Starting phenix.real_space_refine on Sat Sep 12 00:18:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5aey_2850/09_2026/5aey_2850.cif Found real_map, /net/cci-nas-00/data/ceres_data/5aey_2850/09_2026/5aey_2850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5aey_2850/09_2026/5aey_2850.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5aey_2850/09_2026/5aey_2850.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5aey_2850/09_2026/5aey_2850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5aey_2850/09_2026/5aey_2850.map" model { file = "/net/cci-nas-00/data/ceres_data/5aey_2850/09_2026/5aey_2850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5aey_2850/09_2026/5aey_2850.cif" } resolution = 4.3 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 ------------------------------------------------------------------------------- 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= 1.000 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 P 15 5.49 5 S 40 5.16 5 C 7950 2.51 5 N 2140 2.21 5 O 2530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12675 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "B" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "C" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "D" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "E" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2504 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.84, per 1000 atoms: 0.22 Number of scatterers: 12675 At special positions: 0 Unit cell: (78.11, 98.44, 181.9, 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 40 16.00 P 15 15.00 O 2530 8.00 N 2140 7.00 C 7950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 627.5 milliseconds 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 15 sheets defined 42.5% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.942A pdb=" N GLN A 73 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.835A pdb=" N VAL A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.771A pdb=" N TYR A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 115 through 126 removed outlier: 3.816A pdb=" N PHE A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 152 removed outlier: 3.800A pdb=" N ALA A 152 " --> pdb=" O SER A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 149 through 152' Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.752A pdb=" N GLU A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 213 removed outlier: 3.538A pdb=" N ALA A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 228 Processing helix chain 'A' and resid 231 through 237 Processing helix chain 'A' and resid 244 through 268 removed outlier: 3.877A pdb=" N VAL A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 294 removed outlier: 5.553A pdb=" N ASP A 288 " --> pdb=" O GLU A 284 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'B' and resid 69 through 74 removed outlier: 3.957A pdb=" N GLN B 73 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 88 removed outlier: 3.832A pdb=" N VAL B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.747A pdb=" N TYR B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 115 through 126 removed outlier: 3.816A pdb=" N PHE B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 152 removed outlier: 3.805A pdb=" N ALA B 152 " --> pdb=" O SER B 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 152' Processing helix chain 'B' and resid 153 through 159 removed outlier: 3.751A pdb=" N GLU B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 213 removed outlier: 3.572A pdb=" N ALA B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 228 Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 244 through 268 removed outlier: 3.881A pdb=" N VAL B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 250 " --> pdb=" O SER B 246 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG B 262 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 294 removed outlier: 5.554A pdb=" N ASP B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 299 No H-bonds generated for 'chain 'B' and resid 297 through 299' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 309 through 317 Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.957A pdb=" N GLN C 73 " --> pdb=" O ILE C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 88 removed outlier: 3.819A pdb=" N VAL C 79 " --> pdb=" O SER C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.752A pdb=" N TYR C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 108' Processing helix chain 'C' and resid 115 through 126 removed outlier: 3.818A pdb=" N PHE C 126 " --> pdb=" O LYS C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 152 removed outlier: 3.796A pdb=" N ALA C 152 " --> pdb=" O SER C 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 149 through 152' Processing helix chain 'C' and resid 153 through 159 removed outlier: 3.749A pdb=" N GLU C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 213 removed outlier: 3.573A pdb=" N ALA C 205 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP C 208 " --> pdb=" O SER C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 228 Processing helix chain 'C' and resid 231 through 237 Processing helix chain 'C' and resid 244 through 268 removed outlier: 3.859A pdb=" N VAL C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 294 removed outlier: 5.567A pdb=" N ASP C 288 " --> pdb=" O GLU C 284 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 299 No H-bonds generated for 'chain 'C' and resid 297 through 299' Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 309 through 317 Processing helix chain 'D' and resid 69 through 74 removed outlier: 3.960A pdb=" N GLN D 73 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 88 removed outlier: 3.824A pdb=" N VAL D 79 " --> pdb=" O SER D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.751A pdb=" N TYR D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 115 through 126 removed outlier: 3.818A pdb=" N PHE D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 152 removed outlier: 3.791A pdb=" N ALA D 152 " --> pdb=" O SER D 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 149 through 152' Processing helix chain 'D' and resid 153 through 159 removed outlier: 3.751A pdb=" N GLU D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 213 removed outlier: 3.579A pdb=" N ALA D 205 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP D 208 " --> pdb=" O SER D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 228 Processing helix chain 'D' and resid 231 through 237 Processing helix chain 'D' and resid 244 through 268 removed outlier: 3.853A pdb=" N VAL D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU D 250 " --> pdb=" O SER D 246 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN