chain 'D' and resid 247 through 256 Processing helix chain 'D' and resid 279 through 284 removed outlier: 3.747A pdb=" N ASP D 284 " --> pdb=" O VAL D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 290 Processing helix chain 'D' and resid 323 through 334 removed outlier: 3.607A pdb=" N GLU D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 131 Processing helix chain 'F' and resid 132 through 134 No H-bonds generated for 'chain 'F' and resid 132 through 134' Processing helix chain 'F' and resid 147 through 156 removed outlier: 4.328A pdb=" N LYS F 151 " --> pdb=" O ASN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 173 removed outlier: 3.613A pdb=" N LYS F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 216 through 224 Processing helix chain 'F' and resid 230 through 242 Processing helix chain 'F' and resid 247 through 256 Processing helix chain 'F' and resid 279 through 284 removed outlier: 3.747A pdb=" N ASP F 284 " --> pdb=" O VAL F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 290 Processing helix chain 'F' and resid 323 through 334 removed outlier: 3.608A pdb=" N GLU F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 131 Processing helix chain 'H' and resid 132 through 134 No H-bonds generated for 'chain 'H' and resid 132 through 134' Processing helix chain 'H' and resid 147 through 156 removed outlier: 4.328A pdb=" N LYS H 151 " --> pdb=" O ASN H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 173 removed outlier: 3.612A pdb=" N LYS H 172 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 Processing helix chain 'H' and resid 213 through 215 No H-bonds generated for 'chain 'H' and resid 213 through 215' Processing helix chain 'H' and resid 216 through 224 Processing helix chain 'H' and resid 230 through 242 Processing helix chain 'H' and resid 247 through 256 Processing helix chain 'H' and resid 279 through 284 removed outlier: 3.747A pdb=" N ASP H 284 " --> pdb=" O VAL H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 290 Processing helix chain 'H' and resid 323 through 334 removed outlier: 3.607A pdb=" N GLU H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 6.259A pdb=" N VAL A 118 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU A 142 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 120 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.287A pdb=" N ILE A 317 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL A 296 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A 319 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 158 through 161 removed outlier: 6.259A pdb=" N VAL C 118 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU C 142 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE C 120 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.287A pdb=" N ILE C 317 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL C 296 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU C 319 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 158 through 161 removed outlier: 6.260A pdb=" N VAL E 118 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU E 142 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE E 120 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 263 through 268 removed outlier: 6.287A pdb=" N ILE E 317 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL E 296 " --> pdb=" O ILE E 317 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU E 319 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 158 through 161 removed outlier: 6.260A pdb=" N VAL G 118 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU G 142 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE G 120 " --> pdb=" O LEU G 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 263 through 268 removed outlier: 6.287A pdb=" N ILE G 317 " --> pdb=" O VAL G 296 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL G 296 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU G 319 " --> pdb=" O ILE G 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 161 removed outlier: 6.591A pdb=" N VAL B 118 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU B 142 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE B 120 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 181 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLU B 210 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL B 183 " --> pdb=" O GLU B 210 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 263 through 268 removed outlier: 3.520A pdb=" N ARG B 263 " --> pdb=" O GLY B 322 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 322 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 158 through 161 removed outlier: 6.592A pdb=" N VAL D 118 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU D 142 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE D 120 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL