Starting phenix.real_space_refine on Sun Jun 15 08:15:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fz7_29605/06_2025/8fz7_29605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fz7_29605/06_2025/8fz7_29605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fz7_29605/06_2025/8fz7_29605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fz7_29605/06_2025/8fz7_29605.map" model { file = "/net/cci-nas-00/data/ceres_data/8fz7_29605/06_2025/8fz7_29605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fz7_29605/06_2025/8fz7_29605.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16971 Number of models: 1 Model: "" Number of chains: 3 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: "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: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' K': 2, 'PGW': 1, 'YQ1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, E, G, D, F, H Time building chain proxies: 8.22, per 1000 atoms: 0.48 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: 4.13 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.24 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: 6.25 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5601 1.34 - 1.45: 1781 1.45 - 1.57: 9706 1.57 - 1.69: 4 1.69 - 1.80: 116 Bond restraints: 17208 Sorted by residual: bond pdb=" O12 PGW E 401 " pdb=" P PGW E 401 " ideal model delta sigma weight residual 1.636 1.693 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" O12 PGW C 401 " pdb=" P PGW C 401 " ideal model delta sigma weight residual 1.636 1.693 -0.057 2.00e-02 2.50e+03 7.98e+00 bond pdb=" O12 PGW A 401 " pdb=" P PGW A 401 " ideal model delta sigma weight residual 1.636 1.692 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" O12 PGW G 401 " pdb=" P PGW G 401 " ideal model delta sigma weight residual 1.636 1.692 -0.056 2.00e-02 2.50e+03 7.88e+00 bond pdb=" C01 YQ1 A 402 " pdb=" N01 YQ1 A 402 " ideal model delta sigma weight residual 1.524 1.468 0.056 2.00e-02 2.50e+03 7.78e+00 ... (remaining 17203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 22546 1.43 - 2.86: 530 2.86 - 4.28: 97 4.28 - 5.71: 40 5.71 - 7.14: 25 Bond angle restraints: 23238 Sorted by residual: angle pdb=" C SER A 273 " pdb=" N LYS A 274 " pdb=" CA LYS A 274 " ideal model delta sigma weight residual 121.54 126.20 -4.66 1.91e+00 2.74e-01 5.94e+00 angle pdb=" C SER E 273 " pdb=" N LYS E 274 " pdb=" CA LYS E 274 " ideal model delta sigma weight residual 121.54 126.19 -4.65 1.91e+00 2.74e-01 5.94e+00 angle pdb=" C SER C 273 " pdb=" N LYS C 274 " pdb=" CA LYS C 274 " ideal model delta sigma weight residual 121.54 126.19 -4.65 1.91e+00 2.74e-01 5.91e+00 angle pdb=" C SER G 273 " pdb=" N LYS G 274 " pdb=" CA LYS G 274 " ideal model delta sigma weight residual 121.54 126.17 -4.63 1.91e+00 2.74e-01 5.87e+00 angle pdb=" O13 PGW E 401 " pdb=" P PGW E 401 " pdb=" O14 PGW E 401 " ideal model delta sigma weight residual 119.81 126.95 -7.14 3.00e+00 1.11e-01 5.66e+00 ... (remaining 23233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.41: 10363 28.41 - 56.82: 113 56.82 - 85.22: 16 85.22 - 113.63: 0 113.63 - 142.04: 12 Dihedral angle restraints: 10504 sinusoidal: 4352 harmonic: 6152 Sorted by residual: dihedral pdb=" C03 PGW C 401 " pdb=" C01 PGW C 401 " pdb=" C02 PGW C 401 " pdb=" O03 PGW C 401 " ideal model delta sinusoidal sigma weight residual 295.35 153.31 142.04 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C03 PGW A 401 " pdb=" C01 PGW A 401 " pdb=" C02 PGW A 401 " pdb=" O03 PGW A 401 " ideal model delta sinusoidal sigma weight residual 295.35 153.32 142.03 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C03 PGW E 401 " pdb=" C01 PGW E 401 " pdb=" C02 PGW E 401 " pdb=" O03 PGW E 401 " ideal model delta sinusoidal sigma weight residual 295.35 153.36 141.99 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 10501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1626 0.038 - 0.077: 700 0.077 - 0.115: 303 0.115 - 0.153: 59 0.153 - 0.191: 4 Chirality restraints: 2692 Sorted by residual: chirality pdb=" CA PHE G 88 " pdb=" N PHE G 88 " pdb=" C PHE G 88 " pdb=" CB PHE G 88 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.15e-01 chirality pdb=" CA PHE C 88 " pdb=" N PHE C 88 " pdb=" C PHE C 88 " pdb=" CB PHE C 88 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CA PHE E 88 " pdb=" N PHE E 88 " pdb=" C PHE E 88 " pdb=" CB PHE E 88 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.95e-01 ... (remaining 2689 not shown) Planarity restraints: 3004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 47 " -0.034 2.00e-02 