D 261 " --> pdb=" O ARG D 257 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG D 262 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 294 removed outlier: 5.568A pdb=" N ASP D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA D 289 " --> pdb=" O LEU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 299 No H-bonds generated for 'chain 'D' and resid 297 through 299' Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 309 through 317 Processing helix chain 'E' and resid 69 through 74 removed outlier: 3.949A pdb=" N GLN E 73 " --> pdb=" O ILE E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 88 removed outlier: 3.822A pdb=" N VAL E 79 " --> pdb=" O SER E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.751A pdb=" N TYR E 107 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 115 through 126 removed outlier: 3.817A pdb=" N PHE E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 152 removed outlier: 3.834A pdb=" N ALA E 152 " --> pdb=" O SER E 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 149 through 152' Processing helix chain 'E' and resid 153 through 159 removed outlier: 3.732A pdb=" N GLU E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 213 removed outlier: 3.575A pdb=" N ALA E 205 " --> pdb=" O LEU E 201 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 228 Processing helix chain 'E' and resid 231 through 237 Processing helix chain 'E' and resid 244 through 268 removed outlier: 3.854A pdb=" N VAL E 248 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU E 250 " --> pdb=" O SER E 246 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU E 260 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN E 261 " --> pdb=" O ARG E 257 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG E 262 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 294 removed outlier: 5.562A pdb=" N ASP E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA E 289 " --> pdb=" O LEU E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 299 No H-bonds generated for 'chain 'E' and resid 297 through 299' Processing helix chain 'E' and resid 306 through 308 No H-bonds generated for 'chain 'E' and resid 306 through 308' Processing helix chain 'E' and resid 309 through 317 Processing sheet with id=AA, first strand: chain 'A' and resid 22 through 29 removed outlier: 5.514A pdb=" N GLN A 17 " --> pdb=" O LEU A 2 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU A 2 " --> pdb=" O GLN A 17 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 101 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP A 7 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE A 98 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL A 143 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N CYS A 100 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL A 145 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 102 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AC, first strand: chain 'A' and resid 187 through 194 removed outlier: 5.540A pdb=" N ILE A 188 " --> pdb=" O MET A 182 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N MET A 182 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 278 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 22 through 29 removed outlier: 5.454A pdb=" N GLN B 17 " --> pdb=" O LEU B 2 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU B 2 " --> pdb=" O GLN B 17 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR B 101 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP B 7 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE B 98 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL B 143 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N CYS B 100 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL B 145 " --> pdb=" O CYS B 100 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B 102 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=BB, first strand: chain 'B' and resid 32 through 33 Processing sheet with id=BC, first strand: chain 'B' and resid 187 through 194 removed outlier: 5.529A pdb=" N ILE B 188 " --> pdb=" O MET B 182 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N MET B 182 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 278 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing sheet with id=CA, first strand: chain 'C' and resid 22 through 29 removed outlier: 5.483A pdb=" N GLN C 17 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU C 2 " --> pdb=" O GLN C 17 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR C 101 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASP C 7 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 98 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL C 143 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N CYS C 100 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL C 145 " --> pdb=" O CYS C 100 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU C 102 " --> pdb=" O VAL C 145 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=CC, first strand: chain 'C' and resid 187 through 194 removed outlier: 5.534A pdb=" N ILE C 188 " --> pdb=" O MET C 182 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N MET C 182 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 278 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Processing sheet with id=DA, first strand: chain 'D' and resid 22 through 29 removed outlier: 5.496A pdb=" N GLN D 17 " --> pdb=" O LEU D 2 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU D 2 " --> pdb=" O GLN D 17 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR D 101 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP D 7 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE D 98 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL D 143 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N CYS D 100 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL D 145 " --> pdb=" O CYS D 100 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU D 102 " --> pdb=" O VAL D 145 " (cutoff:3.500A) Processing sheet with id=DB, first strand: chain 'D' and resid 32 through 33 Processing sheet with id=DC, first strand: chain 'D' and resid 187 through 194 removed outlier: 5.547A pdb=" N ILE D 188 " --> pdb=" O MET D 182 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N MET D 182 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D 278 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing sheet with id=EA, first strand: chain 'E' and resid 22 through 29 removed outlier: 5.481A pdb=" N GLN E 17 " --> pdb=" O LEU E 2 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU E 2 " --> pdb=" O GLN E 17 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR E 101 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP E 7 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE E 98 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL E 143 " --> pdb=" O ILE E 98 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N CYS E 100 " --> pdb=" O VAL E 143 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL E 145 " --> pdb=" O CYS E 100 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU E 102 " --> pdb=" O VAL E 145 " (cutoff:3.500A) Processing sheet with id=EB, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=EC, first strand: chain 'E' and resid 187 through 194 removed outlier: 5.556A pdb=" N ILE E 188 " --> pdb=" O MET E 182 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N MET E 182 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL E 278 " --> pdb=" O PHE E 302 " (cutoff:3.500A) 545 hydrogen bonds defined for protein. 