Starting phenix.real_space_refine on Thu Sep 18 00:48:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ngq_49390/09_2025/9ngq_49390_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ngq_49390/09_2025/9ngq_49390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ngq_49390/09_2025/9ngq_49390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ngq_49390/09_2025/9ngq_49390.map" model { file = "/net/cci-nas-00/data/ceres_data/9ngq_49390/09_2025/9ngq_49390_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ngq_49390/09_2025/9ngq_49390_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians S 30 5.16 5 Na 6 4.78 5 C 8180 2.51 5 N 2085 2.21 5 O 2250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12551 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 8 Unusual residues: {' NA': 4, '3CN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.27, per 1000 atoms: 0.18 Number of scatterers: 12551 At special positions: 0 Unit cell: (89.96, 89.095, 123.695, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 Na 6 11.00 O 2250 8.00 N 2085 7.00 C 8180 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 593.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 34.5% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 62 through 70 removed outlier: 4.139A pdb=" N TRP A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 179 Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 227 through 249 removed outlier: 3.600A pdb=" N ARG A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR A 249 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 260 through 285 Processing helix chain 'A' and resid 303 through 317 removed outlier: 3.596A pdb=" N ILE A 317 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 removed outlier: 4.139A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 208 through 221 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 227 through 249 removed outlier: 3.600A pdb=" N ARG B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR B 249 " --> pdb=" O TYR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 260 through 285 Processing helix chain 'B' and resid 303 through 317 removed outlier: 3.596A pdb=" N ILE B 317 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 70 removed outlier: 4.139A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 227 through 249 removed outlier: 3.600A pdb=" N ARG C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR C 241 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR C 249 " --> pdb=" O TYR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 260 through 285 Processing helix chain 'C' and resid 303 through 317 removed outlier: 3.596A pdb=" N ILE C 317 " --> pdb=" O CYS C 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 70 removed outlier: 4.140A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 179 Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 208 through 221 Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 227 through 249 removed outlier: 3.600A pdb=" N ARG D 231 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR D 249 " --> pdb=" O TYR D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 252 No H-bonds generated for 'chain 'D' and resid 250 through 252' Processing helix chain 'D' and resid 260 through 285 Processing helix chain 'D' and resid 303 through 317 removed outlier: 3.596A pdb=" N ILE D 317 " --> pdb=" O CYS D 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 70 removed outlier: 4.139A pdb=" N TRP E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 179 Processing helix chain 'E' and resid 201 through 208 Processing helix chain 'E' and resid 208 through 221 Processing helix chain 'E' and resid 222 through 225 Processing helix chain 'E' and resid 227 through 249 removed outlier: 3.599A pdb=" N ARG E 231 " --> pdb=" O SER E 227 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE E 247 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR E 249 " --> pdb=" O TYR E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 252 No H-bonds generated for 'chain 'E' and resid 250 through 252' Processing helix chain 'E' and resid 260 through 285 Processing helix chain 'E' and resid 303 through 317 removed outlier: 3.596A pdb=" N ILE E 317 " --> pdb=" O CYS E 313 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 27 removed outlier: 6.868A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 108 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 37 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER A 109 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 3.512A pdb=" N GLY A 37 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 108 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL A 16 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE A 145 " --> pdb=" O VAL A 16 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.572A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE A 188 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N SER A 171 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG A 190 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N HIS A 169 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR A 192 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER A 167 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG A 194 " --> pdb=" O LYS A 165 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS A 165 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP A 196 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 19 through 27 removed outlier: 