2.50e+03 6.72e-02 4.52e+01 pdb=" C THR C 47 " 0.116 2.00e-02 2.50e+03 pdb=" O THR C 47 " -0.043 2.00e-02 2.50e+03 pdb=" N VAL C 48 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 47 " 0.034 2.00e-02 2.50e+03 6.72e-02 4.51e+01 pdb=" C THR A 47 " -0.116 2.00e-02 2.50e+03 pdb=" O THR A 47 " 0.043 2.00e-02 2.50e+03 pdb=" N VAL A 48 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 47 " -0.034 2.00e-02 2.50e+03 6.72e-02 4.51e+01 pdb=" C THR E 47 " 0.116 2.00e-02 2.50e+03 pdb=" O THR E 47 " -0.043 2.00e-02 2.50e+03 pdb=" N VAL E 48 " -0.039 2.00e-02 2.50e+03 ... (remaining 3001 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 5026 2.83 - 3.41: 17605 3.41 - 3.99: 30081 3.99 - 4.56: 42504 4.56 - 5.14: 65028 Nonbonded interactions: 160244 Sorted by model distance: nonbonded pdb=" OE1 GLU C 133 " pdb=" OG SER D 240 " model vdw 2.255 3.040 nonbonded pdb=" OE1 GLU A 133 " pdb=" OG SER B 240 " model vdw 2.295 3.040 nonbonded pdb=" OE1 GLU E 133 " pdb=" OG SER F 240 " model vdw 2.301 3.040 nonbonded pdb=" OG SER B 279 " pdb=" OD1 ASP B 282 " model vdw 2.331 3.040 nonbonded pdb=" NH2 ARG E 308 " pdb=" OD2 ASP F 287 " model vdw 2.331 3.120 ... (remaining 160239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 336 or resid 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: 1.220 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: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 38.200 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.060 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:14.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17208 Z= 0.288 Angle : 0.617 7.139 23238 Z= 0.327 Chirality : 0.050 0.191 2692 Planarity : 0.007 0.067 3004 Dihedral : 10.715 142.041 6552 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.14 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.013 0.002 TRP C 52 HIS 0.004 0.001 HIS F 117 PHE 0.010 0.002 PHE C 88 TYR 0.015 0.002 TYR G 247 ARG 0.006 0.001 ARG C 221 Details of bonding type rmsd hydrogen bonds : bond 0.20885 ( 816) hydrogen bonds : angle 6.82121 ( 2352) covalent geometry : bond 0.00630 (17208) covalent geometry : angle 0.61708 (23238) *********************** 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 : 1.740 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: 1.7343 time to fit residues: 602.4974 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 : 1.831 ------------------------------------------------------------------------------- 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 179 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 192 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 HIS D 161 HIS F 161 HIS H 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.107509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.073300 restraints weight = 30384.506| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.84 r_work: 0.2896 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17208 Z= 0.146 Angle : 0.568 8.809 23238 Z= 0.294 Chirality : 0.047 0.214 2692 Planarity : 0.003 0.029 3004 Dihedral : 12.430 145.619 2546 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.88 % Allowed : 10.92 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2140 helix: 0.91 (0.16), residues: 1052 sheet: 3.04 (0.26), residues: 312 loop : -1.58 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 123 HIS 0.002 0.001 HIS A 39 PHE 0.010 0.001 PHE E 88 TYR 0.017 0.001 TYR G 33 ARG 0.009 0.001 ARG F 241 Details of bonding type rmsd hydrogen bonds : bond 0.04454 ( 816) hydrogen bonds : angle 4.98778 ( 2352) covalent geometry : bond 0.00319 (17208) covalent geometry : angle 0.56834 (23238) *********************** 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 228 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 1.838 Fit side-chains REVERT: A 73 MET cc_start: 0.4617 (OUTLIER) cc_final: 0.4134 (mpt) REVERT: A 222 MET cc_start: 0.8107 (tmt) cc_final: 0.7887 (tmm) REVERT: C 73 MET cc_start: 0.4630 (OUTLIER) cc_final: 0.4120 (mpt) REVERT: C 222 MET cc_start: 0.8057 (tmt) cc_final: 0.7819 (tmm) REVERT: E 73 MET cc_start: 0.4626 (OUTLIER) cc_final: 0.4102 (mpt) REVERT: G 53 THR cc_start: 0.8472 (m) cc_final: 0.8047 (p) REVERT: G 73 MET cc_start: 0.4591 (OUTLIER) cc_final: 0.4098 (mpt) REVERT: G 222 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8248 (tmt) REVERT: B 325 GLU cc_start: 0.8442 (mp0) cc_final: 0.7969 (tp30) REVERT: D 325 GLU cc_start: 0.8430 (mp0) cc_final: 0.8195 (tm-30) REVERT: F 222 MET cc_start: 0.8624 (mtt) cc_final: 0.8419 (mtp) REVERT: H 325 GLU cc_start: 0.8440 (mp0) cc_final: 0.8191 (tm-30) outliers start: 53 outliers final: 7 residues processed: 202 average time/residue: 1.3260 time to fit residues: 298.0743 Evaluate side-chains 165 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 2.059 ------------------------------------------------------------------------------- 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 53 THR Chi-restraints excluded: chain E residue 73 MET 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 28 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 160 optimal weight: 0.0270 overall best weight: 1.7044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.104068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.069416 restraints weight = 30567.349| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.82 r_work: 0.2811 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17208 Z= 0.164 Angle : 0.532 8.908 23238 Z= 0.281 Chirality : 0.047 0.198 2692 Planarity : 0.004 0.029 3004 Dihedral : 11.721 145.032 2540 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.93 % Allowed : 11.63 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 2140 helix: 1.24 (0.16), residues: 1048 sheet: 2.70 (0.26), residues: 320 loop : -1.49 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 123 HIS 0.004 0.001 HIS F 117 PHE 0.020 0.001 PHE G 75 TYR 0.019 0.001 TYR A 33 ARG 0.005 0.001 ARG F 241 Details of bonding type rmsd hydrogen bonds : bond 0.05229 ( 816) hydrogen bonds : angle 4.74264 ( 2352) covalent geometry : bond 0.00386 (17208) covalent geometry : angle 0.53221 (23238) *********************** 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 229 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 175 time to evaluate : 1.827 Fit side-chains revert: symmetry clash REVERT: A 65 TYR cc_start: 0.7618 (m-80) cc_final: 0.7290 (m-80) REVERT: A 73 MET cc_start: 0.4601 (OUTLIER) cc_final: 0.4104 (mpt) REVERT: C 65 TYR cc_start: 0.7624 (m-80) cc_final: 0.7290 (m-80) REVERT: E 222 MET cc_start: 0.8897 (tpp) cc_final: 0.8599 (mmm) REVERT: E 250 MET cc_start: 0.8267 (mtp) cc_final: 0.7822 (mtp) REVERT: G 222 MET cc_start: 0.9008 (mpp) cc_final: 0.8698 (mmm) REVERT: B 116 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.8061 (ttm-80) REVERT: B 325 GLU cc_start: 0.8514 (mp0) cc_final: 0.8098 (tp30) REVERT: D 116 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.8074 (ttm-80) REVERT: D 325 GLU cc_start: 0.8491 (mp0) cc_final: 0.8072 (tp30) REVERT: F 116 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.8015 (ttm-80) REVERT: H 325 GLU cc_start: 0.8490 (mp0) cc_final: 0.8076 (tp30) outliers start: 54 outliers final: 11 residues processed: 210 average time/residue: 1.4748 time to fit residues: 340.7899 Evaluate side-chains 157 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 25 LEU 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 150 LYS Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain F residue 116 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 123 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 177 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 185 optimal weight: 0.0770 chunk 121 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.104781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.070531 restraints weight = 30645.351| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.88 r_work: 0.2812 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17208 Z= 0.101 Angle : 0.478 7.260 23238 Z= 0.248 Chirality : 0.045 0.179 2692 Planarity : 0.003 0.022 3004 Dihedral : 11.424 143.868 2540 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.28 % Allowed : 12.93 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.18), residues: 2140 helix: 1.65 (0.16), residues: 1028 sheet: 2.62 (0.27), residues: 320 loop : -1.40 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 123 HIS 0.002 0.000 HIS B 117 PHE 0.009 0.001 PHE G 75 TYR 0.019 0.001 TYR A 33 ARG 0.004 0.000 ARG F 241 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 816) hydrogen bonds : angle 4.47405 ( 2352) covalent geometry : bond 0.00214 (17208) covalent geometry : angle 0.47760 (23238) *********************** 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 201 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 1.886 Fit side-chains REVERT: A 65 TYR cc_start: 0.7618 (m-80) cc_final: 0.7290 (m-80) REVERT: A 73 MET cc_start: 0.4691 (OUTLIER) cc_final: 0.4152 (mpt) REVERT: A 103 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7669 (tp-100) REVERT: C 65 TYR cc_start: 0.7573 (m-80) cc_final: 0.7231 (m-80) REVERT: C 103 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7644 (tp-100) REVERT: E 103 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7593 (tp-100) REVERT: E 222 MET cc_start: 0.8945 (tpp) cc_final: 0.8673 (mmm) REVERT: E 250 MET cc_start: 0.8199 (mtp) cc_final: 0.7774 (mtp) REVERT: G 73 MET cc_start: 0.4841 (OUTLIER) cc_final: 0.4325 (mpt) REVERT: G 103 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7714 (tp-100) REVERT: G 222 MET cc_start: 0.8991 (mpp) cc_final: 0.8693 (mmm) REVERT: B 116 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.8015 (ttm-80) REVERT: B 325 GLU cc_start: 0.8526 (mp0) cc_final: 0.8076 (tp30) REVERT: D 116 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.8024 (ttm-80) REVERT: D 325 GLU cc_start: 0.8517 (mp0) cc_final: 0.8080 (tp30) REVERT: H 325 GLU cc_start: 0.8518 (mp0) cc_final: 0.8069 (tp30) outliers start: 42 outliers final: 12 residues processed: 187 average time/residue: 1.5652 time to fit residues: 321.6728 Evaluate side-chains 155 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 73 MET 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 25 LEU Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 150 LYS Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain F residue 266 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 41 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 209 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN C 39 HIS G 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.100481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.065994 restraints weight = 30592.090| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.83 r_work: 0.2708 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 17208 Z= 0.245 Angle : 0.590 7.058 23238 Z= 0.311 Chirality : 0.050 0.154 2692 Planarity : 0.004 0.043 3004 Dihedral : 11.526 144.757 2540 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.12 % Allowed : 13.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.18), residues: 2140 helix: 1.55 (0.16), residues: 1024 sheet: 2.82 (0.29), residues: 256 loop : -1.16 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 123 HIS 0.004 0.002 HIS D 117 PHE 0.018 0.002 PHE G 75 TYR 0.019 0.002 TYR F 333 ARG 0.004 0.001 ARG F 199 Details of bonding type rmsd hydrogen bonds : bond 0.05506 ( 816) hydrogen bonds : angle 4.76227 ( 2352) covalent geometry : bond 0.00596 (17208) covalent geometry : angle 0.59031 (23238) *********************** 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 191 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 1.766 Fit side-chains revert: symmetry clash REVERT: A 46 TRP cc_start: 0.7535 (m100) cc_final: 0.7208 (m100) REVERT: A 65 TYR cc_start: 0.7977 (m-80) cc_final: 0.7663 (m-80) REVERT: A 103 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7825 (tp-100) REVERT: A 274 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8689 (ptpt) REVERT: C 46 TRP cc_start: 0.7453 (m100) cc_final: 0.7176 (m100) REVERT: C 65 TYR cc_start: 0.7932 (m-80) cc_final: 0.7566 (m-80) REVERT: C 103 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7855 (tp-100) REVERT: E 46 TRP cc_start: 0.7487 (m100) cc_final: 0.7162 (m100) REVERT: E 103 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7842 (tp-100) REVERT: E 222 MET cc_start: 0.8949 (tpp) cc_final: 0.8677 (mmm) REVERT: E 250 MET cc_start: 0.8470 (mtp) cc_final: 0.8134 (mtp) REVERT: G 46 TRP cc_start: 0.7550 (m100) cc_final: 0.7270 (m100) REVERT: G 103 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7829 (tp-100) REVERT: G 222 MET cc_start: 0.8955 (mpp) cc_final: 0.8676 (mmm) REVERT: B 325 GLU cc_start: 0.8596 (mp0) cc_final: 0.8304 (tp30) REVERT: D 274 LYS cc_start: 0.8993 (mttp) cc_final: 0.8564 (mptt) REVERT: D 325 GLU cc_start: 0.8594 (mp0) cc_final: 0.8132 (tp30) REVERT: H 325 GLU cc_start: 0.8597 (mp0) cc_final: 0.8365 (tm-30) outliers start: 39 outliers final: 11 residues processed: 176 average time/residue: 1.7145 time to fit residues: 329.5959 Evaluate side-chains 145 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 150 LYS Chi-restraints excluded: chain D residue 150 LYS Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain H residue 150 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 182 optimal weight: 0.1980 chunk 180 optimal weight: 0.0770 chunk 81 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 332 ASN E 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.104242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.069763 restraints weight = 30518.823| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.82 