1545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2456 1.32 - 1.45: 3160 1.45 - 1.57: 7164 1.57 - 1.70: 40 1.70 - 1.82: 70 Bond restraints: 12890 Sorted by residual: bond pdb=" C PHE B 4 " pdb=" N ILE B 5 " ideal model delta sigma weight residual 1.329 1.444 -0.115 1.37e-02 5.33e+03 7.07e+01 bond pdb=" N3B ANP B 500 " pdb=" PG ANP B 500 " ideal model delta sigma weight residual 1.795 1.643 0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" N3B ANP C 500 " pdb=" PG ANP C 500 " ideal model delta sigma weight residual 1.795 1.645 0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" N3B ANP D 500 " pdb=" PG ANP D 500 " ideal model delta sigma weight residual 1.795 1.647 0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" N3B ANP E 500 " pdb=" PG ANP E 500 " ideal model delta sigma weight residual 1.795 1.648 0.147 2.00e-02 2.50e+03 5.39e+01 ... (remaining 12885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 16130 3.00 - 6.00: 1204 6.00 - 9.00: 135 9.00 - 11.99: 16 11.99 - 14.99: 10 Bond angle restraints: 17495 Sorted by residual: angle pdb=" C PHE B 4 " pdb=" N ILE B 5 " pdb=" CA ILE B 5 " ideal model delta sigma weight residual 123.11 112.68 10.43 1.36e+00 5.41e-01 5.88e+01 angle pdb=" N VAL E 66 " pdb=" CA VAL E 66 " pdb=" CB VAL E 66 " ideal model delta sigma weight residual 110.53 117.03 -6.50 1.09e+00 8.42e-01 3.56e+01 angle pdb=" N VAL A 66 " pdb=" CA VAL A 66 " pdb=" CB VAL A 66 " ideal model delta sigma weight residual 110.53 117.02 -6.49 1.09e+00 8.42e-01 3.55e+01 angle pdb=" N VAL C 66 " pdb=" CA VAL C 66 " pdb=" CB VAL C 66 " ideal model delta sigma weight residual 110.53 116.91 -6.38 1.09e+00 8.42e-01 3.42e+01 angle pdb=" N VAL D 66 " pdb=" CA VAL D 66 " pdb=" CB VAL D 66 " ideal model delta sigma weight residual 110.53 116.89 -6.36 1.09e+00 8.42e-01 3.40e+01 ... (remaining 17490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.21: 6956 30.21 - 60.41: 694 60.41 - 90.62: 60 90.62 - 120.83: 0 120.83 - 151.03: 5 Dihedral angle restraints: 7715 sinusoidal: 3090 harmonic: 4625 Sorted by residual: dihedral pdb=" CA LEU B 317 " pdb=" C LEU B 317 " pdb=" N ILE B 318 " pdb=" CA ILE B 318 " ideal model delta harmonic sigma weight residual 180.00 142.63 37.37 0 5.00e+00 4.00e-02 5.59e+01 dihedral pdb=" CA LEU A 317 " pdb=" C LEU A 317 " pdb=" N ILE A 318 " pdb=" CA ILE A 318 " ideal model delta harmonic sigma weight residual 180.00 142.75 37.25 0 5.00e+00 4.00e-02 5.55e+01 dihedral pdb=" CA LEU D 317 " pdb=" C LEU D 317 " pdb=" N ILE D 318 " pdb=" CA ILE D 318 " ideal model delta harmonic sigma weight residual 180.00 142.89 37.11 0 5.00e+00 4.00e-02 5.51e+01 ... (remaining 7712 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1180 0.073 - 0.146: 514 0.146 - 0.219: 185 0.219 - 0.292: 84 0.292 - 0.365: 57 Chirality restraints: 2020 Sorted by residual: chirality pdb=" CA ARG A 262 " pdb=" N ARG A 262 " pdb=" C ARG A 262 " pdb=" CB ARG A 262 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA ASN D 268 " pdb=" N ASN D 268 " pdb=" C ASN D 268 " pdb=" CB ASN D 268 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA PHE B 46 " pdb=" N PHE B 46 " pdb=" C PHE B 46 " pdb=" CB PHE B 46 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 2017 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 107 " -0.046 2.00e-02 2.50e+03 2.47e-02 1.22e+01 pdb=" CG TYR E 107 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR E 107 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR E 107 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR E 107 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 107 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 107 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 107 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 107 " -0.046 2.00e-02 2.50e+03 2.47e-02 1.22e+01 pdb=" CG TYR A 107 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 107 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 107 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 107 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 107 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 107 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 107 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 107 " 0.042 2.00e-02 2.50e+03 2.23e-02 9.95e+00 pdb=" CG TYR D 107 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR D 107 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR D 107 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR D 107 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 107 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 107 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 107 " 0.018 2.00e-02 2.50e+03 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 839 2.74 - 3.28: 13239 3.28 - 3.82: 21743 3.82 - 4.36: 26447 4.36 - 4.90: 41415 Nonbonded interactions: 103683 Sorted by model distance: nonbonded pdb=" N ARG A 297 " pdb=" OD2 ASP C 241 " model vdw 2.197 3.120 nonbonded pdb=" N ARG C 297 " pdb=" OD2 ASP E 241 " model vdw 2.220 3.120 nonbonded pdb=" N ARG B 297 " pdb=" OD2 ASP D 241 " model vdw 2.222 3.120 nonbonded pdb=" O ASP B 164 " pdb=" N GLY B 183 " model vdw 2.303 3.120 nonbonded pdb=" O ASP E 164 " pdb=" N GLY E 183 " model vdw 2.303 3.120 ... (remaining 103678 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.690 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.011 0.152 12890 Z= 0.741 Angle : 1.714 14.993 17495 Z= 1.035 Chirality : 0.110 0.365 2020 Planarity : 0.006 0.047 2220 Dihedral : 21.882 151.032 4735 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 2.85 % Allowed : 8.67 % Favored : 88.48 % Rotamer: Outliers : 18.45 % Allowed : 22.90 % Favored : 58.66 % Cbeta Deviations : 2.