Starting phenix.real_space_refine on Thu Sep 18 00:18:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5aey_2850/09_2025/5aey_2850.cif Found real_map, /net/cci-nas-00/data/ceres_data/5aey_2850/09_2025/5aey_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5aey_2850/09_2025/5aey_2850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5aey_2850/09_2025/5aey_2850.map" model { file = "/net/cci-nas-00/data/ceres_data/5aey_2850/09_2025/5aey_2850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5aey_2850/09_2025/5aey_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-2.0-5805/lib/python3.9/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: 3.13, per 1000 atoms: 0.25 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: 0.81 Conformation dependent library (CDL) restraints added in 570.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.46 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: 2.09 Time building geometry restraints manager: 1.11 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: 7054 30.21 - 60.41: 731 60.41 - 90.62: 65 90.62 - 120.83: 0 120.83 - 151.03: 5 Dihedral angle restraints: 7855 sinusoidal: 3230 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 7852 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: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.610 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 22.055 151.032 4875 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 aren 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 covalent geometry : bond 0.01143 (12890) covalent geometry : angle 1.71384 (17495) hydrogen bonds : bond 0.20531 ( 545) hydrogen bonds : angle 7.74110 ( 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 : 0.517 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: 0.8362 (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: 0.6723 (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: 0.8212 (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: 0.6880 (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: 0.5350 (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: 0.8435 (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: 0.8694 (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: 0.8053 (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: 0.1387 time to fit residues: 109.2311 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 : 0.631 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3344 r_free = 0.3344 target = 0.085746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.077996 restraints weight = 48314.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.079660 restraints weight = 29387.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.080774 restraints weight = 19984.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.081494 restraints weight = 14660.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.081998 restraints weight = 11442.452| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12890 Z= 0.181 Angle : 0.806 8.220 17495 Z= 0.419 Chirality : 0.047 0.213 2020 Planarity : 0.005 0.073 2220 Dihedral : 13.539 169.100 1860 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.25 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 aren not related in a simple way. whole: -1.79 (0.19), residues: 1580 helix: -0.67 (0.20), residues: 595 sheet: -0.24 (0.27), residues: 355 loop : -2.19 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 297 TYR 0.021 0.002 TYR B 107 PHE 0.025 0.002 PHE A 4 TRP 0.013 0.002 TRP B 72 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00397 (12890) covalent geometry : angle 0.80569 (17495) hydrogen bonds : bond 0.04896 ( 545) hydrogen bonds : angle 5.69568 ( 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 361 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 0.517 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: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.7475 (m-80) cc_final: 0.7071 (m-10) REVERT: A 126 PHE cc_start: 0.7645 (m-10) cc_final: 0.7346 (m-80) REVERT: A 146 MET cc_start: 0.7140 (mtp) cc_final: 0.6756 (mtp) REVERT: A 148 GLU cc_start: 0.4213 (tt0) cc_final: 0.3934 (tt0) REVERT: A 176 LEU cc_start: 0.8754 (tt) cc_final: 0.6920 (tt) REVERT: B 74 TYR cc_start: 0.6626 (m-80) cc_final: 0.6210 (m-10) REVERT: B 106 GLU cc_start: 0.7213 (mm-30) cc_final: 0.7000 (mm-30) REVERT: B 126 PHE cc_start: 0.7417 (m-10) cc_final: 0.6801 (m-80) REVERT: B 142 ASP cc_start: 0.7010 (t70) cc_final: 0.6604 (t0) REVERT: B 148 GLU cc_start: 0.3922 (tt0) cc_final: 0.3634 (tt0) REVERT: B 176 LEU cc_start: 0.8855 (tt) cc_final: 0.6901 (tt) REVERT: B 234 TYR cc_start: 0.8604 (t80) cc_final: 0.8312 (t80) REVERT: B 261 GLN cc_start: 0.7871 (tp40) cc_final: 0.7290 (tp-100) REVERT: B 265 ASN cc_start: 0.7574 (m110) cc_final: 0.6998 (m-40) REVERT: B 286 ILE cc_start: 0.8811 (pt) cc_final: 0.8589 (mp) REVERT: C 74 TYR cc_start: 0.7120 (m-80) cc_final: 0.6695 (m-10) REVERT: C 126 PHE cc_start: 0.7697 (m-10) cc_final: 0.7314 (m-80) REVERT: C 142 ASP cc_start: 0.6838 (t70) cc_final: 0.6356 (t0) REVERT: C 201 LEU cc_start: 0.8582 (tt) cc_final: 0.8240 (tt) REVERT: D 126 PHE cc_start: 0.7441 (m-10) cc_final: 0.7212 (m-80) REVERT: D 142 ASP cc_start: 0.7069 (t70) cc_final: 0.6435 (t70) REVERT: D 261 GLN cc_start: 0.8244 (tp40) cc_final: 0.7957 (tp40) REVERT: E 176 LEU cc_start: 0.8687 (tt) cc_final: 0.7141 (tt) REVERT: E 194 ASP cc_start: 0.7696 (t0) cc_final: 0.7370 (p0) REVERT: E 315 MET cc_start: 0.7515 (mtm) cc_final: 0.7007 (ptp) outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.1480 time to fit residues: 72.1932 Evaluate side-chains 217 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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: 30.0000 chunk 142 optimal weight: 30.0000 chunk 15 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 10 optimal weight: 0.0010 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 130 optimal weight: 0.0060 chunk 80 optimal weight: 40.0000 overall best weight: 4.2010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.081994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.074348 restraints weight = 48573.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.075939 restraints weight = 29315.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.077068 restraints weight = 19779.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.077841 restraints weight = 14482.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.078391 restraints weight = 11252.549| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12890 Z= 0.145 Angle : 0.745 8.539 17495 Z= 0.385 Chirality : 0.046 0.264 2020 Planarity : 0.004 0.044 2220 Dihedral : 13.326 176.196 1860 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.49 % Favored : 90.19 % Rotamer: Outliers : 0.21 % Allowed : 3.25 % Favored : 96.54 % 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 aren not related in a simple way. whole: -1.35 (0.20), residues: 1580 helix: -0.11 (0.22), residues: 555 sheet: -0.11 (0.25), residues: 385 loop : -2.06 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 34 TYR 0.017 0.002 TYR A 234 PHE 0.011 0.001 PHE A 4 TRP 0.014 0.002 TRP D 72 HIS 0.004 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00315 (12890) covalent geometry : angle 0.74473 (17495) hydrogen bonds : bond 0.04538 ( 545) hydrogen bonds : angle 5.14763 ( 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 322 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 319 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7661 (m-30) cc_final: 0.7460 (m-30) REVERT: B 74 TYR cc_start: 0.6375 (m-80) cc_final: 0.5982 (m-10) REVERT: B 148 GLU cc_start: 0.2827 (tt0) cc_final: 0.2456 (tt0) REVERT: B 154 TYR cc_start: 0.7770 (t80) cc_final: 0.7433 (t80) REVERT: B 197 LEU cc_start: 0.7985 (mp) cc_final: 0.7521 (mp) REVERT: B 266 THR cc_start: 0.8639 (m) cc_final: 0.8413 (m) REVERT: C 118 ASN cc_start: 0.7401 (m110) cc_final: 0.6945 (m110) REVERT: C 146 MET cc_start: 0.7723 (ttp) cc_final: 0.7479 (ptm) REVERT: C 208 ASP cc_start: 0.6913 (p0) cc_final: 0.6712 (p0) REVERT: D 146 MET cc_start: 0.6954 (mtp) cc_final: 0.6192 (mtp) REVERT: D 261 GLN cc_start: 0.8415 (tp40) cc_final: 0.8120 (tp40) REVERT: D 315 MET cc_start: 0.7868 (ptp) cc_final: 0.7167 (ptp) REVERT: E 116 THR cc_start: 0.8715 (p) cc_final: 0.8487 (p) REVERT: E 121 ARG cc_start: 0.7710 (mtp-110) cc_final: 0.7332 (mtp-110) REVERT: E 146 MET cc_start: 0.8336 (ttp) cc_final: 0.7180 (ttm) REVERT: E 176 LEU cc_start: 0.8950 (tt) cc_final: 0.7598 (tt) REVERT: E 194 ASP cc_start: 0.7635 (t0) cc_final: 0.7247 (p0) outliers start: 3 outliers final: 0 residues processed: 322 average time/residue: 0.1151 time to fit residues: 53.4780 Evaluate side-chains 211 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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: 7.9990 chunk 28 optimal weight: 6.9990 chunk 143 optimal weight: 40.0000 chunk 153 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 91 optimal weight: 0.1980 chunk 34 optimal weight: 30.0000 chunk 110 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 147 optimal weight: 5.9990 overall best weight: 5.