6.868A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 108 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 37 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 81 through 82 removed outlier: 4.124A pdb=" N SER B 109 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 37 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 108 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR B 44 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP B 13 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL B 16 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE B 145 " --> pdb=" O VAL B 16 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.572A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N PHE B 188 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER B 171 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG B 190 " --> pdb=" O HIS B 169 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS B 169 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR B 192 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER B 167 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG B 194 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS B 165 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP B 196 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 19 through 27 removed outlier: 6.868A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY C 108 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 37 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 81 through 82 removed outlier: 4.124A pdb=" N SER C 109 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 37 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY C 108 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL C 16 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE C 145 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.572A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE C 188 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER C 171 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG C 190 " --> pdb=" O HIS C 169 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N HIS C 169 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR C 192 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER C 167 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG C 194 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS C 165 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP C 196 " --> pdb=" O ARG C 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 19 through 27 removed outlier: 6.868A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY D 108 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY D 37 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER D 109 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 56 through 58 removed outlier: 3.512A pdb=" N GLY D 37 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY D 108 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL D 16 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE D 145 " --> pdb=" O VAL D 16 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.572A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE D 188 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N SER D 171 " --> pdb=" O PHE D 188 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG D 190 " --> pdb=" O HIS D 169 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS D 169 " --> pdb=" O ARG D 190 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR D 192 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER D 167 " --> pdb=" O THR D 192 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG D 194 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS D 165 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP D 196 " --> pdb=" O ARG D 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 19 through 27 removed outlier: 6.867A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY E 108 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY E 37 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER E 109 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 56 through 58 removed outlier: 3.512A pdb=" N GLY E 37 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY E 108 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR E 44 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP E 13 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL E 16 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE E 145 " --> pdb=" O VAL E 16 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.572A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE E 188 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N SER E 171 " --> pdb=" O PHE E 188 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG E 190 " --> pdb=" O HIS E 169 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N HIS E 169 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR E 192 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N SER E 167 " --> pdb=" O THR E 192 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG E 194 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS E 165 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP E 196 " --> pdb=" O ARG E 163 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1662 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: 1.43 Time building geometry restraints manager: 1.44 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: 3982 1.34 - 1.46: 2649 1.46 - 1.57: 6199 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 