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.68 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.18), residues: 1580 helix: -2.13 (0.17), residues: 555 sheet: -1.14 (0.26), residues: 365 loop : -2.70 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 127 TYR 0.047 0.007 TYR E 107 PHE 0.028 0.004 PHE A 138 TRP 0.029 0.004 TRP A 72 HIS 0.007 0.002 HIS E 293 Details of bonding type rmsd/Z covalent geometry : bond 0.01143 / 0.74 (12890) covalent geometry : angle 1.71384 / 1.03 (17495) hydrogen bonds : bond 0.20531 / 13.71 ( 545) hydrogen bonds : angle 7.74110 / 5.42 ( 1545) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 261 poor density : 370 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8575 (mpp) cc_final: 0.7635 (ttt) REVERT: A 101 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7580 (t) REVERT: A 106 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8361 (tp30) REVERT: A 107 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: A 111 ASN cc_start: 0.8894 (OUTLIER) cc_final: 0.8560 (p0) REVERT: A 121 ARG cc_start: 0.8905 (mtp85) cc_final: 0.8635 (mtp85) REVERT: A 148 GLU cc_start: 0.5993 (tt0) cc_final: 0.5241 (tt0) REVERT: A 158 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8447 (mm-40) REVERT: A 194 ASP cc_start: 0.7425 (t0) cc_final: 0.7049 (t0) REVERT: A 238 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8634 (mmt180) REVERT: A 261 GLN cc_start: 0.9011 (tp-100) cc_final: 0.8263 (tp40) REVERT: A 262 ARG cc_start: 0.8642 (ptt180) cc_final: 0.8301 (ptm160) REVERT: A 292 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8211 (ptpt) REVERT: A 302 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.6880 (m-80) REVERT: A 308 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8161 (tp-100) REVERT: A 315 MET cc_start: 0.8961 (mtp) cc_final: 0.8732 (mtm) REVERT: B 1 MET cc_start: 0.8708 (mpp) cc_final: 0.8105 (ttt) REVERT: B 54 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7502 (pp30) REVERT: B 101 THR cc_start: 0.7471 (OUTLIER) cc_final: 0.6890 (t) REVERT: B 106 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8125 (tp30) REVERT: B 107 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.7169 (m-80) REVERT: B 111 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8429 (p0) REVERT: B 125 ASN cc_start: 0.7929 (OUTLIER) cc_final: 0.7358 (t0) REVERT: B 148 GLU cc_start: 0.5037 (tt0) cc_final: 0.4498 (tt0) REVERT: B 194 ASP cc_start: 0.7018 (t0) cc_final: 0.6724 (t0) REVERT: B 208 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7958 (t70) REVERT: B 234 TYR cc_start: 0.9070 (t80) cc_final: 0.8284 (t80) REVERT: B 261 GLN cc_start: 0.9052 (tp-100) cc_final: 0.8264 (tp-100) REVERT: B 292 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8209 (ptpt) REVERT: B 302 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: B 316 TYR cc_start: 0.8488 (t80) cc_final: 0.8189 (t80) REVERT: C 1 MET cc_start: 0.8735 (mpp) cc_final: 0.8211 (ttt) REVERT: C 31 SER cc_start: 0.7913 (OUTLIER) cc_final: 0.7660 (t) REVERT: C 74 TYR cc_start: 0.8150 (m-80) cc_final: 0.7668 (m-80) REVERT: C 97 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7756 (m-30) REVERT: C 101 THR cc_start: 0.7589 (OUTLIER) cc_final: 0.7049 (t) REVERT: C 106 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8002 (tp30) REVERT: C 107 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.6879 (m-80) REVERT: C 111 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8218 (p0) REVERT: C 139 THR cc_start: 0.7327 (OUTLIER) cc_final: 0.6874 (p) REVERT: C 140 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8222 (pt) REVERT: C 148 GLU cc_start: 0.5864 (tt0) cc_final: 0.5349 (tt0) REVERT: C 194 ASP cc_start: 0.7218 (t0) cc_final: 0.6911 (t70) REVERT: C 219 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8644 (p) REVERT: C 234 TYR cc_start: 0.8973 (t80) cc_final: 0.8667 (t80) REVERT: C 247 ILE cc_start: 0.8692 (tt) cc_final: 0.8436 (tt) REVERT: C 262 ARG cc_start: 0.8758 (ptt180) cc_final: 0.8490 (mtm-85) REVERT: C 292 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8151 (pttt) REVERT: D 1 MET cc_start: 0.8758 (mpp) cc_final: 0.8316 (ttt) REVERT: D 31 SER cc_start: 0.7766 (OUTLIER) cc_final: 0.7427 (t) REVERT: D 53 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7686 (mt-10) REVERT: D 74 TYR cc_start: 0.7967 (m-80) cc_final: 0.7452 (m-80) REVERT: D 101 THR cc_start: 0.7588 (OUTLIER) cc_final: 0.7122 (t) REVERT: D 106 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8223 (tp30) REVERT: D 121 ARG cc_start: 0.8515 (mtp85) cc_final: 0.8300 (mtp85) REVERT: D 125 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7555 (t0) REVERT: D 148 GLU cc_start: 0.5630 (tt0) cc_final: 0.4961 (tt0) REVERT: D 158 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8693 (mm-40) REVERT: D 216 LYS cc_start: 0.9041 (ttmp) cc_final: 0.8786 (tttp) REVERT: D 261 GLN cc_start: 0.9129 (tp-100) cc_final: 0.8600 (tp40) REVERT: D 292 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8277 (mmtm) REVERT: D 310 ASP cc_start: 0.8549 (m-30) cc_final: 0.8253 (m-30) REVERT: E 1 MET cc_start: 0.8977 (mpp) cc_final: 0.8545 (ttt) REVERT: E 31 SER cc_start: 0.7571 (OUTLIER) cc_final: 0.7155 (t) REVERT: E 40 PHE cc_start: 0.7398 (t80) cc_final: 0.7087 (t80) REVERT: E 54 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.6499 (pp30) REVERT: E 106 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8276 (tp30) REVERT: E 110 ARG cc_start: 0.7393 (mmp80) cc_final: 0.7101 (ttt180) REVERT: E 121 ARG cc_start: 0.8540 (mtp85) cc_final: 0.8054 (mtp85) REVERT: E 158 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8638 (mm-40) REVERT: E 247 ILE cc_start: 0.8774 (tt) cc_final: 0.8531 (tp) REVERT: E 261 GLN cc_start: 0.9309 (tp-100) cc_final: 0.8711 (tp40) REVERT: E 262 ARG cc_start: 0.8780 (ptt180) cc_final: 0.8469 (mtt180) REVERT: E 296 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.6700 (mp) REVERT: E 302 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7738 (m-80) outliers start: 261 outliers final: 78 residues processed: 576 average time/residue: 0.1331 time to fit residues: 105.3181 Evaluate side-chains 345 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 231 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 HIS A 118 ASN A 261 GLN A 308 GLN B 83 HIS B 261 GLN B 308 GLN C 83 HIS C 118 ASN C 308 GLN D 83 HIS D 118 ASN D 261 GLN D 308 GLN E 83 HIS E 115 ASN E 118 ASN E 125 ASN E 261 GLN E 308 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.086681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.078915 restraints weight = 48230.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.080549 restraints weight = 29469.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.081662 restraints weight = 20064.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.082382 restraints weight = 14719.