Starting phenix.real_space_refine on Sat Jul 4 00:13:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fz7_29605/07_2026/8fz7_29605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fz7_29605/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fz7_29605/07_2026/8fz7_29605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fz7_29605/07_2026/8fz7_29605.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fz7_29605/07_2026/8fz7_29605.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fz7_29605/07_2026/8fz7_29605.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fz7_29605/07_2026/8fz7_29605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fz7_29605/07_2026/8fz7_29605.map" } 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-6108/lib/python3.11/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: 9 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: 9 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: 9 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: 9 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.22, per 1000 atoms: 0.19 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: 1.27 Conformation dependent library (CDL) restraints added in 906.3 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: 0.48 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: 3.54 Time building geometry restraints manager: 1.70 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 - 25.26: 10295 25.26 - 50.53: 157 50.53 - 75.79: 4 75.79 - 101.06: 8 101.06 - 126.32: 4 Dihedral angle restraints: 10468 sinusoidal: 4316 harmonic: 6152 Sorted by residual: dihedral pdb=" C01 PGW C 401 " pdb=" C19 PGW C 401 " pdb=" O03 PGW C 401 " pdb=" O04 PGW C 401 " ideal model delta sinusoidal sigma weight residual 9.00 -117.32 126.32 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C01 PGW G 401 " pdb=" C19 PGW G 401 " pdb=" O03 PGW G 401 " pdb=" O04 PGW G 401 " ideal model delta sinusoidal sigma weight residual 9.00 -117.28 126.28 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C01 PGW E 401 " pdb=" C19 PGW E 401 " pdb=" O03 PGW E 401 " pdb=" O04 PGW E 401 " ideal model delta sinusoidal sigma weight residual 9.00 -117.28 126.28 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 10465 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.600 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 : 9.143 126.324 6516 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/Z covalent geometry : bond 0.00630 / 0.29 (17208) covalent geometry : angle 0.61708 / 0.33 (23238) hydrogen bonds : bond 0.20885 / 13.72 ( 816) hydrogen bonds : angle 6.82121 / 4.86 ( 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 : 0.717 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: 0.8469 time to fit residues: 294.5099 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 : 0.656 ------------------------------------------------------------------------------- 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... 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 = 0.107296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.072921 restraints weight = 30436.142| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.85 r_work: 0.2890 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2971 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= 0.149 Angle : 0.564 8.938 23238 Z= 0.292 Chirality : 0.047 0.221 2692 Planarity : 0.003 0.030 3004 Dihedral : 8.332 123.266 2510 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.93 % Allowed : 10.65 % Favored : 86.41 % 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: 0.51 (0.18), residues: 2140 helix: 0.86 (0.16), residues: 1052 sheet: 2.88 (0.26), residues: 320 loop : -1.56 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 241 TYR 0.015 0.001 TYR G 33 PHE 0.009 0.001 PHE C 88 TRP 0.005 0.001 TRP G 123 HIS 0.003 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (17208) covalent geometry : angle 0.56406 / 0.29 (23238) hydrogen bonds : bond 0.04551 / 2.94 ( 816) hydrogen bonds : angle 5.00277 / 3.53 ( 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 232 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 178 time to evaluate : 0.695 Fit side-chains REVERT: A 73 MET cc_start: 0.4790 (OUTLIER) cc_final: 0.4327 (mpt) REVERT: A 222 MET cc_start: 0.8110 (tmt) cc_final: 0.7891 (tmm) REVERT: C 73 MET cc_start: 0.4641 (OUTLIER) cc_final: 0.4137 (mpt) REVERT: C 222 MET cc_start: 0.8101 (tmt) cc_final: 0.7866 (tmm) REVERT: G 33 TYR cc_start: 0.7377 (t80) cc_final: 0.6991 (t80) REVERT: G 53 THR cc_start: 0.8497 (m) cc_final: 0.8070 (p) REVERT: G 73 MET cc_start: 0.4754 (OUTLIER) cc_final: 0.4272 (mpt) REVERT: G 222 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8251 (tmt) REVERT: B 325 GLU cc_start: 0.8448 (mp0) cc_final: 0.7996 (tp30) REVERT: D 325 GLU cc_start: 0.8440 (mp0) cc_final: 0.8219 (tm-30) REVERT: F 222 MET cc_start: 0.8631 (mtt) cc_final: 0.8425 (mtp) REVERT: H 325 GLU cc_start: 0.8445 (mp0) cc_final: 0.7988 (tp30) outliers start: 54 outliers final: 6 residues