r_work: 0.2814 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17208 Z= 0.101 Angle : 0.485 8.810 23238 Z= 0.251 Chirality : 0.045 0.149 2692 Planarity : 0.003 0.027 3004 Dihedral : 11.283 145.086 2540 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.20 % Allowed : 14.84 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.19), residues: 2140 helix: 1.80 (0.17), residues: 1028 sheet: 2.63 (0.27), residues: 320 loop : -1.33 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 52 HIS 0.004 0.000 HIS C 39 PHE 0.013 0.001 PHE G 75 TYR 0.009 0.001 TYR C 51 ARG 0.003 0.000 ARG F 241 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 816) hydrogen bonds : angle 4.40263 ( 2352) covalent geometry : bond 0.00213 (17208) covalent geometry : angle 0.48493 (23238) *********************** 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 175 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 2.110 Fit side-chains revert: symmetry clash REVERT: A 65 TYR cc_start: 0.7773 (m-80) cc_final: 0.7417 (m-80) REVERT: A 103 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7841 (tp-100) REVERT: A 274 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8459 (ptpp) REVERT: C 46 TRP cc_start: 0.7385 (m100) cc_final: 0.7121 (m100) REVERT: C 65 TYR cc_start: 0.7728 (m-80) cc_final: 0.7388 (m-80) REVERT: C 103 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7798 (tp-100) REVERT: E 103 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7849 (tp-100) REVERT: E 222 MET cc_start: 0.8903 (tpp) cc_final: 0.8606 (mmm) REVERT: E 250 MET cc_start: 0.8268 (mtp) cc_final: 0.7826 (mtp) REVERT: G 46 TRP cc_start: 0.7493 (m100) cc_final: 0.7155 (m100) REVERT: G 103 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7846 (tp-100) REVERT: G 222 MET cc_start: 0.8916 (mpp) cc_final: 0.8619 (mmm) REVERT: H 325 GLU cc_start: 0.8607 (mp0) cc_final: 0.8144 (tp30) outliers start: 22 outliers final: 10 residues processed: 171 average time/residue: 1.6867 time to fit residues: 314.7110 Evaluate side-chains 143 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 1.838 ------------------------------------------------------------------------------- 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 E residue 24 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 150 LYS Chi-restraints excluded: chain F residue 266 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 93 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 chunk 57 optimal weight: 0.4980 chunk 166 optimal weight: 6.9990 chunk 193 optimal weight: 4.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 332 ASN E 39 HIS E 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.103419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.069034 restraints weight = 30987.454| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.89 r_work: 0.2775 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.5110 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= 0.104 Angle : 0.475 7.711 23238 Z= 0.246 Chirality : 0.045 0.153 2692 Planarity : 0.003 0.027 3004 Dihedral : 11.032 142.269 2540 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.47 % Allowed : 14.78 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.19), residues: 2140 helix: 1.93 (0.17), residues: 1032 sheet: 2.60 (0.27), residues: 320 loop : -1.30 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 52 HIS 0.004 0.001 HIS C 39 PHE 0.012 0.001 PHE G 75 TYR 0.008 0.001 TYR A 51 ARG 0.004 0.000 ARG E 135 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 816) hydrogen bonds : angle 4.25571 ( 2352) covalent geometry : bond 0.00228 (17208) covalent geometry : angle 0.47540 (23238) *********************** 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 174 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.7796 (m-80) cc_final: 0.7457 (m-80) REVERT: A 103 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7860 (tp-100) REVERT: A 274 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8545 (ptpp) REVERT: C 65 TYR cc_start: 0.7758 (m-80) cc_final: 0.7413 (m-80) REVERT: C 103 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7858 (tp-100) REVERT: C 274 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8849 (ptpt) REVERT: E 46 TRP cc_start: 0.7455 (m100) cc_final: 0.7187 (m100) REVERT: E 103 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7828 (tp-100) REVERT: E 222 MET cc_start: 0.8954 (tpp) cc_final: 0.8666 (mmm) REVERT: E 250 MET cc_start: 0.8230 (mtp) cc_final: 0.7828 (mtp) REVERT: G 103 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7828 (tp-100) REVERT: G 222 MET cc_start: 0.8959 (mpp) cc_final: 0.8667 (mmm) REVERT: G 274 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8448 (ptpp) REVERT: B 237 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8068 (mtp-110) REVERT: D 172 LYS cc_start: 0.8820 (mtpp) cc_final: 0.8579 (mtpt) REVERT: D 237 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8070 (mtp-110) REVERT: D 328 GLU cc_start: 0.8367 (pt0) cc_final: 0.8092 (tp30) REVERT: F 237 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8232 (mtp-110) REVERT: H 237 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8054 (mtp-110) REVERT: H 328 GLU cc_start: 0.8347 (pt0) cc_final: 0.8091 (tp30) outliers start: 27 outliers final: 12 residues processed: 170 average time/residue: 1.7735 time to fit residues: 328.3782 Evaluate side-chains 157 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.961 ------------------------------------------------------------------------------- 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 24 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain G residue 150 LYS Chi-restraints excluded: chain G residue 274 LYS Chi-restraints excluded: chain B residue 237 ARG 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 237 ARG Chi-restraints excluded: chain H residue 309 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 94 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 210 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 204 optimal weight: 0.9980 chunk 206 optimal weight: 0.0040 chunk 8 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.102872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.069351 restraints weight = 31025.003| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.76 r_work: 0.2774 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.5196 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= 0.098 Angle : 0.480 8.819 23238 Z= 0.245 Chirality : 0.045 0.177 2692 Planarity : 0.003 0.029 3004 Dihedral : 10.840 139.046 2540 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.58 % Allowed : 15.11 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.19), residues: 2140 helix: 2.02 (0.17), residues: 1032 sheet: 2.59 (0.27), residues: 320 loop : -1.29 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 52 HIS 0.005 0.001 HIS E 39 PHE 0.012 0.001 PHE G 75 TYR 0.008 0.001 TYR C 51 ARG 0.005 0.000 ARG G 135 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 816) hydrogen bonds : angle 4.17989 ( 2352) covalent geometry : bond 0.00211 (17208) covalent geometry : angle 0.48022 (23238) *********************** 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 179 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.7893 (m-80) cc_final: 0.7552 (m-80) REVERT: A 103 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7930 (tp-100) REVERT: A 172 LYS cc_start: 0.8828 (tppt) cc_final: 0.8556 (ttmm) REVERT: A 274 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8715 (ptpt) REVERT: C 25 LEU cc_start: 0.8357 (pp) cc_final: 0.7736 (mm) REVERT: C 65 TYR cc_start: 0.7768 (m-80) cc_final: 0.7321 (m-80) REVERT: C 103 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7839 (tp-100) REVERT: C 274 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8821 (ptpt) REVERT: E 46 TRP cc_start: 0.7485 (m100) cc_final: 0.7186 (m100) REVERT: E 103 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7894 (tp-100) REVERT: E 151 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8522 (mttt) REVERT: E 222 MET cc_start: 0.9186 (tpp) cc_final: 0.8893 (mmm) REVERT: E 250 MET cc_start: 0.8253 (mtp) cc_final: 0.7926 (mtp) REVERT: E 274 LYS cc_start: 0.9085 (ptpt) cc_final: 0.8661 (ptpp) REVERT: G 103 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7881 (tp-100) REVERT: G 172 LYS cc_start: 0.8789 (tppt) cc_final: 0.8525 (ttmm) REVERT: G 222 MET cc_start: 0.9169 (mpp) cc_final: 0.8885 (mmm) REVERT: G 274 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8727 (ptpt) REVERT: B 172 LYS cc_start: 0.8787 (mtpp) cc_final: 0.8569 (mtpt) REVERT: B 237 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8207 (mtp-110) REVERT: D 237 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8198 (mtp-110) REVERT: D 328 GLU cc_start: 0.8581 (pt0) cc_final: 0.8152 (tp30) REVERT: F 172 LYS cc_start: 0.8783 (mtpp) cc_final: 0.8565 (mtpt) REVERT: F 237 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8335 (mtp-110) REVERT: H 172 LYS cc_start: 0.8794 (mtpp) cc_final: 0.8560 (mtpt) REVERT: H 237 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8197 (mtp-110) REVERT: H 328 GLU