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.082905 restraints weight = 11527.944| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12890 Z= 0.181 Angle : 0.809 8.173 17495 Z= 0.420 Chirality : 0.047 0.213 2020 Planarity : 0.005 0.072 2220 Dihedral : 11.865 162.231 1720 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.70 % Allowed : 9.18 % Favored : 90.13 % Rotamer: Outliers : 0.07 % Allowed : 4.73 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.19), residues: 1580 helix: -0.66 (0.20), residues: 595 sheet: -0.25 (0.27), residues: 355 loop : -2.18 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 297 TYR 0.023 0.002 TYR B 107 PHE 0.025 0.002 PHE A 4 TRP 0.012 0.002 TRP B 72 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (12890) covalent geometry : angle 0.80929 / 0.42 (17495) hydrogen bonds : bond 0.05001 / 3.27 ( 545) hydrogen bonds : angle 5.70396 / 4.00 ( 1545) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 356 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.7525 (m-80) cc_final: 0.7051 (m-10) REVERT: A 126 PHE cc_start: 0.7635 (m-10) cc_final: 0.7335 (m-80) REVERT: A 146 MET cc_start: 0.7165 (mtp) cc_final: 0.6816 (mtp) REVERT: A 148 GLU cc_start: 0.4222 (tt0) cc_final: 0.3937 (tt0) REVERT: A 176 LEU cc_start: 0.8742 (tt) cc_final: 0.6910 (tt) REVERT: B 74 TYR cc_start: 0.6653 (m-80) cc_final: 0.6180 (m-10) REVERT: B 106 GLU cc_start: 0.7227 (mm-30) cc_final: 0.7001 (mm-30) REVERT: B 126 PHE cc_start: 0.7356 (m-10) cc_final: 0.6783 (m-80) REVERT: B 142 ASP cc_start: 0.7009 (t70) cc_final: 0.6611 (t0) REVERT: B 148 GLU cc_start: 0.3954 (tt0) cc_final: 0.3645 (tt0) REVERT: B 176 LEU cc_start: 0.8848 (tt) cc_final: 0.6919 (tt) REVERT: B 234 TYR cc_start: 0.8640 (t80) cc_final: 0.8345 (t80) REVERT: B 261 GLN cc_start: 0.7826 (tp40) cc_final: 0.7256 (tp-100) REVERT: B 265 ASN cc_start: 0.7559 (m110) cc_final: 0.7010 (m-40) REVERT: C 74 TYR cc_start: 0.7172 (m-80) cc_final: 0.6710 (m-10) REVERT: C 126 PHE cc_start: 0.7715 (m-10) cc_final: 0.7282 (m-80) REVERT: C 142 ASP cc_start: 0.6784 (t70) cc_final: 0.6338 (t0) REVERT: C 201 LEU cc_start: 0.8604 (tt) cc_final: 0.8266 (tt) REVERT: D 126 PHE cc_start: 0.7386 (m-10) cc_final: 0.7144 (m-80) REVERT: D 142 ASP cc_start: 0.7025 (t70) cc_final: 0.6397 (t70) REVERT: D 176 LEU cc_start: 0.8847 (tt) cc_final: 0.7460 (tt) REVERT: D 261 GLN cc_start: 0.8240 (tp40) cc_final: 0.7946 (tp40) REVERT: E 121 ARG cc_start: 0.7512 (mtp85) cc_final: 0.6898 (mtp85) REVERT: E 176 LEU cc_start: 0.8691 (tt) cc_final: 0.7093 (tt) REVERT: E 194 ASP cc_start: 0.7690 (t0) cc_final: 0.7356 (p0) outliers start: 1 outliers final: 0 residues processed: 357 average time/residue: 0.1387 time to fit residues: 67.9599 Evaluate side-chains 216 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 15 optimal weight: 40.0000 chunk 84 optimal weight: 6.9990 chunk 10 optimal weight: 30.0000 chunk 71 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 130 optimal weight: 0.2980 chunk 80 optimal weight: 40.0000 overall best weight: 6.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN D 118 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.080262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.072742 restraints weight = 49053.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.074322 restraints weight = 29528.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.075454 restraints weight = 19885.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.076220 restraints weight = 14519.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.076749 restraints weight = 11263.002| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12890 Z= 0.165 Angle : 0.766 8.763 17495 Z= 0.398 Chirality : 0.047 0.272 2020 Planarity : 0.004 0.044 2220 Dihedral : 11.774 173.129 1720 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.62 % Favored : 90.06 % Rotamer: Outliers : 0.21 % Allowed : 3.82 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.20), residues: 1580 helix: -0.16 (0.22), residues: 555 sheet: -0.16 (0.25), residues: 385 loop : -2.07 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 34 TYR 0.019 0.002 TYR A 234 PHE 0.013 0.001 PHE C 4 TRP 0.015 0.002 TRP D 72 HIS 0.006 0.002 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (12890) covalent geometry : angle 0.76570 / 0.40 (17495) hydrogen bonds : bond 0.04780 / 3.15 ( 545) hydrogen bonds : angle 5.24886 / 3.68 ( 1545) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 307 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 TYR cc_start: 0.6344 (m-80) cc_final: 0.5901 (m-10) REVERT: B 106 GLU cc_start: 0.7246 (mm-30) cc_final: 0.7038 (mm-30) REVERT: B 148 GLU cc_start: 0.2950 (tt0) cc_final: 0.2501 (tt0) REVERT: B 154 TYR cc_start: 0.7649 (t80) cc_final: 0.7411 (t80) REVERT: B 266 THR cc_start: 0.8653 (m) cc_final: 0.8450 (m) REVERT: C 118 ASN cc_start: 0.7479 (m110) cc_final: 0.7019 (m110) REVERT: C 146 MET cc_start: 0.7859 (ttp) cc_final: 0.7450 (ptm) REVERT: C 208 ASP cc_start: 0.6924 (p0) cc_final: 0.6652 (p0) REVERT: D 261 GLN cc_start: 0.8403 (tp40) cc_final: 0.8149 (tp40) REVERT: D 315 MET cc_start: 0.7957 (ptp) cc_final: 0.7295 (ptp) REVERT: E 194 ASP cc_start: 0.7575 (t0) cc_final: 0.7184 (p0) outliers start: 3 outliers final: 1 residues processed: 310 average time/residue: 0.1113 time to fit residues: 50.4278 Evaluate side-chains 210 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 113 optimal weight: 4.9990 chunk 28 optimal weight: 40.0000 chunk 143 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 26 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 34 optimal weight: 0.0870 chunk 110 optimal weight: 40.0000 chunk 57 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 overall best weight: 5.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN B 15 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.081195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.073757 restraints weight = 49442.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.075342 restraints weight = 30128.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.076419 restraints weight = 20372.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.077187 restraints weight = 14843.