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 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 ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3338 r_free = 0.3338 target = 0.087563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.080615 restraints weight = 50470.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.082152 restraints weight = 30520.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.083229 restraints weight = 20466.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.083950 restraints weight = 14699.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.084521 restraints weight = 11267.517| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12890 Z= 0.158 Angle : 0.735 8.958 17495 Z= 0.379 Chirality : 0.045 0.178 2020 Planarity : 0.004 0.044 2220 Dihedral : 13.247 179.556 1860 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.92 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.20), residues: 1580 helix: -0.02 (0.22), residues: 535 sheet: 0.48 (0.27), residues: 345 loop : -1.96 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 34 TYR 0.031 0.002 TYR D 234 PHE 0.012 0.001 PHE A 4 TRP 0.016 0.002 TRP D 72 HIS 0.004 0.001 HIS E 293 Details of bonding type rmsd covalent geometry : bond 0.00352 (12890) covalent geometry : angle 0.73549 (17495) hydrogen bonds : bond 0.04338 ( 545) hydrogen bonds : angle 5.13400 ( 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 277 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.570 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 34 ARG cc_start: 0.6955 (mtp180) cc_final: 0.6512 (ttm110) REVERT: B 48 TYR cc_start: 0.8867 (m-80) cc_final: 0.8472 (m-80) REVERT: B 74 TYR cc_start: 0.6504 (m-80) cc_final: 0.6283 (m-10) REVERT: B 106 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6739 (mm-30) REVERT: B 315 MET cc_start: 0.7640 (ptp) cc_final: 0.6830 (ptp) REVERT: C 162 GLU cc_start: 0.7787 (pp20) cc_final: 0.7566 (tp30) REVERT: D 74 TYR cc_start: 0.6715 (m-10) cc_final: 0.6502 (m-10) REVERT: D 106 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7173 (mm-30) REVERT: D 230 LYS cc_start: 0.7508 (mmtm) cc_final: 0.7000 (mmtm) REVERT: D 261 GLN cc_start: 0.8315 (tp40) cc_final: 0.8038 (tp40) REVERT: D 315 MET cc_start: 0.7760 (ptp) cc_final: 0.7317 (ptp) REVERT: E 176 LEU cc_start: 0.9097 (tt) cc_final: 0.8199 (tt) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.1189 time to fit residues: 47.7941 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 : 0.689 ------------------------------------------------------------------------------- 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: 30.0000 chunk 16 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN A 265 ASN B 158 GLN C 17 GLN D 78 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.086082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.079033 restraints weight = 50871.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.080615 restraints weight = 30351.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.081693 restraints weight = 20192.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.082459 restraints weight = 14432.