D 181 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N GLU D 210 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL D 183 " --> pdb=" O GLU D 210 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 263 through 268 removed outlier: 3.521A pdb=" N ARG D 263 " --> pdb=" O GLY D 322 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 322 " --> pdb=" O ARG D 263 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.592A pdb=" N VAL F 118 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU F 142 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE F 120 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL F 181 " --> pdb=" O ILE F 208 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N GLU F 210 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL F 183 " --> pdb=" O GLU F 210 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 263 through 268 removed outlier: 3.521A pdb=" N ARG F 263 " --> pdb=" O GLY F 322 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY F 322 " --> pdb=" O ARG F 263 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 158 through 161 removed outlier: 6.592A pdb=" N VAL H 118 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU H 142 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE H 120 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL H 181 " --> pdb=" O ILE H 208 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLU H 210 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL H 183 " --> pdb=" O GLU H 210 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 263 through 268 removed outlier: 3.521A pdb=" N ARG H 263 " --> pdb=" O GLY H 322 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY H 322 " --> pdb=" O ARG H 263 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2352 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: 2.88 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5601 1.34 - 1.45: 1781 1.45 - 1.57: 9706 1.57 - 1.69: 4 1.69 - 1.80: 116 Bond restraints: 17208 Sorted by residual: bond pdb=" O12 PGW E 401 " pdb=" P PGW E 401 " ideal model delta sigma weight residual 1.636 1.693 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" O12 PGW C 401 " pdb=" P PGW C 401 " ideal model delta sigma weight residual 1.636 1.693 -0.057 2.00e-02 2.50e+03 7.98e+00 bond pdb=" O12 PGW A 401 " pdb=" P PGW A 401 " ideal model delta sigma weight residual 1.636 1.692 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" O12 PGW G 401 " pdb=" P PGW G 401 " ideal model delta sigma weight residual 1.636 1.692 -0.056 2.00e-02 2.50e+03 7.88e+00 bond pdb=" C01 YQ1 A 402 " pdb=" N01 YQ1 A 402 " ideal model delta sigma weight residual 1.524 1.468 0.056 2.00e-02 2.50e+03 7.78e+00 ... (remaining 17203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 22546 1.43 - 2.86: 530 2.86 - 4.28: 97 4.28 - 5.71: 40 5.71 - 7.14: 25 Bond angle restraints: 23238 Sorted by residual: angle pdb=" C SER A 273 " pdb=" N LYS A 274 " pdb=" CA LYS A 274 " ideal model delta sigma weight residual 121.54 126.20 -4.66 1.91e+00 2.74e-01 5.94e+00 angle pdb=" C SER E 273 " pdb=" N LYS E 274 " pdb=" CA LYS E 274 " ideal model delta sigma weight residual 121.54 126.19 -4.65 1.91e+00 2.74e-01 5.94e+00 angle pdb=" C SER C 273 " pdb=" N LYS C 274 " pdb=" CA LYS C 274 " ideal model delta sigma weight residual 121.54 126.19 -4.65 1.91e+00 2.74e-01 5.91e+00 angle pdb=" C SER G 273 " pdb=" N LYS G 274 " pdb=" CA LYS G 274 " ideal model delta sigma weight residual 121.54 126.17 -4.63 1.91e+00 2.74e-01 5.87e+00 angle pdb=" O13 PGW E 401 " pdb=" P PGW E 401 " pdb=" O14 PGW E 401 " ideal model delta sigma weight residual 119.81 126.95 -7.14 3.00e+00 1.11e-01 5.66e+00 ... (remaining 23233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.41: 10363 28.41 - 56.82: 113 56.82 - 85.22: 16 85.22 - 113.63: 0 113.63 - 142.04: 12 Dihedral angle restraints: 10504 sinusoidal: 4352 harmonic: 6152 Sorted by residual: dihedral pdb=" C03 PGW C 401 " pdb=" C01 PGW C 401 " pdb=" C02 PGW C 401 " pdb=" O03 PGW C 401 " ideal model delta sinusoidal sigma weight residual 295.35 153.31 142.04 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C03 PGW A 401 " pdb=" C01 PGW A 401 " pdb=" C02 PGW A 401 " pdb=" O03 PGW A 401 " ideal model delta sinusoidal sigma weight residual 295.35 153.32 142.03 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C03 PGW E 401 " pdb=" C01 PGW E 401 " pdb=" C02 PGW E 401 " pdb=" O03 PGW E 401 " ideal model delta sinusoidal sigma weight residual 295.35 153.36 141.99 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 10501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1626 0.038 - 0.077: 700 0.077 - 0.115: 303 0.115 - 0.153: 59 0.153 - 0.191: 4 Chirality restraints: 2692 Sorted by residual: chirality pdb=" CA PHE G 88 " pdb=" N PHE G 88 " pdb=" C PHE G 88 " pdb=" CB PHE G 88 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.15e-01 