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.077750 restraints weight = 11609.728| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.5793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12890 Z= 0.149 Angle : 0.727 8.403 17495 Z= 0.376 Chirality : 0.045 0.199 2020 Planarity : 0.004 0.044 2220 Dihedral : 11.697 173.921 1720 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.92 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.20), residues: 1580 helix: -0.03 (0.23), residues: 535 sheet: 0.38 (0.27), residues: 345 loop : -1.92 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 238 TYR 0.030 0.002 TYR D 234 PHE 0.012 0.001 PHE A 4 TRP 0.014 0.002 TRP C 72 HIS 0.004 0.001 HIS E 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (12890) covalent geometry : angle 0.72735 / 0.38 (17495) hydrogen bonds : bond 0.04262 / 2.78 ( 545) hydrogen bonds : angle 5.13006 / 3.58 ( 1545) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.7565 (m-80) cc_final: 0.7055 (m-10) REVERT: A 148 GLU cc_start: 0.5051 (pt0) cc_final: 0.4702 (pt0) REVERT: A 230 LYS cc_start: 0.7980 (mmtm) cc_final: 0.7365 (pttm) REVERT: B 48 TYR cc_start: 0.8837 (m-80) cc_final: 0.8550 (m-80) REVERT: D 230 LYS cc_start: 0.7424 (mmtm) cc_final: 0.6841 (mmtm) REVERT: D 261 GLN cc_start: 0.8363 (tp40) cc_final: 0.8075 (tp40) REVERT: D 315 MET cc_start: 0.7867 (ptp) cc_final: 0.7360 (ptp) REVERT: E 176 LEU cc_start: 0.9149 (tt) cc_final: 0.8051 (tt) REVERT: E 315 MET cc_start: 0.7657 (ptp) cc_final: 0.7402 (ptm) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1100 time to fit residues: 43.3929 Evaluate side-chains 203 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 149 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 104 optimal weight: 0.0970 chunk 87 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 126 optimal weight: 9.9990 chunk 15 optimal weight: 0.0770 chunk 150 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.9538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 ASN B 158 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.091077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.083820 restraints weight = 49111.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.085462 restraints weight = 29535.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.086619 restraints weight = 19681.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.087408 restraints weight = 14053.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.087982 restraints weight = 10652.893| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.6298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12890 Z= 0.121 Angle : 0.687 8.219 17495 Z= 0.353 Chirality : 0.044 0.220 2020 Planarity : 0.005 0.081 2220 Dihedral : 11.405 179.682 1720 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.42 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.20), residues: 1580 helix: -0.19 (0.22), residues: 585 sheet: 0.58 (0.27), residues: 345 loop : -2.17 (0.21), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 238 TYR 0.017 0.002 TYR D 234 PHE 0.010 0.001 PHE C 138 TRP 0.014 0.002 TRP D 72 HIS 0.003 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (12890) covalent geometry : angle 0.68653 / 0.35 (17495) hydrogen bonds : bond 0.03926 / 2.58 ( 545) hydrogen bonds : angle 4.75292 / 3.32 ( 1545) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.7909 (mmtm) cc_final: 0.7330 (pttm) REVERT: A 315 MET cc_start: 0.8263 (mtp) cc_final: 0.8023 (mtm) REVERT: B 148 GLU cc_start: 0.3274 (tt0) cc_final: 0.2504 (tt0) REVERT: B 178 ILE cc_start: 0.8709 (mm) cc_final: 0.8433 (mm) REVERT: C 208 ASP cc_start: 0.6632 (p0) cc_final: 0.6392 (p0) REVERT: D 74 TYR cc_start: 0.6785 (m-80) cc_final: 0.6509 (m-10) REVERT: D 106 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7123 (mm-30) REVERT: D 194 ASP cc_start: 0.7721 (p0) cc_final: 0.7362 (p0) REVERT: D 230 LYS cc_start: 0.7470 (mmtm) cc_final: 0.6984 (mmtm) REVERT: D 261 GLN cc_start: 0.8324 (tp40) cc_final: 0.7934 (tp40) REVERT: D 262 ARG cc_start: 0.7752 (ptp-110) cc_final: 0.7542 (ptp-110) REVERT: D 315 MET cc_start: 0.7701 (ptp) cc_final: 0.7224 (ptp) REVERT: E 194 ASP cc_start: 0.6918 (p0) cc_final: 0.6674 (p0) REVERT: E 315 MET cc_start: 0.7525 (ptp) cc_final: 0.7082 (ptm) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.1113 time to fit residues: 48.3953 Evaluate side-chains 213 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 83 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 135 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 15 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 79 optimal weight: 30.0000 chunk 121 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 overall best weight: 6.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 ASN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.081653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.074300 restraints weight = 49458.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.075869 restraints weight = 29833.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.076983 restraints weight = 20094.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.077770 restraints weight = 14585.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.078299 restraints weight = 11213.950| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12890 Z= 0.165 Angle : 0.714 8.421 17495 Z= 0.372 Chirality : 0.045 0.216 2020 Planarity : 0.006 0.114 2220 Dihedral : 11.653 175.970 1720 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.99 % Favored : 90.70 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.20), residues: 1580 helix: -0.04 (0.22), residues: 555 sheet: 0.65 (0.27), residues: 325 loop : -2.03 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 238 TYR 0.020 0.002 TYR A 107 PHE 0.013 0.002 PHE E 4 TRP 0.027 0.002 TRP E 16 HIS 0.005 0.001 HIS E 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (12890) covalent geometry : angle 0.71419 / 0.37 (17495) hydrogen bonds : bond 0.04214 / 2.78 ( 545) hydrogen bonds : angle 4.95083 / 3.43 ( 1545) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.7920 (mmtm) cc_final: 0.7313 (pttm) REVERT: B 106 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6367 (mm-30) REVERT: B 168 ILE cc_start: 0.8797 (mp) cc_final: 0.8347 (tp) REVERT: B 178 ILE cc_start: 0.8755 (mm) cc_final: 0.8382 (mm) REVERT: B 179 SER cc_start: 0.8601 (p) cc_final: 0.8363 (p) REVERT: C 74 TYR cc_start: 0.6360 (m-10) cc_final: 0.5693 (m-10) REVERT: C 106 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6807 (tp30) REVERT: C 154 TYR cc_start: 0.7653 (t80) cc_final: 0.7216 (t80) REVERT: D 230 LYS cc_start: 0.7518 (mmtm) cc_final: 0.6923 (mmtm) REVERT: D 261 GLN cc_start: 0.8398 (tp40) cc_final: 0.8193 (tp40) REVERT: D 265 ASN cc_start: 0.8305 (m-40) cc_final: 0.7994 (m-40) REVERT: D 315 MET cc_start: 0.7813 (ptp) cc_final: 0.7231 (ptp) REVERT: E 146 MET cc_start: 0.8243 (ttt) cc_final: 0.7666 (ttt) REVERT: E 315 MET cc_start: 0.7706 (ptp) cc_final: 0.6995 (ptm) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1057 time to fit residues: 42.6289 Evaluate side-chains 210 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 129 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 107 optimal weight: 0.0470 chunk 36 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 62 optimal weight: 30.0000 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 ASN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.088730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.081595 restraints weight = 49114.