12880 Sorted by residual: bond pdb=" N ILE E 162 " pdb=" CA ILE E 162 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.17e-02 7.31e+03 9.29e+00 bond pdb=" N ILE D 162 " pdb=" CA ILE D 162 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.17e-02 7.31e+03 9.12e+00 bond pdb=" N ILE C 162 " pdb=" CA ILE C 162 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.17e-02 7.31e+03 8.96e+00 bond pdb=" N ILE A 162 " pdb=" CA ILE A 162 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.17e-02 7.31e+03 8.94e+00 bond pdb=" N ILE B 162 " pdb=" CA ILE B 162 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.17e-02 7.31e+03 8.69e+00 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 16484 1.46 - 2.91: 846 2.91 - 4.37: 150 4.37 - 5.83: 45 5.83 - 7.28: 20 Bond angle restraints: 17545 Sorted by residual: angle pdb=" CA ASP A 158 " pdb=" CB ASP A 158 " pdb=" CG ASP A 158 " ideal model delta sigma weight residual 112.60 116.15 -3.55 1.00e+00 1.00e+00 1.26e+01 angle pdb=" CA ASP E 158 " pdb=" CB ASP E 158 " pdb=" CG ASP E 158 " ideal model delta sigma weight residual 112.60 116.15 -3.55 1.00e+00 1.00e+00 1.26e+01 angle pdb=" CA ASP D 158 " pdb=" CB ASP D 158 " pdb=" CG ASP D 158 " ideal model delta sigma weight residual 112.60 116.14 -3.54 1.00e+00 1.00e+00 1.25e+01 angle pdb=" CA ASP B 158 " pdb=" CB ASP B 158 " pdb=" CG ASP B 158 " ideal model delta sigma weight residual 112.60 116.14 -3.54 1.00e+00 1.00e+00 1.25e+01 angle pdb=" CA ASP C 158 " pdb=" CB ASP C 158 " pdb=" CG ASP C 158 " ideal model delta sigma weight residual 112.60 116.12 -3.52 1.00e+00 1.00e+00 1.24e+01 ... (remaining 17540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6790 17.92 - 35.85: 622 35.85 - 53.77: 83 53.77 - 71.70: 30 71.70 - 89.62: 5 Dihedral angle restraints: 7530 sinusoidal: 3025 harmonic: 4505 Sorted by residual: dihedral pdb=" CA SER D 227 " pdb=" C SER D 227 " pdb=" N PHE D 228 " pdb=" CA PHE D 228 " ideal model delta harmonic sigma weight residual -180.00 -156.00 -24.00 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA SER C 227 " pdb=" C SER C 227 " pdb=" N PHE C 228 " pdb=" CA PHE C 228 " ideal model delta harmonic sigma weight residual -180.00 -156.02 -23.98 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA SER E 227 " pdb=" C SER E 227 " pdb=" N PHE E 228 " pdb=" CA PHE E 228 " ideal model delta harmonic sigma weight residual 180.00 -156.03 -23.97 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 7527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1207 0.040 - 0.080: 441 0.080 - 0.121: 228 0.121 - 0.161: 54 0.161 - 0.201: 20 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CA ILE A 157 " pdb=" N ILE A 157 " pdb=" C ILE A 157 " pdb=" CB ILE A 157 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE B 157 " pdb=" N ILE B 157 " pdb=" C ILE B 157 " pdb=" CB ILE B 157 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE E 157 " pdb=" N ILE E 157 " pdb=" C ILE E 157 " pdb=" CB ILE E 157 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1947 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 210 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.44e+00 pdb=" N PRO B 211 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 211 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 211 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 210 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.42e+00 pdb=" N PRO C 211 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 211 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 211 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 210 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO A 211 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 211 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 211 " -0.036 5.00e-02 4.00e+02 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 931 2.74 - 3.28: 11703 3.28 - 3.82: 20553 3.82 - 4.36: 24004 4.36 - 4.90: 42881 Nonbonded interactions: 100072 Sorted by model distance: nonbonded pdb=" OE2 GLU D 131 " pdb=" ND 3CN D 401 " model vdw 2.202 3.120 nonbonded pdb=" OE2 GLU C 131 " pdb=" ND 3CN C 401 " model vdw 2.202 3.120 nonbonded pdb=" OE2 GLU B 131 " pdb=" ND 3CN B 401 " model vdw 2.202 3.120 nonbonded pdb=" OE2 GLU E 131 " pdb=" ND 3CN E 401 " model vdw 2.202 3.120 nonbonded pdb=" ND2 ASN B 60 " pdb=" OD1 ASN B 89 " model vdw 2.401 3.120 ... (remaining 100067 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 11 through 401) selection = (chain 'B' and resid 11 through 401) selection = chain 'C' selection = chain 'D' selection = (chain 'E' and resid 11 through 401) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.800 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.902 12881 Z= 0.846 Angle : 0.778 7.282 17545 Z= 0.445 Chirality : 0.055 0.201 1950 Planarity : 0.008 0.069 2235 Dihedral : 14.013 89.622 4620 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.20), residues: 1525 helix: -0.40 (0.21), residues: 505 sheet: -0.17 (0.25), residues: 485 loop : -2.46 (0.22), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 123 TYR 0.009 0.001 TYR A 204 PHE 0.015 0.002 PHE B 304 TRP 0.025 0.001 TRP A 206 HIS 0.001 0.000 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00522 (12880) covalent geometry : angle 0.77825 (17545) hydrogen bonds : bond 0.16921 ( 527) hydrogen bonds : angle 7.35204 ( 1662) Misc. bond : bond 0.90192 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.475 Fit side-chains REVERT: A 27 ASN cc_start: 0.8329 (t0) cc_final: 0.8022 (t0) REVERT: A 65 ARG cc_start: 0.7211 (ttm170) cc_final: 0.6720 (ttt180) REVERT: A 158 ASP cc_start: 0.6034 (m-30) cc_final: 0.5779 (m-30) REVERT: B 27 ASN cc_start: 0.8408 (t0) cc_final: 0.8022 (t0) REVERT: B 65 ARG cc_start: 0.7331 (ttm170) cc_final: 0.6878 (ttt180) REVERT: B 158 ASP cc_start: 0.6053 (m-30) cc_final: 0.5837 (m-30) REVERT: C 27 ASN cc_start: 0.8451 (t0) cc_final: 0.8102 (t0) REVERT: C 65 ARG cc_start: 0.7342 (ttm170) cc_final: 0.6884 (ttt180) REVERT: C 158 ASP cc_start: 0.6065 (m-30) cc_final: 0.5799 (m-30) REVERT: D 27 ASN cc_start: 0.8385 (t0) cc_final: 0.7947 (t0) REVERT: D 65 ARG cc_start: 0.7312 (ttm170) cc_final: 0.6838 (ttt180) REVERT: D 158 ASP cc_start: 0.6034 (m-30) cc_final: 0.5807 (m-30) REVERT: E 27 ASN cc_start: 0.8410 (t0) cc_final: 0.8020 (t0) REVERT: E 65 ARG cc_start: 0.7357 (ttm170) cc_final: 0.6895 (ttt180) REVERT: E 158 ASP cc_start: 0.6207 (m-30) cc_final: 0.5937 (m-30) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1283 time to fit residues: 34.4700 Evaluate side-chains 140 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.0070 chunk 149 optimal weight: 0.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.133158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.122077 restraints weight = 15042.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.122102 restraints weight = 12133.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.122102 restraints weight = 11947.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.122102 restraints weight = 11947.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.122102 restraints weight = 11947.197| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12881 Z= 0.104 Angle : 0.503 4.475 17545 Z= 0.267 Chirality : 0.045 0.127 1950 Planarity : 0.004 0.056 2235 Dihedral : 4.299 21.427 1690 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.44 % Allowed : 5.82 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.21), residues: 1525 helix: 0.85 (0.23), residues: 500 sheet: 0.03 (0.26), residues: 465 loop : -2.36 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 255 TYR 0.012 0.001 TYR D 245 PHE 0.016 0.001 PHE B 282 TRP 0.019 0.001 TRP C 206 HIS 0.001 0.000 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00223 (12880) covalent geometry : angle 0.50344 (17545) hydrogen bonds : bond 0.03569 ( 527) hydrogen bonds : angle 5.00758 ( 1662) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 182 time to evaluate : 0.491 Fit side-chains REVERT: A 27 ASN cc_start: 0.8338 (t0) cc_final: 0.7996 (t0) REVERT: A 65 ARG cc_start: 0.7255 (ttm170) cc_final: 0.6770 (ttt180) REVERT: A 158 ASP cc_start: 0.6033 (m-30) cc_final: 0.5727 (m-30) REVERT: B 27 ASN cc_start: 0.8422 (t0) cc_final: 0.8052 (t0) REVERT: B 62 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7665 (tm-30) REVERT: B 65 ARG cc_start: 0.7417 (ttm170) cc_final: 0.7005 (ttt180) REVERT: B 158 ASP cc_start: 0.6165 (m-30) cc_final: 0.5864 (m-30) REVERT: C 27 ASN cc_start: 0.8455 (t0) cc_final: 0.8118 (t0) REVERT: C 65 ARG cc_start: 0.7441 (ttm170) cc_final: 0.6943 (ttt180) REVERT: C 158 ASP cc_start: 0.6231 (m-30) cc_final: 0.5916 (m-30) REVERT: D 27 ASN cc_start: 0.8403 (t0) cc_final: 0.7974 (t0) REVERT: D 65 ARG cc_start: 0.7392 (ttm170) cc_final: 0.6840 (ttt180) REVERT: D 87 THR cc_start: 0.8689 (t) cc_final: 0.8024 (m) REVERT: D 158 ASP cc_start: 0.6200 (m-30) cc_final: 0.5944 (m-30) REVERT: E 27 ASN cc_start: 0.8452 (t0) cc_final: 0.8034 (t0) REVERT: E 65 ARG cc_start: 0.7291 (ttm170) cc_final: 0.6843 (ttt180) REVERT: E 158 ASP cc_start: 0.6286 (m-30) cc_final: 0.6043 (m-30) outliers start: 6 outliers final: 6 residues processed: 188 average time/residue: 0.1109 time to fit residues: 30.6406 Evaluate side-chains 170 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 164 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain E residue 266 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 130 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 126 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.3185 r_free = 0.3185 target = 0.124182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.112524 restraints weight = 15657.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.112524 restraints weight = 13185.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.112524 restraints weight = 13184.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.112524 restraints weight = 13184.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.112524 restraints weight = 13184.944| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12881 Z= 0.203 Angle : 0.579 4.802 17545 Z= 0.311 Chirality : 0.048 0.146 1950 Planarity : 0.005 0.061 2235 Dihedral : 4.895 49.340 1690 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.75 % Allowed : 10.18 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.22), residues: 1525 helix: 1.37 (0.24), residues: 475 sheet: -0.20 (0.24), residues: 495 loop : -1.93 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 123 TYR 0.012 0.002 TYR D 204 PHE 0.013 0.002 PHE C 304 TRP 0.016 0.001 TRP E 206 HIS 0.001 0.000 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00492 (12880) covalent geometry : angle 0.57920 (17545) hydrogen bonds : bond 0.04107 ( 527) hydrogen bonds : angle 4.87311 ( 1662) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.507 Fit side-chains REVERT: A 27 ASN cc_start: 0.8450 (t0) cc_final: 0.8025 (t0) REVERT: A 65 ARG cc_start: 0.7288 (ttm170) cc_final: 0.6824 (ttt180) REVERT: A 161 TRP cc_start: 0.7417 (t60) cc_final: 0.7197 (t60) REVERT: B 27 ASN cc_start: 0.8506 (t0) cc_final: 0.8084 (t0) REVERT: B 62 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7724 (tm-30) REVERT: B 65 ARG cc_start: 0.7499 (ttm170) cc_final: 0.7052 (ttt180) REVERT: B 158 ASP cc_start: 0.6364 (m-30) cc_final: 0.6160 (m-30) REVERT: B 245 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: C 27 ASN cc_start: 0.8504 (t0) cc_final: 0.8128 (t0) REVERT: C 65 ARG cc_start: 0.7455 (ttm170) cc_final: 0.6983 (ttt180) REVERT: C 158 ASP cc_start: 0.6414 (m-30) cc_final: 0.6177 (m-30) REVERT: D 27 ASN cc_start: 0.8429 (t0) cc_final: 0.8014 (t0) REVERT: D 65 ARG cc_start: 0.7474 (ttm170) cc_final: 0.6892 (ttt180) REVERT: E 27 ASN cc_start: 0.8489 (t0) cc_final: 0.8075 (t0) REVERT: E 65 ARG cc_start: 0.7370 (ttm170) cc_final: 0.6956 (ttt180) REVERT: E 158 ASP cc_start: 0.6584 (m-30) cc_final: 0.6346 (m-30) outliers start: 24 outliers final: 22 residues processed: 176 average time/residue: 0.1154 time to fit residues: 29.9211 Evaluate side-chains 177 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 266 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 133 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3250 r_free = 0.3250 target = 0.129607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.118547 restraints weight = 15149.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.119642 restraints weight = 11593.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.120301 restraints weight = 9542.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.120487 restraints weight = 8891.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.120572 restraints weight = 8500.408| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12881 Z= 0.096 Angle : 0.474 5.617 17545 Z= 0.248 Chirality : 0.045 0.131 1950 Planarity : 0.004 0.054 2235 Dihedral : 4.415 50.434 1690 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.16 % Allowed : 12.36 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.22), residues: 1525 helix: 1.88 (0.24), residues: 475 sheet: 0.05 (0.25), residues: 495 loop : -1.83 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 123 TYR 0.008 0.001 TYR B 38 PHE 0.024 0.001 PHE C 282 TRP 0.018 0.001 TRP A 206 HIS 0.001 0.000 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00216 (12880) covalent geometry : angle 0.47356 (17545) hydrogen bonds : bond 0.03060 ( 527) hydrogen bonds : angle 4.41812 ( 1662) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.357 Fit side-chains REVERT: A 27 ASN cc_start: 0.8431 (t0) cc_final: 0.8010 (t0) REVERT: A 65 ARG cc_start: 0.7249 (ttm170) cc_final: 0.6718 (ttt180) REVERT: A 245 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.8129 (t80) REVERT: B 27 ASN cc_start: 0.8469 (t0) cc_final: 0.8070 (t0) REVERT: B 62 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7579 (tm-30) REVERT: B 65 ARG cc_start: 0.7450 (ttm170) cc_final: 0.6940 (ttt180) REVERT: B 158 ASP cc_start: 0.6313 (m-30) cc_final: 0.6070 (m-30) REVERT: B 245 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: C 27 ASN cc_start: 0.8456 (t0) cc_final: 0.8111 (t0) REVERT: C 62 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7345 (tm-30) REVERT: D 27 ASN cc_start: 0.8392 (t0) cc_final: 0.7948 (t0) REVERT: D 65 ARG cc_start: 0.7317 (ttm170) cc_final: 0.6832 (ttt180) REVERT: E 27 ASN cc_start: 0.8487 (t0) cc_final: 0.8075 (t0) REVERT: E 65 ARG cc_start: 0.7263 (ttm170) cc_final: 0.6871 (ttt180) REVERT: E 158 ASP cc_start: 0.6420 (m-30) cc_final: 0.6187 (m-30) outliers start: 16 outliers final: 13 residues processed: 179 average time/residue: 0.1119 time to fit residues: 29.0650 Evaluate side-chains 166 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 259 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 138 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 87 optimal weight: 0.0270 chunk 133 optimal weight: 0.0370 chunk 15 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 146 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.5920 ------------------------------------------------------------------------------- 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 = 0.3207 r_free = 0.3207 target = 0.125531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.114597 restraints weight = 15478.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.114639 restraints weight = 12050.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.114642 restraints weight = 11903.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.114642 restraints weight = 11891.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.114642 restraints weight = 11891.746| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12881 Z= 0.145 Angle : 0.529 6.281 17545 Z= 0.279 Chirality : 0.046 0.135 1950 Planarity : 0.004 0.055 2235 Dihedral : 4.454 53.655 1690 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.96 % Allowed : 12.87 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.22), residues: 1525 helix: 1.85 (0.24), residues: 475 sheet: 0.01 (0.25), residues: 495 loop : -1.82 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 123 TYR 0.012 0.001 TYR B 38 PHE 0.013 0.001 PHE C 282 TRP 0.017 0.001 TRP B 206 HIS 0.001 0.000 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00347 (12880) covalent geometry : angle 0.52910 (17545) hydrogen bonds : bond 0.03475 ( 527) hydrogen bonds : angle 4.48226 ( 1662) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.357 Fit side-chains REVERT: A 27 ASN cc_start: 0.8411 (t0) cc_final: 