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.082988 restraints weight = 10901.200| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.6094 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= 0.187 Angle : 0.742 8.978 17495 Z= 0.386 Chirality : 0.045 0.243 2020 Planarity : 0.005 0.078 2220 Dihedral : 13.278 179.509 1860 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.24 % Favored : 90.44 % Rotamer: Outliers : 0.07 % Allowed : 3.75 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.20), residues: 1580 helix: -0.16 (0.22), residues: 555 sheet: 0.37 (0.27), residues: 345 loop : -2.19 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 34 TYR 0.029 0.002 TYR A 107 PHE 0.014 0.002 PHE D 4 TRP 0.019 0.002 TRP C 16 HIS 0.006 0.002 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00419 (12890) covalent geometry : angle 0.74183 (17495) hydrogen bonds : bond 0.04497 ( 545) hydrogen bonds : angle 5.15745 ( 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 259 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 0.523 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 74 TYR cc_start: 0.6901 (m-10) cc_final: 0.6259 (m-10) REVERT: A 148 GLU cc_start: 0.5113 (pt0) cc_final: 0.4746 (pt0) REVERT: A 315 MET cc_start: 0.7886 (mtm) cc_final: 0.7521 (ptp) REVERT: B 48 TYR cc_start: 0.8817 (m-80) cc_final: 0.8469 (m-80) REVERT: B 178 ILE cc_start: 0.8749 (mm) cc_final: 0.8477 (mm) REVERT: C 208 ASP cc_start: 0.6781 (p0) cc_final: 0.6565 (p0) REVERT: D 182 MET cc_start: 0.8169 (ptt) cc_final: 0.7764 (ptm) REVERT: D 265 ASN cc_start: 0.8347 (m-40) cc_final: 0.8078 (m-40) REVERT: D 315 MET cc_start: 0.7824 (ptp) cc_final: 0.7282 (ptp) REVERT: E 121 ARG cc_start: 0.7799 (mtp-110) cc_final: 0.7372 (mtp-110) REVERT: E 315 MET cc_start: 0.7948 (ptp) cc_final: 0.7276 (ptp) outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.1164 time to fit residues: 43.8000 Evaluate side-chains 189 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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: 6.9990 chunk 48 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 15 optimal weight: 5.9990 chunk 99 optimal weight: 40.0000 chunk 79 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 overall best weight: 9.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 118 ASN D 51 ASN D 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.079431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.072307 restraints weight = 50653.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.073817 restraints weight = 30389.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.074944 restraints weight = 20414.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.075682 restraints weight = 14682.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.076208 restraints weight = 11222.296| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.6290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12890 Z= 0.202 Angle : 0.757 8.245 17495 Z= 0.396 Chirality : 0.046 0.208 2020 Planarity : 0.006 0.111 2220 Dihedral : 13.324 179.243 1860 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.49 % Favored : 90.19 % Rotamer: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.20), residues: 1580 helix: -0.26 (0.21), residues: 555 sheet: 0.36 (0.27), residues: 345 loop : -2.17 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 262 TYR 0.042 0.003 TYR A 107 PHE 0.013 0.002 PHE A 4 TRP 0.015 0.002 TRP D 72 HIS 0.006 0.002 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00449 (12890) covalent geometry : angle 0.75669 (17495) hydrogen bonds : bond 0.04594 ( 545) hydrogen bonds : angle 5.27810 ( 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 251 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.7942 (mmtm) cc_final: 0.7610 (mppt) REVERT: B 48 TYR cc_start: 0.8821 (m-80) cc_final: 0.8460 (m-80) REVERT: B 74 TYR cc_start: 0.6393 (m-10) cc_final: 0.6125 (m-10) REVERT: B 178 ILE cc_start: 0.8827 (mm) cc_final: 0.8575 (mm) REVERT: C 176 LEU cc_start: 0.8304 (tt) cc_final: 0.8022 (tt) REVERT: D 182 MET cc_start: 0.8203 (ptt) cc_final: 0.7774 (ptm) REVERT: D 277 MET cc_start: 0.8210 (tpp) cc_final: 0.8007 (tpt) REVERT: D 315 MET cc_start: 0.7938 (ptp) cc_final: 0.7332 (ptp) REVERT: E 194 ASP cc_start: 0.7620 (p0) cc_final: 0.7246 (p0) REVERT: E 230 LYS cc_start: 0.7819 (mmtm) cc_final: 0.7537 (mmtm) REVERT: E 315 MET cc_start: 0.7903 (ptp) cc_final: 0.7559 (ptm) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.1219 time to fit residues: 44.3033 Evaluate side-chains 194 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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: 6.9990 chunk 24 optimal weight: 7.9990 chunk 66 optimal weight: 40.0000 chunk 38 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 36 optimal weight: 30.0000 chunk 3 optimal weight: 8.9990 chunk 99 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 14 optimal weight: 0.0870 chunk 62 optimal weight: 30.0000 overall best weight: 5.