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.083140 restraints weight = 29877.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.084243 restraints weight = 20170.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.085022 restraints weight = 14573.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.085609 restraints weight = 11176.069| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.6667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12890 Z= 0.143 Angle : 0.695 8.378 17495 Z= 0.361 Chirality : 0.044 0.218 2020 Planarity : 0.005 0.078 2220 Dihedral : 11.562 178.742 1720 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.24 % Favored : 90.63 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.20), residues: 1580 helix: -0.09 (0.21), residues: 590 sheet: 0.71 (0.27), residues: 325 loop : -1.94 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 238 TYR 0.022 0.002 TYR A 107 PHE 0.013 0.001 PHE D 270 TRP 0.028 0.002 TRP E 16 HIS 0.004 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (12890) covalent geometry : angle 0.69538 / 0.36 (17495) hydrogen bonds : bond 0.04071 / 2.66 ( 545) hydrogen bonds : angle 4.95640 / 3.43 ( 1545) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.7164 (m-10) cc_final: 0.6377 (m-10) REVERT: A 178 ILE cc_start: 0.8562 (mm) cc_final: 0.8195 (mm) REVERT: A 230 LYS cc_start: 0.7858 (mmtm) cc_final: 0.7283 (pttm) REVERT: B 168 ILE cc_start: 0.8808 (mp) cc_final: 0.8339 (tp) REVERT: B 178 ILE cc_start: 0.8751 (mm) cc_final: 0.8397 (mm) REVERT: B 179 SER cc_start: 0.8553 (p) cc_final: 0.8293 (p) REVERT: C 74 TYR cc_start: 0.6579 (m-10) cc_final: 0.6286 (m-10) REVERT: C 106 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6819 (mm-30) REVERT: C 208 ASP cc_start: 0.6713 (p0) cc_final: 0.6420 (p0) REVERT: D 43 LYS cc_start: 0.7750 (tptt) cc_final: 0.7491 (tptt) REVERT: D 230 LYS cc_start: 0.7579 (mmtm) cc_final: 0.7156 (mmtm) REVERT: D 261 GLN cc_start: 0.8349 (tp40) cc_final: 0.8133 (tp40) REVERT: D 265 ASN cc_start: 0.8295 (m-40) cc_final: 0.7976 (m-40) REVERT: D 315 MET cc_start: 0.7784 (ptp) cc_final: 0.7167 (ptp) REVERT: E 223 ASP cc_start: 0.8242 (t70) cc_final: 0.7875 (t70) REVERT: E 230 LYS cc_start: 0.7783 (mmtm) cc_final: 0.7324 (mmtm) REVERT: E 315 MET cc_start: 0.7822 (ptp) cc_final: 0.7118 (ptm) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1190 time to fit residues: 46.0126 Evaluate side-chains 202 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 112 optimal weight: 40.0000 chunk 70 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 ASN B 158 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.088125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.080841 restraints weight = 49069.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.082443 restraints weight = 29588.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.083537 restraints weight = 19841.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.084309 restraints weight = 14339.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.084840 restraints weight = 11020.056| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.6837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12890 Z= 0.153 Angle : 0.691 8.058 17495 Z= 0.361 Chirality : 0.045 0.252 2020 Planarity : 0.005 0.053 2220 Dihedral : 11.661 178.882 1720 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.11 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.20), residues: 1580 helix: -0.08 (0.21), residues: 590 sheet: 0.62 (0.27), residues: 325 loop : -1.90 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 238 TYR 0.033 0.002 TYR A 107 PHE 0.014 0.001 PHE D 138 TRP 0.015 0.002 TRP D 72 HIS 0.005 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (12890) covalent geometry : angle 0.69115 / 0.36 (17495) hydrogen bonds : bond 0.04202 / 2.77 ( 545) hydrogen bonds : angle 4.96047 / 3.43 ( 1545) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.7063 (m-10) cc_final: 0.6734 (m-10) REVERT: A 178 ILE cc_start: 0.8606 (mm) cc_final: 0.8303 (mm) REVERT: A 230 LYS cc_start: 0.7849 (mmtm) cc_final: 0.7327 (pttm) REVERT: B 48 TYR cc_start: 0.8864 (m-80) cc_final: 0.8654 (m-80) REVERT: B 168 ILE cc_start: 0.8764 (mp) cc_final: 0.8374 (tp) REVERT: B 178 ILE cc_start: 0.8789 (mm) cc_final: 0.8412 (mm) REVERT: B 179 SER cc_start: 0.8585 (p) cc_final: 0.8374 (p) REVERT: C 34 ARG cc_start: 0.8473 (mtt-85) cc_final: 0.8100 (mtt-85) REVERT: C 74 TYR cc_start: 0.6674 (m-10) cc_final: 0.6299 (m-10) REVERT: C 106 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6724 (mm-30) REVERT: C 208 ASP cc_start: 0.6786 (p0) cc_final: 0.6555 (p0) REVERT: D 230 LYS cc_start: 0.7615 (mmtm) cc_final: 0.7275 (mmtm) REVERT: D 261 GLN cc_start: 0.8460 (tp40) cc_final: 0.8123 (tp40) REVERT: D 265 ASN cc_start: 0.8301 (m-40) cc_final: 0.7945 (m-40) REVERT: D 315 MET cc_start: 0.7879 (ptp) cc_final: 0.7282 (ptp) REVERT: E 34 ARG cc_start: 0.8444 (mtm180) cc_final: 0.8181 (mtt90) REVERT: E 120 GLU cc_start: 0.7057 (tp30) cc_final: 0.5993 (tp30) REVERT: E 223 ASP cc_start: 0.8213 (t70) cc_final: 0.7860 (t70) REVERT: E 229 ARG cc_start: 0.7678 (mtp85) cc_final: 0.7315 (mtm180) REVERT: E 315 MET cc_start: 0.7861 (ptp) cc_final: 0.7177 (ptm) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.1116 time to fit residues: 42.6711 Evaluate side-chains 203 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 123 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 41 optimal weight: 30.0000 chunk 28 optimal weight: 0.0370 chunk 144 optimal weight: 6.9990 chunk 8 optimal weight: 30.0000 chunk 109 optimal weight: 20.0000 chunk 18 optimal weight: 30.0000 chunk 86 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 overall best weight: 5.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 ASN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.088992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.081850 restraints weight = 49669.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.083389 restraints weight = 30370.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.084455 restraints weight = 20445.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.085222 restraints weight = 14863.