0.8019 (t0) REVERT: A 65 ARG cc_start: 0.7195 (ttm170) cc_final: 0.6709 (ttt180) REVERT: A 266 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8872 (mt) REVERT: B 27 ASN cc_start: 0.8445 (t0) cc_final: 0.8100 (t0) REVERT: B 62 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7685 (tm-30) REVERT: B 65 ARG cc_start: 0.7499 (ttm170) cc_final: 0.7013 (ttt180) REVERT: B 158 ASP cc_start: 0.6392 (m-30) cc_final: 0.6160 (m-30) REVERT: B 245 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: C 27 ASN cc_start: 0.8405 (t0) cc_final: 0.8134 (t0) REVERT: C 62 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7432 (tm-30) REVERT: C 65 ARG cc_start: 0.7867 (ttm170) cc_final: 0.7337 (ttt180) REVERT: C 266 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8806 (mt) REVERT: D 27 ASN cc_start: 0.8386 (t0) cc_final: 0.8025 (t0) REVERT: D 65 ARG cc_start: 0.7334 (ttm170) cc_final: 0.6878 (ttt180) REVERT: E 27 ASN cc_start: 0.8473 (t0) cc_final: 0.8095 (t0) REVERT: E 65 ARG cc_start: 0.7343 (ttm170) cc_final: 0.6885 (ttt180) REVERT: E 158 ASP cc_start: 0.6525 (m-30) cc_final: 0.6290 (m-30) outliers start: 27 outliers final: 22 residues processed: 173 average time/residue: 0.1157 time to fit residues: 29.2509 Evaluate side-chains 166 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 266 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 119 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 36 optimal weight: 0.0980 chunk 28 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 148 optimal weight: 0.0770 overall best weight: 0.5940 ------------------------------------------------------------------------------- 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 = 0.3251 r_free = 0.3251 target = 0.129252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.118313 restraints weight = 15175.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.119380 restraints weight = 11514.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.119834 restraints weight = 9441.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.120032 restraints weight = 9211.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.120105 restraints weight = 8734.995| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12881 Z= 0.096 Angle : 0.480 6.306 17545 Z= 0.250 Chirality : 0.044 0.123 1950 Planarity : 0.004 0.051 2235 Dihedral : 4.142 57.831 1690 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.18 % Allowed : 13.16 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.22), residues: 1525 helix: 1.99 (0.24), residues: 475 sheet: 0.21 (0.25), residues: 495 loop : -1.77 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 123 TYR 0.011 0.001 TYR B 38 PHE 0.009 0.001 PHE C 282 TRP 0.018 0.001 TRP A 206 HIS 0.001 0.000 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00218 (12880) covalent geometry : angle 0.47954 (17545) hydrogen bonds : bond 0.02948 ( 527) hydrogen bonds : angle 4.23755 ( 1662) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.478 Fit side-chains REVERT: A 27 ASN cc_start: 0.8373 (t0) cc_final: 0.7975 (t0) REVERT: A 65 ARG cc_start: 0.7090 (ttm170) cc_final: 0.6667 (ttt180) REVERT: A 245 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.8172 (t80) REVERT: B 27 ASN cc_start: 0.8433 (t0) cc_final: 0.8175 (t0) REVERT: B 62 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7645 (tm-30) REVERT: B 65 ARG cc_start: 0.7470 (ttm170) cc_final: 0.6958 (ttt180) REVERT: B 158 ASP cc_start: 0.6328 (m-30) cc_final: 0.6092 (m-30) REVERT: B 245 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: C 27 ASN cc_start: 0.8401 (t0) cc_final: 0.8148 (t0) REVERT: C 62 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7230 (tm-30) REVERT: C 65 ARG cc_start: 0.7734 (ttm170) cc_final: 0.7232 (ttt180) REVERT: C 245 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.8321 (t80) REVERT: D 27 ASN cc_start: 0.8367 (t0) cc_final: 0.8019 (t0) REVERT: D 65 ARG cc_start: 0.7232 (ttm170) cc_final: 0.6814 (ttt180) REVERT: E 27 ASN cc_start: 0.8475 (t0) cc_final: 0.8091 (t0) REVERT: E 65 ARG cc_start: 0.7213 (ttm170) cc_final: 0.6793 (ttt180) REVERT: E 158 ASP cc_start: 0.6429 (m-30) cc_final: 0.6192 (m-30) outliers start: 30 outliers final: 20 residues processed: 177 average time/residue: 0.1024 time to fit residues: 27.4409 Evaluate side-chains 177 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 259 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 61 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.126573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.115757 restraints weight = 15388.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.116798 restraints weight = 11830.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.117051 restraints weight = 9832.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.117317 restraints weight = 9437.