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN D 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.081569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.074213 restraints weight = 49126.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.075775 restraints weight = 29729.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.076868 restraints weight = 20062.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.077617 restraints weight = 14582.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.078154 restraints weight = 11281.823| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.6596 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= 0.151 Angle : 0.717 8.057 17495 Z= 0.375 Chirality : 0.045 0.191 2020 Planarity : 0.005 0.061 2220 Dihedral : 13.043 179.242 1860 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.30 % Favored : 90.51 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.20), residues: 1580 helix: -0.04 (0.22), residues: 555 sheet: 0.42 (0.27), residues: 345 loop : -2.04 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 229 TYR 0.029 0.002 TYR A 107 PHE 0.014 0.001 PHE A 138 TRP 0.014 0.002 TRP C 72 HIS 0.004 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00335 (12890) covalent geometry : angle 0.71741 (17495) hydrogen bonds : bond 0.04436 ( 545) hydrogen bonds : angle 5.06349 ( 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 266 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.7240 (m-10) cc_final: 0.6407 (m-10) REVERT: A 208 ASP cc_start: 0.6930 (p0) cc_final: 0.6715 (p0) REVERT: A 230 LYS cc_start: 0.7893 (mmtm) cc_final: 0.7431 (mmtm) REVERT: A 315 MET cc_start: 0.7827 (ptp) cc_final: 0.7589 (ptp) REVERT: B 48 TYR cc_start: 0.8782 (m-80) cc_final: 0.8437 (m-80) REVERT: B 54 GLN cc_start: 0.8641 (pt0) cc_final: 0.8310 (pt0) REVERT: B 121 ARG cc_start: 0.7481 (ptp-170) cc_final: 0.7098 (ptm160) REVERT: B 168 ILE cc_start: 0.8791 (mp) cc_final: 0.8368 (tp) REVERT: B 178 ILE cc_start: 0.8785 (mm) cc_final: 0.8408 (mm) REVERT: B 179 SER cc_start: 0.8585 (p) cc_final: 0.8357 (p) REVERT: C 74 TYR cc_start: 0.6507 (m-10) cc_final: 0.6213 (m-10) REVERT: C 106 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7468 (mm-30) REVERT: C 208 ASP cc_start: 0.6828 (p0) cc_final: 0.6601 (p0) REVERT: D 74 TYR cc_start: 0.6685 (m-10) cc_final: 0.6372 (m-10) REVERT: D 182 MET cc_start: 0.8104 (ptt) cc_final: 0.7615 (ptm) REVERT: D 234 TYR cc_start: 0.7921 (t80) cc_final: 0.7315 (t80) REVERT: D 315 MET cc_start: 0.7725 (ptp) cc_final: 0.7261 (ptp) REVERT: E 120 GLU cc_start: 0.7054 (tp30) cc_final: 0.6360 (tp30) REVERT: E 194 ASP cc_start: 0.7633 (p0) cc_final: 0.7199 (p0) REVERT: E 229 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7454 (mtm180) REVERT: E 315 MET cc_start: 0.7811 (ptp) cc_final: 0.7453 (ptm) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1219 time to fit residues: 46.6494 Evaluate side-chains 192 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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: 7.9990 chunk 70 optimal weight: 30.0000 chunk 71 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 12 optimal weight: 0.5980 chunk 116 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 GLN ** 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 = 0.3385 r_free = 0.3385 target = 0.089581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.082142 restraints weight = 49029.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.083751 restraints weight = 29923.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.084862 restraints weight = 20192.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.085672 restraints weight = 14669.