processed: 205 average time/residue: 0.6344 time to fit residues: 144.9101 Evaluate side-chains 163 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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: 0.6980 chunk 147 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 2 optimal weight: 0.0870 chunk 136 optimal weight: 0.6980 chunk 157 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.6964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.106195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.072146 restraints weight = 31198.179| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.91 r_work: 0.2843 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17208 Z= 0.103 Angle : 0.468 8.106 23238 Z= 0.246 Chirality : 0.045 0.182 2692 Planarity : 0.003 0.023 3004 Dihedral : 7.335 94.006 2504 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.34 % Allowed : 12.28 % Favored : 85.38 % 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: 0.89 (0.18), residues: 2140 helix: 1.35 (0.16), residues: 1052 sheet: 2.83 (0.26), residues: 312 loop : -1.51 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 241 TYR 0.019 0.001 TYR A 33 PHE 0.008 0.001 PHE A 75 TRP 0.003 0.000 TRP E 52 HIS 0.002 0.000 HIS B 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (17208) covalent geometry : angle 0.46764 / 0.25 (23238) hydrogen bonds : bond 0.03957 / 2.58 ( 816) hydrogen bonds : angle 4.58628 / 3.25 ( 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 208 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.4452 (OUTLIER) cc_final: 0.4013 (mpt) REVERT: C 33 TYR cc_start: 0.7387 (t80) cc_final: 0.7028 (t80) REVERT: C 73 MET cc_start: 0.4522 (OUTLIER) cc_final: 0.4036 (mpt) REVERT: C 172 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8333 (tppt) REVERT: G 53 THR cc_start: 0.8388 (m) cc_final: 0.7960 (p) REVERT: G 73 MET cc_start: 0.4604 (OUTLIER) cc_final: 0.4155 (mpt) REVERT: B 116 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7761 (ttm-80) REVERT: B 239 MET cc_start: 0.8929 (mtt) cc_final: 0.8702 (mtt) REVERT: B 325 GLU cc_start: 0.8491 (mp0) cc_final: 0.8063 (tp30) REVERT: D 116 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7826 (ttm-80) REVERT: D 239 MET cc_start: 0.8913 (mtt) cc_final: 0.8678 (mtt) REVERT: D 325 GLU cc_start: 0.8474 (mp0) cc_final: 0.8058 (tp30) REVERT: F 116 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7701 (ttm-80) REVERT: H 116 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7852 (ttm-80) REVERT: H 325 GLU cc_start: 0.8487 (mp0) cc_final: 0.8055 (tp30) outliers start: 43 outliers final: 6 residues processed: 194 average time/residue: 0.6663 time to fit residues: 142.3823 Evaluate side-chains 149 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 172 LYS 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 23 ILE Chi-restraints excluded: chain G residue 25 LEU 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 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: 2.9990 chunk 92 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.104070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.069691 restraints weight = 30943.811| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.90 r_work: 0.2788 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17208 Z= 0.127 Angle : 0.507 8.713 23238 Z= 0.262 Chirality : 0.046 0.210 2692 Planarity : 0.003 0.023 3004 Dihedral : 6.998 88.420 2504 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.66 % Allowed : 12.72 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.18), residues: 2140 helix: 1.68 (0.16), residues: 1032 sheet: 2.84 (0.26), residues: 312 loop : -1.39 (0.21), residues: 796 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 0.022 0.001 PHE G 75 TRP 0.002 0.000 TRP C 123 HIS 0.003 0.001 HIS H 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (17208) covalent geometry : angle 0.50699 / 0.26 (23238) hydrogen bonds : bond 0.03968 / 2.58 ( 816) hydrogen bonds : angle 4.48653 / 3.19 ( 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 211 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 162 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.4677 (OUTLIER) cc_final: 0.4144 (mpt) REVERT: A 222 MET cc_start: 0.8270 (tmt) cc_final: 0.8035 (tmm) REVERT: C 73 MET cc_start: 0.4661 (OUTLIER) cc_final: 0.4152 (mpt) REVERT: C 103 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7584 (tp-100) REVERT: C 222 MET cc_start: 0.8224 (tmt) cc_final: 0.7971 (tmm) REVERT: E 73 MET cc_start: 0.4928 (OUTLIER) cc_final: 0.4468 (mpt) REVERT: E 103 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7619 (tp-100) REVERT: E 172 LYS cc_start: 0.8644 (tppt) cc_final: 0.8422 (tppt) REVERT: E 222 MET cc_start: 0.8980 (tpp) cc_final: 0.8696 (mmm) REVERT: G 73 MET cc_start: 0.4625 (OUTLIER) cc_final: 0.4121 (mpt) REVERT: G 103 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7575 (tp-100) REVERT: G 222 MET cc_start: 0.8978 (tpp) cc_final: 0.8688 (mmm) REVERT: B 116 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.8025 (ttm-80) REVERT: B 239 MET cc_start: 0.8961 (mtt) cc_final: 0.8710 (mtt) REVERT: B 325 GLU cc_start: 0.8522 (mp0) cc_final: 0.8121 (tp30) REVERT: D 116 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.8034 (ttm-80) REVERT: D 239 MET cc_start: 0.8941 (mtt) cc_final: 0.8690 (mtt) REVERT: D 325 GLU cc_start: 0.8518 (mp0) cc_final: 0.8122 (tp30) REVERT: F 116 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.8018 (ttm-80) REVERT: F 200 LYS cc_start: 0.8876 (mmmm) cc_final: 0.8577 (ttpt) REVERT: F 274 LYS cc_start: 0.8986 (mttp) cc_final: 0.8733 (mptt) REVERT: H 116 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.8009 (ttm-80) REVERT: H 274 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8796 (mtmm) REVERT: H 325 GLU cc_start: 0.8528 (mp0) cc_final: 0.8118 (tp30) outliers start: 49 outliers final: 12 residues processed: 193 average time/residue: 0.7165 time to fit residues: 151.4509 Evaluate side-chains 162 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 C residue 25 LEU Chi-restraints excluded: chain C residue 41 ILE 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 41 ILE 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 23 ILE 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 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 Chi-restraints excluded: chain H residue 274 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 186 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 77 optimal weight: 0.0060 overall best weight: 1.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 ASN C 39 HIS C 332 ASN G 332 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.103502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.068953 restraints weight = 31007.367| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.90 r_work: 0.2774 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17208 Z= 0.140 Angle : 0.489 6.774 23238 Z= 0.257 Chirality : 0.046 0.166 2692 Planarity : 0.003 0.024 3004 Dihedral : 6.811 86.709 2504 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.66 % Allowed : 13.04 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.18), residues: 2140 helix: 1.80 (0.17), residues: 1032 sheet: 2.76 (0.27), residues: 320 loop : -1.29 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 241 TYR 0.014 0.001 TYR C 33 PHE 0.032 0.001 PHE C 54 TRP 0.004 0.001 TRP G 52 HIS 0.003 0.001 HIS B 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (17208) covalent geometry : angle 0.48862 / 0.26 (23238) hydrogen bonds : bond 0.03951 / 2.57 ( 816) hydrogen bonds : angle 4.47272 / 3.17 ( 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 201 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 152 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.7699 (m-80) cc_final: 0.7329 (m-80) REVERT: A 103 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7844 (tp-100) REVERT: A 274 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8517 (ptpp) REVERT: C 103 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7683 (tp-100) REVERT: E 103 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7756 (tp-100) REVERT: E 222 MET cc_start: 0.8949 (tpp) cc_final: 0.8666 (mmm) REVERT: G 103 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7642 (tp-100) REVERT: G 172 LYS cc_start: 0.8728 (tppt) cc_final: 0.8522 (tppt) REVERT: G 222 MET cc_start: 0.9014 (tpp) cc_final: 0.8721 (mmm) REVERT: B 116 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.8065 (ttm-80) REVERT: B 325 GLU cc_start: 0.8622 (mp0) cc_final: 0.8112 (tp30) REVERT: D 116 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8071 (ttm-80) REVERT: D 325 GLU cc_start: 0.8606 (mp0) cc_final: 0.8309 (tm-30) REVERT: H 116 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8088 (ttm-80) REVERT: H 274 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8757 (mtmm) REVERT: H 325 GLU cc_start: 0.8606 (mp0) cc_final: 0.8309 (tm-30) outliers start: 49 outliers final: 11 residues processed: 186 average time/residue: 0.7412 time to fit residues: 151.0428 Evaluate side-chains 152 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 150 LYS 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 41 ILE Chi-restraints excluded: chain E residue 150 LYS 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 Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 274 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 204 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 206 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 12 optimal weight: 0.2980 chunk 96 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3566 r_free = 0.3566 target = 0.103871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.069326 restraints weight = 30851.736| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.90 r_work: 0.2788 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.4746 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= 0.110 Angle : 0.471 7.488 23238 Z= 0.246 Chirality : 0.045 0.153 2692 Planarity : 0.003 0.027 3004 