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.117424 restraints weight = 9422.361| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12881 Z= 0.125 Angle : 0.498 5.924 17545 Z= 0.262 Chirality : 0.046 0.131 1950 Planarity : 0.004 0.051 2235 Dihedral : 4.195 59.502 1690 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.04 % Allowed : 14.18 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.22), residues: 1525 helix: 1.95 (0.24), residues: 475 sheet: 0.28 (0.25), residues: 465 loop : -1.65 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 123 TYR 0.010 0.001 TYR B 38 PHE 0.008 0.001 PHE E 274 TRP 0.018 0.001 TRP A 206 HIS 0.001 0.000 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00296 (12880) covalent geometry : angle 0.49766 (17545) hydrogen bonds : bond 0.03196 ( 527) hydrogen bonds : angle 4.27241 ( 1662) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.496 Fit side-chains REVERT: A 27 ASN cc_start: 0.8330 (t0) cc_final: 0.7980 (t0) REVERT: A 65 ARG cc_start: 0.7120 (ttm170) cc_final: 0.6717 (ttt180) REVERT: A 245 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.8154 (t80) REVERT: B 27 ASN cc_start: 0.8403 (t0) cc_final: 0.8193 (t0) REVERT: B 62 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7499 (tm-30) REVERT: B 65 ARG cc_start: 0.7486 (ttm170) cc_final: 0.6983 (ttt180) REVERT: B 158 ASP cc_start: 0.6396 (m-30) cc_final: 0.6160 (m-30) REVERT: B 245 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: C 27 ASN cc_start: 0.8382 (t0) cc_final: 0.8126 (t0) REVERT: C 62 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7091 (tm-30) REVERT: C 65 ARG cc_start: 0.7758 (ttm170) cc_final: 0.7245 (ttt180) REVERT: D 27 ASN cc_start: 0.8372 (t0) cc_final: 0.8005 (t0) REVERT: D 65 ARG cc_start: 0.7296 (ttm170) cc_final: 0.6837 (ttt180) REVERT: E 27 ASN cc_start: 0.8458 (t0) cc_final: 0.8089 (t0) REVERT: E 65 ARG cc_start: 0.7261 (ttm170) cc_final: 0.6908 (ttt180) REVERT: E 158 ASP cc_start: 0.6486 (m-30) cc_final: 0.6238 (m-30) outliers start: 28 outliers final: 22 residues processed: 173 average time/residue: 0.1139 time to fit residues: 29.3412 Evaluate side-chains 181 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 259 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 89 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 117 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3235 r_free = 0.3235 target = 0.127993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.116704 restraints weight = 15310.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.116800 restraints weight = 13461.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.116800 restraints weight = 12959.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.116800 restraints weight = 12957.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.116800 restraints weight = 12957.844| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12881 Z= 0.107 Angle : 0.484 5.544 17545 Z= 0.254 Chirality : 0.045 0.126 1950 Planarity : 0.004 0.050 2235 Dihedral : 4.040 56.541 1690 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.18 % Allowed : 14.47 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.22), residues: 1525 helix: 2.00 (0.24), residues: 475 sheet: 0.36 (0.25), residues: 465 loop : -1.64 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 123 TYR 0.010 0.001 TYR B 38 PHE 0.017 0.001 PHE D 282 TRP 0.019 0.001 TRP A 206 HIS 0.001 0.000 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00250 (12880) covalent geometry : angle 0.48368 (17545) hydrogen bonds : bond 0.03001 ( 527) hydrogen bonds : angle 4.18069 ( 1662) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.490 Fit side-chains REVERT: A 27 ASN cc_start: 0.8278 (t0) cc_final: 0.7904 (t0) REVERT: A 65 ARG cc_start: 0.7134 (ttm170) cc_final: 0.6759 (ttt180) REVERT: A 245 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.8173 (t80) REVERT: B 27 ASN cc_start: 0.8331 (t0) cc_final: 0.8088 (t0) REVERT: B 62 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7450 (tm-30) REVERT: B 65 ARG cc_start: 0.7493 (ttm170) cc_final: 0.6966 (ttt180) REVERT: B 245 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: C 27 ASN cc_start: 0.8367 (t0) cc_final: 0.8107 (t0) REVERT: C 62 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7096 (tm-30) REVERT: C 65 ARG cc_start: 0.7735 (ttm170) cc_final: 0.7212 (ttt180) REVERT: C 245 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.8335 (t80) REVERT: D 27 ASN cc_start: 0.8347 (t0) cc_final: 0.7973 (t0) REVERT: D 65 ARG cc_start: 0.7317 (ttm170) cc_final: 0.6857 (ttt180) REVERT: E 27 ASN cc_start: 0.8426 (t0) cc_final: 0.8073 (t0) REVERT: E 65 ARG cc_start: 0.7204 (ttm170) cc_final: 0.6884 (ttt180) REVERT: E 158 ASP cc_start: 0.6416 (m-30) cc_final: 0.6189 (m-30) outliers start: 30 outliers final: 21 residues processed: 180 average time/residue: 0.1198 time to fit residues: 31.3028 Evaluate side-chains 182 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 259 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 80 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- 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 = 0.3171 r_free = 0.3171 target = 0.122727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.111575 restraints weight = 15649.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.112664 restraints weight = 13569.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.113245 restraints weight = 10920.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.113839 restraints weight = 9700.