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.085769 restraints weight = 11434.614| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.7013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12890 Z= 0.138 Angle : 0.688 7.953 17495 Z= 0.359 Chirality : 0.045 0.258 2020 Planarity : 0.005 0.050 2220 Dihedral : 11.583 179.389 1720 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.11 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.20), residues: 1580 helix: 0.04 (0.21), residues: 590 sheet: 0.56 (0.27), residues: 325 loop : -1.88 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 238 TYR 0.025 0.002 TYR E 107 PHE 0.015 0.001 PHE E 138 TRP 0.016 0.002 TRP B 72 HIS 0.004 0.001 HIS E 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (12890) covalent geometry : angle 0.68828 / 0.36 (17495) hydrogen bonds : bond 0.04079 / 2.69 ( 545) hydrogen bonds : angle 4.90914 / 3.39 ( 1545) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ILE cc_start: 0.8593 (mm) cc_final: 0.8318 (mm) REVERT: A 208 ASP cc_start: 0.6894 (p0) cc_final: 0.6630 (p0) REVERT: A 230 LYS cc_start: 0.7855 (mmtm) cc_final: 0.7358 (pttm) REVERT: A 261 GLN cc_start: 0.7862 (mt0) cc_final: 0.7469 (mt0) REVERT: B 48 TYR cc_start: 0.8832 (m-80) cc_final: 0.8550 (m-80) REVERT: B 168 ILE cc_start: 0.8723 (mp) cc_final: 0.8419 (tp) REVERT: B 179 SER cc_start: 0.8697 (p) cc_final: 0.8354 (p) REVERT: C 74 TYR cc_start: 0.6776 (m-10) cc_final: 0.6502 (m-10) REVERT: C 106 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6671 (mm-30) REVERT: D 74 TYR cc_start: 0.6758 (m-10) cc_final: 0.6517 (m-10) REVERT: D 106 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6733 (mm-30) REVERT: D 120 GLU cc_start: 0.7224 (tp30) cc_final: 0.6495 (tp30) REVERT: D 230 LYS cc_start: 0.7600 (mmtm) cc_final: 0.7281 (mmtm) REVERT: D 261 GLN cc_start: 0.8444 (tp40) cc_final: 0.8094 (tp40) REVERT: D 265 ASN cc_start: 0.8317 (m-40) cc_final: 0.7831 (m-40) REVERT: D 315 MET cc_start: 0.7882 (ptp) cc_final: 0.7375 (ptp) REVERT: E 34 ARG cc_start: 0.8431 (mtm180) cc_final: 0.8131 (mtt90) REVERT: E 120 GLU cc_start: 0.6987 (tp30) cc_final: 0.6049 (tp30) REVERT: E 178 ILE cc_start: 0.8683 (mm) cc_final: 0.8335 (mm) REVERT: E 223 ASP cc_start: 0.8000 (t70) cc_final: 0.7721 (t70) REVERT: E 229 ARG cc_start: 0.7516 (mtp85) cc_final: 0.6920 (ptp-170) REVERT: E 315 MET cc_start: 0.7763 (ptp) cc_final: 0.7095 (ptm) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.1039 time to fit residues: 40.9854 Evaluate side-chains 199 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 146 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 13 optimal weight: 40.0000 chunk 14 optimal weight: 5.9990 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 HIS ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN D 228 HIS E 228 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.082687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.075367 restraints weight = 49452.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.076878 restraints weight = 30097.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.077923 restraints weight = 20375.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.078667 restraints weight = 14989.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.079192 restraints weight = 11712.447| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.7107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12890 Z= 0.157 Angle : 0.702 8.140 17495 Z= 0.367 Chirality : 0.046 0.269 2020 Planarity : 0.005 0.050 2220 Dihedral : 11.579 179.161 1720 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.07 % Allowed : 0.21 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.20), residues: 1580 helix: -0.04 (0.21), residues: 595 sheet: 0.52 (0.27), residues: 325 loop : -1.90 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 238 TYR 0.031 0.002 TYR E 107 PHE 0.017 0.002 PHE D 270 TRP 0.018 0.002 TRP B 72 HIS 0.005 0.001 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (12890) covalent geometry : angle 0.70181 / 0.37 (17495) hydrogen bonds : bond 0.04206 / 2.77 ( 545) hydrogen bonds : angle 4.95451 / 3.42 ( 1545) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ILE cc_start: 0.8538 (mm) cc_final: 0.8326 (mm) REVERT: A 230 LYS cc_start: 0.7781 (mmtm) cc_final: 0.7354 (pttm) REVERT: A 261 GLN cc_start: 0.7788 (mt0) cc_final: 0.7159 (mt0) REVERT: B 48 TYR cc_start: 0.8813 (m-80) cc_final: 0.8500 (m-80) REVERT: B 168 ILE cc_start: 0.8739 (mp) cc_final: 0.8367 (mm) REVERT: C 74 TYR cc_start: 0.6619 (m-10) cc_final: 0.6334 (m-10) REVERT: C 106 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6734 (mm-30) REVERT: C 223 ASP cc_start: 0.7793 (t0) cc_final: 0.7506 (t70) REVERT: D 74 TYR cc_start: 0.6720 (m-10) cc_final: 0.6479 (m-10) REVERT: D 106 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6690 (mm-30) REVERT: D 315 MET cc_start: 0.7744 (ptp) cc_final: 0.7050 (ptp) REVERT: E 1 MET cc_start: 0.5467 (ttt) cc_final: 0.5233 (ptp) REVERT: E 34 ARG cc_start: 0.8440 (mtm180) cc_final: 0.8118 (mtt90) REVERT: E 106 GLU cc_start: 0.7160 (tp30) cc_final: 0.6960 (tp30) REVERT: E 120 GLU cc_start: 0.7062 (tp30) cc_final: 0.6097 (tp30) REVERT: E 223 ASP cc_start: 0.8101 (t70) cc_final: 0.7882 (t70) REVERT: E 229 ARG cc_start: 0.7569 (mtp85) cc_final: 0.6878 (ptp-170) REVERT: E 315 MET cc_start: 0.7791 (ptp) cc_final: 0.7177 (ptm) outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.1095 time to fit residues: 39.5942 Evaluate side-chains 190 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 41 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 66 optimal weight: 40.0000 chunk 36 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 80 optimal weight: 30.0000 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 HIS ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.091047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.083680 restraints weight = 49419.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.085293 restraints weight = 29877.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.086382 restraints weight = 20043.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.087184 restraints weight = 14563.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.087737 restraints weight = 11149.385| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.7336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12890 Z= 0.120 Angle : 0.663 7.873 17495 Z= 0.342 Chirality : 0.045 0.256 2020 Planarity : 0.005 0.049 2220 Dihedral : 11.349 178.425 1720 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.20), residues: 1580 helix: 0.19 (0.22), residues: 595 sheet: 0.59 (0.27), residues: 325 loop : -1.83 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 238 TYR 0.019 0.002 TYR B 107 PHE 0.024 0.002 PHE D 270 TRP 0.017 0.002 TRP B 72 HIS 0.004 0.001 HIS E 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (12890) covalent geometry : angle 0.66267 / 0.34 (17495) hydrogen bonds : bond 0.03835 / 2.51 ( 545) hydrogen bonds : angle 4.78457 / 3.31 ( 1545) =============================================================================== Job complete usr+sys time: 1883.56 seconds wall clock time: 33 minutes 47.71 seconds (2027.71 seconds total)