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.086206 restraints weight = 11260.297| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.6880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12890 Z= 0.127 Angle : 0.687 7.889 17495 Z= 0.355 Chirality : 0.044 0.202 2020 Planarity : 0.005 0.054 2220 Dihedral : 12.785 173.729 1860 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.48 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.20), residues: 1580 helix: 0.12 (0.22), residues: 555 sheet: 0.79 (0.27), residues: 325 loop : -1.99 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 229 TYR 0.023 0.002 TYR A 107 PHE 0.015 0.001 PHE D 138 TRP 0.014 0.002 TRP D 72 HIS 0.004 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00277 (12890) covalent geometry : angle 0.68713 (17495) hydrogen bonds : bond 0.03998 ( 545) hydrogen bonds : angle 4.88662 ( 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 257 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ASP cc_start: 0.6824 (p0) cc_final: 0.6621 (p0) REVERT: A 230 LYS cc_start: 0.7878 (mmtm) cc_final: 0.7393 (mmtm) REVERT: A 315 MET cc_start: 0.7998 (ptp) cc_final: 0.7302 (ptp) REVERT: B 48 TYR cc_start: 0.8721 (m-80) cc_final: 0.8470 (m-80) REVERT: B 54 GLN cc_start: 0.8589 (pt0) cc_final: 0.8274 (pt0) REVERT: B 168 ILE cc_start: 0.8810 (mp) cc_final: 0.8376 (tp) REVERT: B 178 ILE cc_start: 0.8754 (mm) cc_final: 0.8327 (mm) REVERT: B 179 SER cc_start: 0.8626 (p) cc_final: 0.8361 (p) REVERT: C 74 TYR cc_start: 0.6552 (m-10) cc_final: 0.6267 (m-10) REVERT: C 98 ILE cc_start: 0.8959 (pt) cc_final: 0.8758 (pt) REVERT: C 106 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7314 (mm-30) REVERT: C 208 ASP cc_start: 0.6795 (p0) cc_final: 0.6562 (p0) REVERT: C 315 MET cc_start: 0.7380 (ptp) cc_final: 0.6582 (ptp) REVERT: D 106 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6664 (mm-30) REVERT: D 182 MET cc_start: 0.7931 (ptt) cc_final: 0.7513 (ptm) REVERT: D 315 MET cc_start: 0.7854 (ptp) cc_final: 0.7333 (ptp) REVERT: E 120 GLU cc_start: 0.7179 (tp30) cc_final: 0.6226 (tp30) REVERT: E 194 ASP cc_start: 0.7770 (p0) cc_final: 0.7408 (p0) REVERT: E 229 ARG cc_start: 0.7648 (mtp85) cc_final: 0.7158 (ptp-170) REVERT: E 315 MET cc_start: 0.7890 (ptp) cc_final: 0.7559 (ptm) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.1197 time to fit residues: 44.7319 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 : 0.594 ------------------------------------------------------------------------------- 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: 8.9990 chunk 85 optimal weight: 10.0000 chunk 104 optimal weight: 0.0070 chunk 41 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 8 optimal weight: 40.0000 chunk 109 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 overall best weight: 5.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.088824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.081629 restraints weight = 49583.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.083199 restraints weight = 30146.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.084244 restraints weight = 20409.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.085040 restraints weight = 14864.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.085501 restraints weight = 11410.689| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.6948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12890 Z= 0.147 Angle : 0.704 8.575 17495 Z= 0.365 Chirality : 0.044 0.198 2020 Planarity : 0.005 0.053 2220 Dihedral : 12.697 174.382 1860 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.92 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.20), residues: 1580 helix: 0.11 (0.22), residues: 555 sheet: 0.88 (0.28), residues: 325 loop : -1.98 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 238 TYR 0.037 0.002 TYR C 154 PHE 0.014 0.001 PHE D 138 TRP 0.016 0.002 TRP B 72 HIS 0.004 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00327 (12890) covalent geometry : angle 0.70425 (17495) hydrogen bonds : bond 0.04065 ( 545) hydrogen bonds : angle 4.94774 ( 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 258 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.7131 (m-10) cc_final: 0.6847 (m-10) REVERT: A 230 LYS cc_start: 0.7953 (mmtm) cc_final: 0.7466 (mmtm) REVERT: A 315 MET cc_start: 0.7992 (ptp) cc_final: 0.7457 (ptp) REVERT: B 48 TYR cc_start: 0.8766 (m-80) cc_final: 0.8468 (m-80) REVERT: B 54 GLN cc_start: 0.8544 (pt0) cc_final: 0.8243 (pt0) REVERT: B 168 ILE cc_start: 0.8802 (mp) cc_final: 0.8381 (tp) REVERT: B 178 ILE cc_start: 0.8832 (mm) cc_final: 0.8495 (mm) REVERT: B 179 SER cc_start: 0.8609 (p) cc_final: 