Dihedral : 6.639 83.447 2504 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.68 % Allowed : 13.80 % 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: 1.43 (0.19), residues: 2140 helix: 1.91 (0.17), residues: 1032 sheet: 2.93 (0.26), residues: 312 loop : -1.28 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 241 TYR 0.010 0.001 TYR C 33 PHE 0.014 0.001 PHE C 54 TRP 0.002 0.000 TRP C 123 HIS 0.004 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (17208) covalent geometry : angle 0.47120 / 0.25 (23238) hydrogen bonds : bond 0.03492 / 2.27 ( 816) hydrogen bonds : angle 4.35739 / 3.09 ( 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 179 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7887 (tp-100) REVERT: A 274 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8483 (ptpp) REVERT: C 103 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7737 (tp-100) REVERT: E 103 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7768 (tp-100) REVERT: E 222 MET cc_start: 0.8987 (tpp) cc_final: 0.8702 (mmm) REVERT: G 103 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7692 (tp-100) REVERT: G 222 MET cc_start: 0.9010 (tpp) cc_final: 0.8726 (mmm) REVERT: B 116 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8046 (ttm-80) REVERT: B 325 GLU cc_start: 0.8641 (mp0) cc_final: 0.8187 (tp30) REVERT: D 116 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8071 (ttm-80) REVERT: D 274 LYS cc_start: 0.8918 (mttt) cc_final: 0.8620 (mttt) REVERT: D 325 GLU cc_start: 0.8637 (mp0) cc_final: 0.8204 (tp30) REVERT: H 116 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8099 (ttm-80) REVERT: H 172 LYS cc_start: 0.8849 (mtpp) cc_final: 0.8631 (mtpt) REVERT: H 325 GLU cc_start: 0.8640 (mp0) cc_final: 0.8161 (tp30) outliers start: 31 outliers final: 13 residues processed: 172 average time/residue: 0.7039 time to fit residues: 132.0522 Evaluate side-chains 152 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 150 LYS 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 41 ILE Chi-restraints excluded: chain E residue 150 LYS 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 B residue 150 LYS Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 150 LYS Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 274 LYS 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: 0.5980 chunk 104 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 332 ASN D 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.102746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.068352 restraints weight = 30803.731| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.88 r_work: 0.2764 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17208 Z= 0.139 Angle : 0.495 7.442 23238 Z= 0.259 Chirality : 0.046 0.154 2692 Planarity : 0.003 0.029 3004 Dihedral : 6.695 83.084 2504 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.63 % Allowed : 14.18 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.19), residues: 2140 helix: 1.91 (0.17), residues: 1032 sheet: 2.97 (0.27), residues: 312 loop : -1.38 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 241 TYR 0.010 0.001 TYR C 33 PHE 0.011 0.001 PHE G 75 TRP 0.003 0.001 TRP C 123 HIS 0.003 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (17208) covalent geometry : angle 0.49513 / 0.26 (23238) hydrogen bonds : bond 0.03937 / 2.55 ( 816) hydrogen bonds : angle 4.39200 / 3.12 ( 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 179 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7930 (tp-100) REVERT: A 151 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8609 (mttm) REVERT: A 172 LYS cc_start: 0.8829 (tppt) cc_final: 0.8507 (ttmm) REVERT: A 274 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8547 (ptpp) REVERT: C 103 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7727 (tp-100) REVERT: C 172 LYS cc_start: 0.8852 (tppt) cc_final: 0.8516 (ttmm) REVERT: E 46 TRP cc_start: 0.7432 (m100) cc_final: 0.7103 (m100) REVERT: E 103 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7800 (tp-100) REVERT: E 222 MET cc_start: 0.8959 (tpp) cc_final: 0.8660 (mmm) REVERT: G 46 TRP cc_start: 0.7518 (m100) cc_final: 0.7179 (m100) REVERT: G 103 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7717 (tp-100) REVERT: G 222 MET cc_start: 0.8961 (tpp) cc_final: 0.8670 (mmm) REVERT: B 116 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8132 (ttm-80) REVERT: B 325 GLU cc_start: 0.8662 (mp0) cc_final: 0.8319 (tm-30) REVERT: D 116 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8150 (ttm-80) REVERT: D 274 LYS cc_start: 0.8964 (mttt) cc_final: 0.8681 (mttt) REVERT: D 325 GLU cc_start: 0.8669 (mp0) cc_final: 0.8315 (tm-30) REVERT: H 116 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8156 (ttm-80) outliers start: 30 outliers final: 18 residues processed: 171 average time/residue: 0.8218 time to fit residues: 152.9380 Evaluate side-chains 154 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain C residue 24 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 24 