chirality pdb=" CA PHE C 88 " pdb=" N PHE C 88 " pdb=" C PHE C 88 " pdb=" CB PHE C 88 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CA PHE E 88 " pdb=" N PHE E 88 " pdb=" C PHE E 88 " pdb=" CB PHE E 88 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.95e-01 ... (remaining 2689 not shown) Planarity restraints: 3004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 47 " -0.034 2.00e-02 2.50e+03 6.72e-02 4.52e+01 pdb=" C THR C 47 " 0.116 2.00e-02 2.50e+03 pdb=" O THR C 47 " -0.043 2.00e-02 2.50e+03 pdb=" N VAL C 48 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 47 " 0.034 2.00e-02 2.50e+03 6.72e-02 4.51e+01 pdb=" C THR A 47 " -0.116 2.00e-02 2.50e+03 pdb=" O THR A 47 " 0.043 2.00e-02 2.50e+03 pdb=" N VAL A 48 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 47 " -0.034 2.00e-02 2.50e+03 6.72e-02 4.51e+01 pdb=" C THR E 47 " 0.116 2.00e-02 2.50e+03 pdb=" O THR E 47 " -0.043 2.00e-02 2.50e+03 pdb=" N VAL E 48 " -0.039 2.00e-02 2.50e+03 ... (remaining 3001 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 5026 2.83 - 3.41: 17605 3.41 - 3.99: 30081 3.99 - 4.56: 42504 4.56 - 5.14: 65028 Nonbonded interactions: 160244 Sorted by model distance: nonbonded pdb=" OE1 GLU C 133 " pdb=" OG SER D 240 " model vdw 2.255 3.040 nonbonded pdb=" OE1 GLU A 133 " pdb=" OG SER B 240 " model vdw 2.295 3.040 nonbonded pdb=" OE1 GLU E 133 " pdb=" OG SER F 240 " model vdw 2.301 3.040 nonbonded pdb=" OG SER B 279 " pdb=" OD1 ASP B 282 " model vdw 2.331 3.040 nonbonded pdb=" NH2 ARG E 308 " pdb=" OD2 ASP F 287 " model vdw 2.331 3.120 ... (remaining 160239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 20 through 401) selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.070 Process input model: 15.790 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 : 0.006 0.057 17208 Z= 0.288 Angle : 0.617 7.139 23238 Z= 0.327 Chirality : 0.050 0.191 2692 Planarity : 0.007 0.067 3004 Dihedral : 10.715 142.041 6552 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.43 % Allowed : 2.39 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.18), residues: 2140 helix: 0.12 (0.16), residues: 1028 sheet: 3.16 (0.26), residues: 344 loop : -1.49 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 221 TYR 0.015 0.002 TYR G 247 PHE 0.010 0.002 PHE C 88 TRP 0.013 0.002 TRP C 52 HIS 0.004 0.001 HIS F 117 Details of bonding type rmsd covalent geometry : bond 0.00630 (17208) covalent geometry : angle 0.61708 (23238) hydrogen bonds : bond 0.20885 ( 816) hydrogen bonds : angle 6.82121 ( 2352) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 317 time to evaluate : 0.632 Fit side-chains REVERT: A 53 THR cc_start: 0.8572 (m) cc_final: 0.8261 (p) REVERT: C 53 THR cc_start: 0.8543 (m) cc_final: 0.8329 (p) REVERT: G 53 THR cc_start: 0.8542 (m) cc_final: 0.8335 (p) outliers start: 8 outliers final: 2 residues processed: 321 average time/residue: 0.8324 time to fit residues: 287.9991 Evaluate side-chains 148 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 248 GLU Chi-restraints excluded: chain H residue 248 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 HIS D 161 HIS F 161 HIS H 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.107302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.073015 restraints weight = 30444.679| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.84 r_work: 0.2895 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17208 Z= 0.146 Angle : 0.563 9.180 23238 Z= 0.291 Chirality : 0.047 0.235 2692 Planarity : 0.003 0.034 3004 Dihedral : 12.461 146.053 2546 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.99 % Allowed : 10.65 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.18), residues: 2140 helix: 0.86 (0.16), residues: 1052 sheet: 2.89 (0.26), residues: 320 loop : -1.56 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 241 TYR 0.017 0.001 TYR G 33 PHE 0.010 0.001 PHE C 88 TRP 0.006 0.001 TRP A 52 HIS 0.004 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00320 (17208) covalent geometry : angle 0.56309 (23238) hydrogen bonds : bond 0.04556 ( 816) hydrogen bonds : angle 4.99180 ( 2352) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 180 time to evaluate : 0.713 Fit side-chains REVERT: A 73 MET cc_start: 0.4791 (OUTLIER) cc_final: 0.4324 (mpt) REVERT: A 222 MET cc_start: 0.8108 (tmt) cc_final: 0.7884 (tmm) REVERT: C 73 MET cc_start: 0.4644 (OUTLIER) cc_final: 0.4138 (mpt) REVERT: C 222 MET cc_start: 0.8108 (tmt) cc_final: 0.7869 (tmm) REVERT: G 33 TYR cc_start: 0.7374 (t80) cc_final: 0.6983 (t80) REVERT: G 53 THR cc_start: 0.8507 (m) cc_final: 0.8084 (p) REVERT: G 73 MET cc_start: 0.4703 (OUTLIER) cc_final: 0.4229 (mpt) REVERT: G 222 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8252 (tmt) REVERT: B 325 GLU cc_start: 0.8446 (mp0) cc_final: 0.8011 (tp30) REVERT: D 325 GLU