cc_start: 0.8576 (pt0) cc_final: 0.8126 (tp30) outliers start: 29 outliers final: 13 residues processed: 177 average time/residue: 1.7232 time to fit residues: 331.8805 Evaluate side-chains 161 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.820 ------------------------------------------------------------------------------- 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 150 LYS Chi-restraints excluded: chain E residue 151 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 237 ARG 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 F residue 309 ASP Chi-restraints excluded: chain H residue 237 ARG Chi-restraints excluded: chain H residue 309 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 77 optimal weight: 0.9990 chunk 146 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 209 optimal weight: 0.4980 chunk 197 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 202 optimal weight: 0.1980 chunk 190 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.103310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.069748 restraints weight = 31026.652| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.77 r_work: 0.2782 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.5282 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= 0.093 Angle : 0.475 7.674 23238 Z= 0.243 Chirality : 0.045 0.150 2692 Planarity : 0.003 0.030 3004 Dihedral : 10.719 136.965 2540 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.30 % Allowed : 16.09 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.19), residues: 2140 helix: 2.11 (0.17), residues: 1032 sheet: 2.57 (0.27), residues: 320 loop : -1.24 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 52 HIS 0.004 0.001 HIS E 39 PHE 0.011 0.001 PHE G 75 TYR 0.008 0.001 TYR C 51 ARG 0.004 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.02989 ( 816) hydrogen bonds : angle 4.10275 ( 2352) covalent geometry : bond 0.00196 (17208) covalent geometry : angle 0.47458 (23238) *********************** 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 166 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.7879 (m-80) cc_final: 0.7525 (m-80) REVERT: A 103 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7883 (tp-100) REVERT: A 172 LYS cc_start: 0.8666 (tppt) cc_final: 0.8359 (ttmm) REVERT: A 274 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8718 (ptpt) REVERT: C 25 LEU cc_start: 0.8348 (pp) cc_final: 0.7743 (mm) REVERT: C 65 TYR cc_start: 0.7728 (m-80) cc_final: 0.7311 (m-80) REVERT: C 103 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7812 (tp-100) REVERT: E 103 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7847 (tp-100) REVERT: E 222 MET cc_start: 0.8964 (tpp) cc_final: 0.8669 (mmm) REVERT: E 250 MET cc_start: 0.8061 (mtp) cc_final: 0.7727 (mtp) REVERT: G 103 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7868 (tp-100) REVERT: G 172 LYS cc_start: 0.8761 (tppt) cc_final: 0.8462 (ttmm) REVERT: G 222 MET cc_start: 0.8969 (mpp) cc_final: 0.8666 (mmm) REVERT: G 274 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8729 (ptpt) REVERT: B 172 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8513 (mtpt) REVERT: B 237 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8018 (mtp-110) REVERT: D 172 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8532 (mtpt) REVERT: D 237 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7999 (mtp-110) REVERT: D 328 GLU cc_start: 0.8443 (pt0) cc_final: 0.8077 (tp30) REVERT: F 172 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8510 (mtpt) REVERT: F 237 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8155 (mtp-110) REVERT: H 172 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8477 (mtpt) REVERT: H 237 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8002 (mtp-110) REVERT: H 328 GLU cc_start: 0.8462 (pt0) cc_final: 0.8133 (tp30) outliers start: 24 outliers final: 7 residues processed: 165 average time/residue: 1.7614 time to fit residues: 316.4825 Evaluate side-chains 152 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain E residue 150 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 237 ARG 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 237 ARG Chi-restraints excluded: chain H residue 309 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 51 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 176 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 chunk 165 optimal weight: 0.1980 chunk 196 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.4524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.101637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.068003 