LEU Chi-restraints excluded: chain E residue 25 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 41 ILE Chi-restraints excluded: chain G residue 150 LYS Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B 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 Chi-restraints excluded: chain H residue 274 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 164 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 180 optimal weight: 0.6980 chunk 140 optimal weight: 0.1980 chunk 74 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.102785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.069188 restraints weight = 31071.248| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.78 r_work: 0.2770 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.5085 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= 0.103 Angle : 0.489 9.996 23238 Z= 0.250 Chirality : 0.045 0.153 2692 Planarity : 0.003 0.032 3004 Dihedral : 6.560 80.321 2504 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.41 % Allowed : 15.05 % Favored : 83.53 % 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: 1.45 (0.19), residues: 2140 helix: 2.01 (0.17), residues: 1032 sheet: 2.65 (0.27), residues: 320 loop : -1.30 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 135 TYR 0.009 0.001 TYR C 33 PHE 0.011 0.001 PHE G 75 TRP 0.002 0.000 TRP A 52 HIS 0.003 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (17208) covalent geometry : angle 0.48872 / 0.25 (23238) hydrogen bonds : bond 0.03275 / 2.13 ( 816) hydrogen bonds : angle 4.26117 / 3.02 ( 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 177 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7803 (tp-100) REVERT: A 172 LYS cc_start: 0.8697 (tppt) cc_final: 0.8337 (ttmm) REVERT: A 274 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8538 (ptpp) REVERT: C 25 LEU cc_start: 0.8261 (pp) cc_final: 0.7670 (mm) REVERT: C 103 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7662 (tp-100) REVERT: C 172 LYS cc_start: 0.8744 (tppt) cc_final: 0.8376 (ttmm) REVERT: E 46 TRP cc_start: 0.7418 (m100) cc_final: 0.7083 (m100) REVERT: E 103 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7763 (tp-100) REVERT: E 222 MET cc_start: 0.8978 (tpp) cc_final: 0.8672 (mmm) REVERT: G 103 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7681 (tp-100) REVERT: G 222 MET cc_start: 0.9011 (tpp) cc_final: 0.8707 (mmm) REVERT: D 116 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8179 (ttm-80) REVERT: D 237 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7927 (mtp-110) REVERT: D 274 LYS cc_start: 0.8982 (mttt) cc_final: 0.8716 (mttt) REVERT: D 325 GLU cc_start: 0.8658 (mp0) cc_final: 0.8200 (tp30) REVERT: F 237 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8146 (mtp-110) REVERT: H 116 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8126 (ttm-80) REVERT: H 172 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8480 (mtpt) REVERT: H 237 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8004 (mtp-110) outliers start: 26 outliers final: 14 residues processed: 172 average time/residue: 0.9057 time to fit residues: 168.3540 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 : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE 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 41 ILE 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 150 LYS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 41 ILE 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 D residue 237 ARG Chi-restraints excluded: chain F residue 237 ARG Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 237 ARG Chi-restraints excluded: chain H residue 274 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 160 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS G 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.102255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.067509 restraints weight = 30485.829| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.82 r_work: 0.2767 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 17208 Z= 0.190 Angle : 0.549 8.276 23238 Z= 0.285 Chirality : 0.048 0.157 2692 Planarity : 0.004 0.035 3004 Dihedral : 6.854 84.158 2504 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.47 % Allowed : 15.11 % Favored : 83.42 % 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: 1.33 (0.19), residues: 2140 helix: 1.88 (0.17), residues: 1032 sheet: 2.99 (0.26), residues: 312 loop : -1.47 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 135 TYR 0.009 0.001 TYR A 51 PHE 0.012 0.001 PHE G 75 TRP 0.005 0.001 TRP C 123 HIS 0.004 0.001 HIS F 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (17208) covalent geometry : angle 0.54889 / 0.28 (23238) hydrogen bonds : bond 0.04666 / 3.03 ( 816) hydrogen bonds : angle 4.47933 / 3.18 ( 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 171 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7941 (tp-100) REVERT: A 172 LYS cc_start: 0.8859 (tppt) cc_final: 0.8547 (ttmm) REVERT: A 274 