cc_start: 0.8440 (mp0) cc_final: 0.8215 (tm-30) REVERT: F 222 MET cc_start: 0.8627 (mtt) cc_final: 0.8418 (mtp) REVERT: H 325 GLU cc_start: 0.8445 (mp0) cc_final: 0.8210 (tm-30) outliers start: 55 outliers final: 6 residues processed: 207 average time/residue: 0.6049 time to fit residues: 138.9789 Evaluate side-chains 165 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 222 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 0.0000 chunk 166 optimal weight: 4.9990 chunk 185 optimal weight: 0.0870 chunk 147 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.0168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.105120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.070854 restraints weight = 31146.298| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.91 r_work: 0.2819 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17208 Z= 0.119 Angle : 0.483 9.154 23238 Z= 0.255 Chirality : 0.046 0.180 2692 Planarity : 0.003 0.029 3004 Dihedral : 11.594 143.322 2540 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.55 % Allowed : 12.17 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.18), residues: 2140 helix: 1.45 (0.16), residues: 1028 sheet: 2.66 (0.26), residues: 320 loop : -1.47 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 241 TYR 0.021 0.001 TYR A 33 PHE 0.023 0.001 PHE A 75 TRP 0.003 0.000 TRP E 52 HIS 0.003 0.001 HIS H 117 Details of bonding type rmsd covalent geometry : bond 0.00264 (17208) covalent geometry : angle 0.48325 (23238) hydrogen bonds : bond 0.04301 ( 816) hydrogen bonds : angle 4.58502 ( 2352) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.4527 (OUTLIER) cc_final: 0.4049 (mpt) REVERT: C 65 TYR cc_start: 0.7487 (m-80) cc_final: 0.7268 (m-80) REVERT: C 73 MET cc_start: 0.4550 (OUTLIER) cc_final: 0.4076 (mpt) REVERT: C 172 LYS cc_start: 0.8554 (tppt) cc_final: 0.8328 (tppt) REVERT: E 172 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8381 (tppt) REVERT: E 222 MET cc_start: 0.8935 (tpp) cc_final: 0.8646 (mmm) REVERT: G 53 THR cc_start: 0.8403 (m) cc_final: 0.8022 (p) REVERT: G 65 TYR cc_start: 0.7395 (m-80) cc_final: 0.7192 (m-80) REVERT: G 73 MET cc_start: 0.4548 (OUTLIER) cc_final: 0.4081 (mpt) REVERT: G 172 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8352 (tppt) REVERT: G 222 MET cc_start: 0.8965 (mpp) cc_final: 0.8647 (mmm) REVERT: B 116 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7913 (ttm-80) REVERT: B 239 MET cc_start: 0.8925 (mtt) cc_final: 0.8667 (mtt) REVERT: B 310 TYR cc_start: 0.7835 (t80) cc_final: 0.7612 (t80) REVERT: B 325 GLU cc_start: 0.8491 (mp0) cc_final: 0.8053 (tp30) REVERT: D 116 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7937 (ttm-80) REVERT: D 239 MET cc_start: 0.8926 (mtt) cc_final: 0.8675 (mtt) REVERT: D 325 GLU cc_start: 0.8475 (mp0) cc_final: 0.8248 (tm-30) REVERT: F 116 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7856 (ttm-80) REVERT: H 116 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7959 (ttm-80) REVERT: H 325 GLU cc_start: 0.8489 (mp0) cc_final: 0.8259 (tm-30) outliers start: 47 outliers final: 8 residues processed: 203 average time/residue: 0.7145 time to fit residues: 158.9972 Evaluate side-chains 164 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain H residue 116 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 54 optimal weight: 0.0070 overall best weight: 1.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.103880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.069578 restraints weight = 31098.667| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.89 r_work: 0.2786 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17208 Z= 0.133 Angle : 0.499 6.729 23238 Z= 0.261 Chirality : 0.046 0.184 2692 Planarity : 0.003 0.024 3004 Dihedral : 11.288 141.121 2540 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.04 % Allowed : 12.39 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.18), residues: 2140 helix: 1.69 (0.16), residues: 1028 sheet: 2.89 (0.26), residues: 312 loop : -1.43 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 241 TYR 0.023 0.001 TYR A 33 PHE 0.012 0.001 PHE A 75 TRP 0.003 0.000 TRP C 123 HIS 0.003 0.001 HIS F 117 Details of bonding type rmsd covalent geometry : bond 0.00308 (17208) covalent geometry : angle 0.49902 (23238) hydrogen bonds : bond 0.03909 ( 816) hydrogen bonds : angle 4.49821 ( 2352) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 160 time to evaluate : 0.594 Fit side-chains REVERT: A 73 MET cc_start: 0.4715 (OUTLIER) cc_final: 0.4180 (mpt) REVERT: A 103 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7774 (tp-100) REVERT: A 274 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8405 (ptpp) REVERT: C 65 TYR cc_start: 0.7713 (m-80) cc_final: 0.7322 (m-80) REVERT: C 103 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7638 (tp-100) REVERT: E 73 MET