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.113898 restraints weight = 9177.111| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12881 Z= 0.201 Angle : 0.572 7.510 17545 Z= 0.303 Chirality : 0.048 0.145 1950 Planarity : 0.004 0.053 2235 Dihedral : 4.535 58.807 1690 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.25 % Allowed : 15.13 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.22), residues: 1525 helix: 1.76 (0.24), residues: 475 sheet: 0.11 (0.25), residues: 465 loop : -1.71 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 123 TYR 0.011 0.001 TYR B 38 PHE 0.015 0.002 PHE D 282 TRP 0.017 0.001 TRP A 206 HIS 0.001 0.000 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00493 (12880) covalent geometry : angle 0.57159 (17545) hydrogen bonds : bond 0.03806 ( 527) hydrogen bonds : angle 4.50075 ( 1662) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.523 Fit side-chains REVERT: A 27 ASN cc_start: 0.8393 (t0) cc_final: 0.8009 (t0) REVERT: A 65 ARG cc_start: 0.7137 (ttm170) cc_final: 0.6754 (ttt180) REVERT: B 27 ASN cc_start: 0.8374 (t0) cc_final: 0.8081 (t0) REVERT: B 62 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7175 (tm-30) REVERT: B 65 ARG cc_start: 0.7578 (ttm170) cc_final: 0.6990 (ttt180) REVERT: B 245 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.8018 (m-80) REVERT: C 27 ASN cc_start: 0.8419 (t0) cc_final: 0.8150 (t0) REVERT: C 62 GLN cc_start: 0.7829 (tm-30) cc_final: 0.6987 (tm-30) REVERT: C 65 ARG cc_start: 0.7802 (ttm170) cc_final: 0.7272 (ttt180) REVERT: D 27 ASN cc_start: 0.8383 (t0) cc_final: 0.8040 (t0) REVERT: D 65 ARG cc_start: 0.7369 (ttm170) cc_final: 0.6892 (ttt180) REVERT: E 27 ASN cc_start: 0.8449 (t0) cc_final: 0.8096 (t0) REVERT: E 65 ARG cc_start: 0.7327 (ttm170) cc_final: 0.6983 (ttt180) outliers start: 31 outliers final: 26 residues processed: 182 average time/residue: 0.1169 time to fit residues: 31.6290 Evaluate side-chains 184 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 161 TRP Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 22 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.124491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.113451 restraints weight = 15499.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.113839 restraints weight = 13322.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.113844 restraints weight = 11689.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.113844 restraints weight = 11673.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.113844 restraints weight = 11673.126| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12881 Z= 0.147 Angle : 0.532 5.506 17545 Z= 0.281 Chirality : 0.046 0.135 1950 Planarity : 0.004 0.051 2235 Dihedral : 4.445 57.253 1690 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.04 % Allowed : 15.56 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.22), residues: 1525 helix: 1.75 (0.24), residues: 475 sheet: 0.15 (0.25), residues: 465 loop : -1.68 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 123 TYR 0.010 0.001 TYR B 38 PHE 0.008 0.001 PHE E 304 TRP 0.018 0.001 TRP A 206 HIS 0.001 0.000 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00353 (12880) covalent geometry : angle 0.53226 (17545) hydrogen bonds : bond 0.03415 ( 527) hydrogen bonds : angle 4.38506 ( 1662) Misc. bond : bond 0.00017 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.484 Fit side-chains REVERT: A 27 ASN cc_start: 0.8353 (t0) cc_final: 0.8009 (t0) REVERT: A 65 ARG cc_start: 0.7122 (ttm170) cc_final: 0.6761 (ttt180) REVERT: B 27 ASN cc_start: 0.8380 (t0) cc_final: 0.8038 (t0) REVERT: B 62 GLN cc_start: 0.7838 (tm-30) cc_final: 0.7319 (tm-30) REVERT: B 245 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: B 266 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8782 (mt) REVERT: C 27 ASN cc_start: 0.8415 (t0) cc_final: 0.8120 (t0) REVERT: C 65 ARG cc_start: 0.7782 (ttm170) cc_final: 0.7279 (ttt180) REVERT: D 27 ASN cc_start: 0.8372 (t0) cc_final: 0.7998 (t0) REVERT: D 62 GLN cc_start: 0.7868 (tm-30) cc_final: 0.7538 (tm-30) REVERT: D 65 ARG cc_start: 0.7355 (ttm170) cc_final: 0.6889 (ttt180) REVERT: E 27 ASN cc_start: 0.8404 (t0) cc_final: 0.8051 (t0) REVERT: E 65 ARG cc_start: 0.7250 (ttm170) cc_final: 0.6970 (ttt180) REVERT: E 158 ASP cc_start: 0.6563 (m-30) cc_final: 0.6323 (m-30) outliers start: 28 outliers final: 25 residues processed: 178 average time/residue: 0.1082 time to fit residues: 28.9235 Evaluate side-chains 185 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 161 TRP Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 259 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 72 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3194 r_free = 0.3194 target = 0.124518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.113407 restraints weight = 15492.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.113962 restraints weight = 12967.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.113954 restraints weight = 11650.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.113954 restraints weight = 11540.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.113954 restraints weight = 11540.076| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12881 Z= 0.143 Angle : 0.529 5.986 17545 Z= 0.279 Chirality : 0.046 0.136 1950 Planarity : 0.004 0.051 2235 Dihedral : 4.452 56.029 1690 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.87 % Favored : 96.07 % Rotamer: Outliers : 2.11 % Allowed : 15.78 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.22), residues: 1525 helix: 1.77 (0.24), residues: 475 sheet: 0.15 (0.25), residues: 465 loop : -1.66 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 123 TYR 0.010 0.001 TYR B 38 PHE 0.019 0.001 PHE D 282 TRP 0.018 0.001 TRP A 206 HIS 0.001 0.000 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00345 (12880) covalent geometry : angle 0.52931 (17545) hydrogen bonds : bond 0.03382 ( 527) hydrogen bonds : angle 4.35699 ( 1662) Misc. bond : bond 0.00019 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1675.60 seconds wall clock time: 29 minutes 52.34 seconds (1792.34 seconds total)