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8690 (ptpt) REVERT: E 103 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7860 (tp-100) REVERT: E 222 MET cc_start: 0.8959 (tpp) cc_final: 0.8674 (mmm) REVERT: G 222 MET cc_start: 0.8964 (tpp) cc_final: 0.8686 (mmm) REVERT: D 274 LYS cc_start: 0.8929 (mttt) cc_final: 0.8633 (mttt) REVERT: F 237 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8297 (mtp-110) REVERT: H 172 LYS cc_start: 0.8865 (mtpp) cc_final: 0.8621 (mtpt) REVERT: H 237 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8257 (mtp-110) outliers start: 27 outliers final: 17 residues processed: 164 average time/residue: 0.8593 time to fit residues: 153.0989 Evaluate side-chains 149 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE 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 150 LYS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 150 LYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain D residue 150 LYS 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 237 ARG Chi-restraints excluded: chain H residue 274 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: 0.8980 chunk 75 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 168 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.102977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.068645 restraints weight = 30563.439| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.79 r_work: 0.2765 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.5364 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= 0.110 Angle : 0.498 8.577 23238 Z= 0.255 Chirality : 0.046 0.149 2692 Planarity : 0.003 0.037 3004 Dihedral : 6.670 81.605 2504 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.20 % Allowed : 15.98 % Favored : 82.83 % 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: 2.00 (0.17), residues: 1032 sheet: 2.67 (0.27), residues: 320 loop : -1.37 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 135 TYR 0.008 0.001 TYR E 51 PHE 0.011 0.001 PHE G 75 TRP 0.027 0.001 TRP E 46 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (17208) covalent geometry : angle 0.49754 / 0.26 (23238) hydrogen bonds : bond 0.03482 / 2.26 ( 816) hydrogen bonds : angle 4.27815 / 3.03 ( 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 159 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7888 (tp-100) REVERT: A 172 LYS cc_start: 0.8804 (tppt) cc_final: 0.8505 (ttmm) REVERT: A 274 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8688 (ptpt) REVERT: C 25 LEU cc_start: 0.8314 (pp) cc_final: 0.7703 (mm) REVERT: C 172 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8372 (ttmm) REVERT: E 103 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7872 (tp-100) REVERT: E 222 MET cc_start: 0.8977 (tpp) cc_final: 0.8691 (mmm) REVERT: G 222 MET cc_start: 0.9010 (tpp) cc_final: 0.8711 (mmm) REVERT: G 274 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8692 (ptpt) REVERT: D 237 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8060 (mtp-110) REVERT: D 274 LYS cc_start: 0.8977 (mttt) cc_final: 0.8672 (mttt) REVERT: F 237 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8118 (mtp-110) REVERT: H 172 LYS cc_start: 0.8801 (mtpp) cc_final: 0.8551 (mtpt) outliers start: 22 outliers final: 12 residues processed: 156 average time/residue: 0.8361 time to fit residues: 142.0355 Evaluate side-chains 148 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE 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 172 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 41 ILE 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 237 ARG 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 H residue 274 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 100 optimal weight: 0.9980 chunk 136 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 183 optimal weight: 0.0060 chunk 19 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.103030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.069478 restraints weight = 30981.680| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.76 r_work: 0.2776 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.5435 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= 0.098 Angle : 0.487 8.510 23238 Z= 0.247 Chirality : 0.045 0.148 2692 Planarity : 0.003 0.036 3004 Dihedral : 6.472 80.377 2504 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.14 % Allowed : 16.09 % Favored : 82.77 % 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: 1.57 (0.19), residues: 2140 helix: 2.15 (0.17), residues: 1032 sheet: 2.63 (0.27), residues: 320 loop : -1.27 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 135 TYR 0.009 0.001 TYR C 33 PHE 0.010 0.001 PHE G 75 TRP 0.012 0.001 TRP E 46 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (17208) covalent geometry : angle 0.48687 / 0.25 (23238) hydrogen bonds : bond 0.03104 / 2.02 ( 816) hydrogen bonds : angle 4.14230 / 2.93 ( 2352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5548.93 seconds wall clock time: 95 minutes 20.62 seconds (5720.62 seconds total)