cc_start: 0.5053 (OUTLIER) cc_final: 0.4571 (mpt) REVERT: E 103 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7630 (tp-100) REVERT: E 222 MET cc_start: 0.8947 (tpp) cc_final: 0.8663 (mmm) REVERT: G 73 MET cc_start: 0.4632 (OUTLIER) cc_final: 0.4086 (mpt) REVERT: G 103 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7725 (tp-100) REVERT: G 222 MET cc_start: 0.8977 (tpp) cc_final: 0.8673 (mmm) REVERT: B 116 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.8026 (ttm-80) REVERT: B 325 GLU cc_start: 0.8534 (mp0) cc_final: 0.8129 (tp30) REVERT: D 116 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.8054 (ttm-80) REVERT: D 239 MET cc_start: 0.8973 (mtt) cc_final: 0.8680 (mtt) REVERT: D 274 LYS cc_start: 0.8955 (mttt) cc_final: 0.8711 (mttt) REVERT: D 325 GLU cc_start: 0.8516 (mp0) cc_final: 0.8105 (tp30) REVERT: H 116 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.8052 (ttm-80) REVERT: H 325 GLU cc_start: 0.8532 (mp0) cc_final: 0.8112 (tp30) outliers start: 56 outliers final: 13 residues processed: 195 average time/residue: 0.7252 time to fit residues: 154.8024 Evaluate side-chains 156 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 150 LYS Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain H residue 116 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 186 optimal weight: 8.9990 chunk 209 optimal weight: 0.0030 chunk 86 optimal weight: 0.0060 chunk 53 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.5006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN C 332 ASN G 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.105056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.071022 restraints weight = 31048.825| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.90 r_work: 0.2817 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17208 Z= 0.091 Angle : 0.457 6.746 23238 Z= 0.239 Chirality : 0.045 0.159 2692 Planarity : 0.003 0.024 3004 Dihedral : 10.996 138.099 2540 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.17 % Allowed : 13.26 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.19), residues: 2140 helix: 1.85 (0.17), residues: 1032 sheet: 2.61 (0.27), residues: 320 loop : -1.23 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 241 TYR 0.008 0.001 TYR E 51 PHE 0.028 0.001 PHE C 54 TRP 0.005 0.000 TRP C 52 HIS 0.004 0.000 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00186 (17208) covalent geometry : angle 0.45746 (23238) hydrogen bonds : bond 0.03125 ( 816) hydrogen bonds : angle 4.33572 ( 2352) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.656 Fit side-chains REVERT: A 73 MET cc_start: 0.4630 (OUTLIER) cc_final: 0.4129 (mpt) REVERT: A 103 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7723 (tp-100) REVERT: A 274 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8433 (ptpp) REVERT: C 65 TYR cc_start: 0.7595 (m-80) cc_final: 0.7187 (m-80) REVERT: C 103 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7767 (tp-100) REVERT: E 73 MET cc_start: 0.4921 (OUTLIER) cc_final: 0.4508 (mpt) REVERT: E 103 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7706 (tp-100) REVERT: E 222 MET cc_start: 0.8938 (tpp) cc_final: 0.8640 (mmm) REVERT: G 73 MET cc_start: 0.4575 (OUTLIER) cc_final: 0.4015 (mpt) REVERT: G 103 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7707 (tp-100) REVERT: G 222 MET cc_start: 0.8985 (mpp) cc_final: 0.8676 (mmm) REVERT: B 116 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7969 (ttm-80) REVERT: B 325 GLU cc_start: 0.8562 (mp0) cc_final: 0.8127 (tp30) REVERT: D 116 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.8003 (ttm-80) REVERT: D 172 LYS cc_start: 0.8850 (mtpp) cc_final: 0.8646 (mtpt) REVERT: D 239 MET cc_start: 0.8917 (mtt) cc_final: 0.8661 (mtt) REVERT: D 325 GLU cc_start: 0.8504 (mp0) cc_final: 0.8066 (tp30) REVERT: F 274 LYS cc_start: 0.8728 (mttp) cc_final: 0.8470 (mttp) REVERT: H 116 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.8011 (ttm-80) REVERT: H 172 LYS cc_start: 0.8859 (mtpp) cc_final: 0.8651 (mtpt) REVERT: H 325 GLU cc_start: 0.8498 (mp0) cc_final: 0.8081 (tp30) outliers start: 40 outliers final: 8 residues processed: 192 average time/residue: 0.7260 time to fit residues: 152.7926 Evaluate side-chains 156 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain H residue 116 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 204 optimal weight: 0.2980 chunk 177 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 163 optimal weight: 0.0670 chunk 12 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 211 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 332 ASN E 332 ASN G 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.103863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.070305 restraints weight = 30875.062| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.80 r_work: 0.2798 