restraints weight = 31014.678| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.76 r_work: 0.2742 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.5332 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= 0.135 Angle : 0.503 7.724 23238 Z= 0.259 Chirality : 0.046 0.153 2692 Planarity : 0.003 0.034 3004 Dihedral : 10.800 136.931 2540 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.98 % Allowed : 16.41 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.19), residues: 2140 helix: 2.06 (0.17), residues: 1032 sheet: 2.65 (0.27), residues: 320 loop : -1.29 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 123 HIS 0.004 0.001 HIS E 39 PHE 0.012 0.001 PHE G 75 TYR 0.009 0.001 TYR A 51 ARG 0.004 0.000 ARG G 154 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 816) hydrogen bonds : angle 4.20800 ( 2352) covalent geometry : bond 0.00320 (17208) covalent geometry : angle 0.50311 (23238) ********************** 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 155 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.7889 (m-80) cc_final: 0.7532 (m-80) REVERT: A 103 GLN cc_start: 0.8217 (mm-40) cc_final: 0.8001 (tp-100) REVERT: A 172 LYS cc_start: 0.8836 (tppt) cc_final: 0.8585 (ttmm) REVERT: A 274 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8696 (ptpt) REVERT: C 65 TYR cc_start: 0.7885 (m-80) cc_final: 0.7433 (m-80) REVERT: C 103 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7930 (tp-100) REVERT: E 103 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7962 (tp-100) REVERT: E 222 MET cc_start: 0.9182 (tpp) cc_final: 0.8874 (mmm) REVERT: E 250 MET cc_start: 0.8239 (mtp) cc_final: 0.7863 (mtp) REVERT: G 103 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7900 (tp-100) REVERT: G 172 LYS cc_start: 0.8788 (tppt) cc_final: 0.8494 (ttmm) REVERT: G 222 MET cc_start: 0.9115 (mpp) cc_final: 0.8825 (mmm) REVERT: G 274 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8711 (ptpt) REVERT: B 172 LYS cc_start: 0.8765 (mtpp) cc_final: 0.8531 (mtpt) REVERT: B 237 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8302 (mtp-110) REVERT: D 172 LYS cc_start: 0.8782 (mtpp) cc_final: 0.8559 (mtpt) REVERT: D 237 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8197 (mtp-110) REVERT: D 328 GLU cc_start: 0.8574 (pt0) cc_final: 0.8222 (tp30) REVERT: F 172 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8535 (mtpt) REVERT: F 237 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8336 (mtp-110) REVERT: H 172 LYS cc_start: 0.8779 (mtpp) cc_final: 0.8531 (mtpt) REVERT: H 237 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8310 (mtp-110) REVERT: H 328 GLU cc_start: 0.8578 (pt0) cc_final: 0.8235 (tp30) outliers start: 18 outliers final: 9 residues processed: 155 average time/residue: 1.8891 time to fit residues: 317.6466 Evaluate side-chains 149 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 150 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 237 ARG 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 F residue 309 ASP Chi-restraints excluded: chain H residue 237 ARG Chi-restraints excluded: chain H residue 309 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 102 optimal weight: 0.0570 chunk 137 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 195 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 139 optimal weight: 0.0370 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.103467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.069960 restraints weight = 30853.152| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.76 r_work: 0.2784 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.5392 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= 0.091 Angle : 0.476 8.282 23238 Z= 0.243 Chirality : 0.045 0.148 2692 Planarity : 0.003 0.032 3004 Dihedral : 10.658 135.033 2540 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.87 % Allowed : 16.79 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.19), residues: 2140 helix: 2.17 (0.17), residues: 1032 sheet: 2.60 (0.27), residues: 320 loop : -1.22 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 52 HIS 0.003 0.001 HIS C 39 PHE 0.011 0.001 PHE G 75 TYR 0.007 0.001 TYR A 51 ARG 0.005 0.000 ARG G 154 Details of bonding type rmsd hydrogen bonds : bond 0.02870 ( 816) hydrogen bonds : angle 4.06566 ( 2352) covalent geometry : bond 0.00189 (17208) covalent geometry : angle 0.47588 (23238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11685.64 seconds wall clock time: 200 minutes 50.52 seconds (12050.52 seconds total)