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17208 Z= 0.095 Angle : 0.460 8.984 23238 Z= 0.238 Chirality : 0.045 0.170 2692 Planarity : 0.003 0.025 3004 Dihedral : 10.778 134.316 2540 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.47 % Allowed : 14.02 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 2140 helix: 1.96 (0.17), residues: 1032 sheet: 2.61 (0.27), residues: 320 loop : -1.22 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 241 TYR 0.009 0.001 TYR C 51 PHE 0.010 0.001 PHE A 75 TRP 0.003 0.000 TRP C 52 HIS 0.004 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00201 (17208) covalent geometry : angle 0.45987 (23238) hydrogen bonds : bond 0.03127 ( 816) hydrogen bonds : angle 4.24924 ( 2352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.743 Fit side-chains REVERT: A 73 MET cc_start: 0.4625 (OUTLIER) cc_final: 0.4130 (mpt) REVERT: A 103 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7712 (tp-100) REVERT: A 274 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8483 (ptpp) REVERT: C 65 TYR cc_start: 0.7565 (m-80) cc_final: 0.7156 (m-80) REVERT: C 103 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7744 (tp-100) REVERT: E 73 MET cc_start: 0.5032 (OUTLIER) cc_final: 0.4592 (mpt) REVERT: E 103 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7736 (tp-100) REVERT: E 222 MET cc_start: 0.8955 (tpp) cc_final: 0.8643 (mmm) REVERT: G 103 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7724 (tp-100) REVERT: G 222 MET cc_start: 0.8988 (tpp) cc_final: 0.8671 (mmm) REVERT: B 116 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7968 (ttm-80) REVERT: B 325 GLU cc_start: 0.8483 (mp0) cc_final: 0.8012 (tp30) REVERT: D 116 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7988 (ttm-80) REVERT: D 239 MET cc_start: 0.8869 (mtt) cc_final: 0.8660 (mtt) REVERT: D 325 GLU cc_start: 0.8489 (mp0) cc_final: 0.8028 (tp30) REVERT: F 274 LYS cc_start: 0.8865 (mttp) cc_final: 0.8596 (mptt) REVERT: H 116 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7979 (ttm-80) REVERT: H 325 GLU cc_start: 0.8489 (mp0) cc_final: 0.8238 (tm-30) outliers start: 27 outliers final: 7 residues processed: 167 average time/residue: 0.8185 time to fit residues: 148.4486 Evaluate side-chains 145 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain H residue 116 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 154 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 104 optimal weight: 0.0370 chunk 181 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 332 ASN E 332 ASN D 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.102513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.067984 restraints weight = 30837.724| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.88 r_work: 0.2757 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17208 Z= 0.162 Angle : 0.528 9.498 23238 Z= 0.272 Chirality : 0.047 0.169 2692 Planarity : 0.003 0.031 3004 Dihedral : 10.878 134.331 2540 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.36 % Allowed : 14.73 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.19), residues: 2140 helix: 1.85 (0.17), residues: 1032 sheet: 2.96 (0.27), residues: 312 loop : -1.35 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 199 TYR 0.009 0.001 TYR C 51 PHE 0.011 0.001 PHE A 75 TRP 0.003 0.001 TRP A 123 HIS 0.004 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00386 (17208) covalent geometry : angle 0.52820 (23238) hydrogen bonds : bond 0.04324 ( 816) hydrogen bonds : angle 4.41700 ( 2352) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7901 (tp-100) REVERT: A 274 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8552 (ptpp) REVERT: C 65 TYR cc_start: 0.7782 (m-80) cc_final: 0.7389 (m-80) REVERT: C 103 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7833 (tp-100) REVERT: E 46 TRP cc_start: 0.7431 (m100) cc_final: 0.7110 (m100) REVERT: E 103 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7841 (tp-100) REVERT: E 222 MET cc_start: 0.8962 (tpp) cc_final: 0.8661 (mmm) REVERT: G 46 TRP cc_start: 0.7483 (m100) cc_final: 0.7161 (m100) REVERT: G 103 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7838 (tp-100) REVERT: G 222 MET cc_start: 0.8957 (tpp) cc_final: 0.8669 (mmm) REVERT: B 172 LYS cc_start: 0.8893 (mtpp) cc_final: 0.8687 (mtpt) REVERT: B 325 GLU cc_start: 0.8565 (mp0) cc_final: 0.8274 (tp30) REVERT: D 116 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8199 (ttm-80) REVERT: D 172 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8599 (mtpt) REVERT: D 239 MET cc_start: 0.8916 (mtt) cc_final: 0.8668 (mtt) REVERT: D 325 GLU cc_start: 0.8667 (mp0) cc_final: 0.8411 (tm-30) REVERT: F 172 LYS cc_start: 0.8902 (mtpp) cc_final: 0.8699 (mtpt) REVERT: H 116 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8206 (ttm-80) REVERT: H 172 LYS cc_start: 0.8838 (mtpp) cc_final: 0.8593 (mtpt) outliers start: 25 outliers final: 13 residues processed: 164 average time/residue: 0.8744 time to fit residues: 154.7974 Evaluate side-chains 150 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 150 LYS Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 150 LYS Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain H residue 116 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 164 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.103125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.068802 restraints weight = 31005.082| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.87 r_work: 0.2773 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17208 Z= 0.126 Angle : 0.494 7.619 23238 Z= 0.254 Chirality : 0.046 0.149 2692 Planarity : 0.003 0.028 3004 Dihedral : 10.836 134.322 2540 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.25 % Allowed : 15.38 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.19), residues: 2140 helix: 1.93 (0.17), residues: 1032 sheet: 2.68 (0.27), residues: 320 loop : -1.33 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 241 TYR 0.008 0.001 TYR E 51 PHE 0.010 0.001 PHE A 75 TRP 0.003 0.000 TRP G 123 HIS 0.003 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00294 (17208) covalent geometry : angle 0.49436 (23238) hydrogen bonds : bond 0.03631 ( 816) hydrogen bonds : angle 4.31346 ( 2352) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.656 Fit side-chains REVERT: A 46 TRP cc_start: 0.7474 (m100) cc_final: 0.7105 (m100) REVERT: A 103 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7911 (tp-100) REVERT: A 274 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8697 (ptpt) REVERT: C 46 TRP cc_start: 0.7397 (m100) cc_final: 0.7092 (m100) REVERT: C 65 TYR cc_start: 0.7764 (m-80) cc_final: 0.7335 (m-80) REVERT: C 103 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7846 (tp-100) REVERT: E 46 TRP cc_start: 0.7475 (m100) cc_final: 0.7099 (m100) REVERT: E 103 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7865 (tp-100) REVERT: E 222 MET cc_start: 0.8951 (tpp) cc_final: 0.8648 (mmm) REVERT: G 46 TRP cc_start: 0.7530 (m100) cc_final: 0.7186 (m100) REVERT: G 103 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7896 (tp-100) REVERT: G 222 MET cc_start: 0.8988 (tpp) cc_final: 0.8690 (mmm) REVERT: B 325 GLU cc_start: 0.8572 (mp0) cc_final: 0.8355 (tp30) REVERT: D 239 MET cc_start: 0.8923 (mtt) cc_final: 0.8688 (mtt) outliers start: 23 outliers final: 13 residues processed: 165 average time/residue: 0.8399 time to fit residues: 150.1532 Evaluate side-chains 148 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 150 LYS Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 309 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 160 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 179 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.102297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.067867 restraints weight = 30889.577| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.87 r_work: 0.2752 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17208 Z= 0.150 Angle : 0.525 7.793 23238 Z= 0.268 Chirality : 0.047 0.154 2692 Planarity : 0.003 0.028 3004 Dihedral : 10.883 134.548 2540 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.25 % Allowed : 15.54 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.19), residues: 2140 helix: 1.96 (0.17), residues: 1028 sheet: 2.69 (0.27), residues: 320 loop : -1.40 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 135 TYR 0.009 0.001 TYR C 51 PHE 0.010 0.001 PHE A 75 TRP 0.004 0.001 TRP E 123 HIS 0.003 0.001 HIS F 117 Details of bonding type rmsd covalent geometry : bond 0.00358 (17208) covalent geometry : angle 0.52531 (23238) hydrogen bonds : bond 0.04074 ( 816) hydrogen bonds : angle 4.34871 ( 2352) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7920 (tp-100) REVERT: A 274 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8702 (ptpt) REVERT: C 25 LEU cc_start: 0.8382 (pp) cc_final: 0.7759 (mm) REVERT: C 65 TYR cc_start: 0.7876 (m-80) cc_final: 0.7540 (m-80) REVERT: C 103 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7860 (tp-100) REVERT: E 46 TRP cc_start: 0.7561 (m100) cc_final: 0.7342 (m100) REVERT: E 103 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7902 (tp-100) REVERT: E 222 MET cc_start: 0.8963 (tpp) cc_final: 0.8662 (mmm) REVERT: G 74 TYR cc_start: 0.8237 (m-80) cc_final: 0.8027 (m-80) REVERT: G 103 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7930 (tp-100) REVERT: G 222 MET cc_start: 0.8948 (tpp) cc_final: 0.8656 (mmm) REVERT: G 274 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8717 (ptpt) REVERT: B 172 LYS cc_start: 0.8840 (mtpp) cc_final: 0.8608 (mtpt) REVERT: D 172 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8616 (mtpt) REVERT: D 239 MET cc_start: 0.8914 (mtt) cc_final: 0.8658 (mtt) REVERT: F 172 LYS cc_start: 0.8841 (mtpp) cc_final: 0.8610 (mtpt) REVERT: F 237 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8266 (mtp-110) REVERT: H 172 LYS cc_start: 0.8850 (mtpp) cc_final: 0.8608 (mtpt) outliers start: 23 outliers final: 13 residues processed: 160 average time/residue: 0.8149 time to fit residues: 141.4077 Evaluate side-chains 151 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 150 LYS Chi-restraints excluded: chain G residue 274 LYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain F residue 237 ARG Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 309 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 72 optimal weight: 3.9990 chunk 201 optimal weight: 0.4980 chunk 75 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 168 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 204 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.102429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.068685 restraints weight = 30670.051| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.77 r_work: 0.2766 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17208 Z= 0.103 Angle : 0.493 7.791 23238 Z= 0.250 Chirality : 0.046 0.158 2692 Planarity : 0.003 0.028 3004 Dihedral : 10.761 133.587 2540 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.76 % Allowed : 16.30 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.19), residues: 2140 helix: 2.06 (0.17), residues: 1032 sheet: 2.66 (0.27), residues: 320 loop : -1.30 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 135 TYR 0.008 0.001 TYR C 51 PHE 0.010 0.001 PHE A 75 TRP 0.003 0.000 TRP E 52 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00226 (17208) covalent geometry : angle 0.49301 (23238) hydrogen bonds : bond 0.03238 ( 816) hydrogen bonds : angle 4.20114 ( 2352) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7902 (tp-100) REVERT: A 274 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8678 (ptpt) REVERT: C 25 LEU cc_start: 0.8350 (pp) cc_final: 0.7742 (mm) REVERT: C 65 TYR cc_start: 0.7733 (m-80) cc_final: 0.7368 (m-80) REVERT: C 103 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7848 (tp-100) REVERT: C 172 LYS cc_start: 0.8815 (ttmt) cc_final: 0.8419 (ttmm) REVERT: E 103 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7887 (tp-100) REVERT: E 172 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8426 (ttmm) REVERT: E 222 MET cc_start: 0.9001 (tpp) cc_final: 0.8707 (mmm) REVERT: G 103 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7888 (tp-100) REVERT: G 172 LYS cc_start: 0.8818 (ttmt) cc_final: 0.8400 (ttmm) REVERT: G 222 MET cc_start: 0.8978 (tpp) cc_final: 0.8669 (mmm) REVERT: G 274 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8692 (ptpt) REVERT: B 172 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8529 (mtpt) REVERT: D 172 LYS cc_start: 0.8757 (mtpp) cc_final: 0.8514 (mtpt) REVERT: D 239 MET cc_start: 0.8876 (mtt) cc_final: 0.8656 (mtt) REVERT: F 172 LYS cc_start: 0.8778 (mtpp) cc_final: 0.8543 (mtpt) REVERT: F 237 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8049 (mtp-110) REVERT: H 172 LYS cc_start: 0.8751 (mtpp) cc_final: 0.8508 (mtpt) REVERT: H 237 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8038 (mtp-110) outliers start: 14 outliers final: 7 residues processed: 160 average time/residue: 0.8374 time to fit residues: 145.2399 Evaluate side-chains 145 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 274 LYS Chi-restraints excluded: chain F residue 237 ARG Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain H residue 237 ARG Chi-restraints excluded: chain H residue 309 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 100 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.102122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.067616 restraints weight = 30822.494| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.85 r_work: 0.2742 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17208 Z= 0.158 Angle : 0.526 7.691 23238 Z= 0.270 Chirality : 0.047 0.149 2692 Planarity : 0.003 0.028 3004 Dihedral : 10.868 133.898 2540 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.44 % Favored : 95.51 % Rotamer: Outliers : 0.92 % Allowed : 16.52 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.19), residues: 2140 helix: 2.02 (0.17), residues: 1028 sheet: 2.71 (0.27), residues: 320 loop : -1.38 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 135 TYR 0.018 0.001 TYR G 74 PHE 0.011 0.001 PHE A 75 TRP 0.004 0.001 TRP E 123 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00377 (17208) covalent geometry : angle 0.52638 (23238) hydrogen bonds : bond 0.04165 ( 816) hydrogen bonds : angle 4.32205 ( 2352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5191.91 seconds wall clock time: 88 minutes 59.14 seconds (5339.14 seconds total)