0.8376 (p) REVERT: B 266 THR cc_start: 0.8392 (m) cc_final: 0.8170 (m) REVERT: C 106 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7254 (mm-30) REVERT: D 182 MET cc_start: 0.7947 (ptt) cc_final: 0.7520 (ptm) REVERT: D 315 MET cc_start: 0.7861 (ptp) cc_final: 0.7340 (ptp) REVERT: E 120 GLU cc_start: 0.7114 (tp30) cc_final: 0.6156 (tp30) REVERT: E 121 ARG cc_start: 0.7775 (mtp-110) cc_final: 0.7519 (mtp-110) REVERT: E 194 ASP cc_start: 0.7638 (p0) cc_final: 0.7240 (p0) REVERT: E 223 ASP cc_start: 0.7966 (t70) cc_final: 0.7632 (t70) REVERT: E 229 ARG cc_start: 0.7680 (mtp85) cc_final: 0.7142 (ptp-170) REVERT: E 315 MET cc_start: 0.7892 (ptp) cc_final: 0.7511 (ptm) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.1264 time to fit residues: 46.7057 Evaluate side-chains 195 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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: 20.0000 chunk 20 optimal weight: 9.9990 chunk 111 optimal weight: 0.0870 chunk 13 optimal weight: 20.0000 chunk 14 optimal weight: 0.5980 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 56 optimal weight: 30.0000 chunk 64 optimal weight: 30.0000 overall best weight: 4.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN ** 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 = 0.3396 r_free = 0.3396 target = 0.089830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.082548 restraints weight = 49375.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.084138 restraints weight = 29887.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.085247 restraints weight = 20138.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.086011 restraints weight = 14535.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.086596 restraints weight = 11193.175| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.7113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12890 Z= 0.131 Angle : 0.691 8.475 17495 Z= 0.354 Chirality : 0.045 0.260 2020 Planarity : 0.005 0.054 2220 Dihedral : 12.614 171.083 1860 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.21), residues: 1580 helix: 0.05 (0.22), residues: 590 sheet: 0.86 (0.28), residues: 325 loop : -1.89 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 297 TYR 0.028 0.002 TYR A 234 PHE 0.015 0.001 PHE B 138 TRP 0.015 0.002 TRP C 72 HIS 0.003 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00290 (12890) covalent geometry : angle 0.69103 (17495) hydrogen bonds : bond 0.03979 ( 545) hydrogen bonds : angle 4.85933 ( 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 256 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ILE cc_start: 0.8434 (pt) cc_final: 0.8231 (pt) REVERT: A 230 LYS cc_start: 0.7940 (mmtm) cc_final: 0.7470 (mmtm) REVERT: A 315 MET cc_start: 0.7982 (ptp) cc_final: 0.7280 (ptp) REVERT: B 48 TYR cc_start: 0.8754 (m-80) cc_final: 0.8470 (m-80) REVERT: B 54 GLN cc_start: 0.8528 (pt0) cc_final: 0.8297 (pt0) REVERT: B 168 ILE cc_start: 0.8893 (mp) cc_final: 0.8505 (tp) REVERT: B 178 ILE cc_start: 0.8812 (mm) cc_final: 0.8515 (mm) REVERT: B 179 SER cc_start: 0.8665 (p) cc_final: 0.8457 (p) REVERT: C 201 LEU cc_start: 0.8435 (tt) cc_final: 0.8199 (pp) REVERT: C 208 ASP cc_start: 0.6616 (p0) cc_final: 0.6346 (p0) REVERT: C 270 PHE cc_start: 0.7611 (m-80) cc_final: 0.7342 (m-80) REVERT: D 74 TYR cc_start: 0.6332 (m-10) cc_final: 0.6020 (m-10) REVERT: D 120 GLU cc_start: 0.6944 (tp30) cc_final: 0.6262 (tp30) REVERT: D 182 MET cc_start: 0.7836 (ptt) cc_final: 0.7417 (ptm) REVERT: D 261 GLN cc_start: 0.8268 (tp40) cc_final: 0.7980 (tp40) REVERT: D 315 MET cc_start: 0.7849 (ptp) cc_final: 0.7312 (ptp) REVERT: E 120 GLU cc_start: 0.7039 (tp30) cc_final: 0.6002 (tp30) REVERT: E 194 ASP cc_start: 0.7535 (p0) cc_final: 0.7225 (p0) REVERT: E 223 ASP cc_start: 0.7869 (t70) cc_final: 0.7601 (t70) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1088 time to fit residues: 41.3706 Evaluate side-chains 195 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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: 0.0030 chunk 82 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 105 optimal weight: 0.0980 chunk 66 optimal weight: 7.9990 chunk 36 optimal weight: 30.0000 chunk 12 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 overall best weight: 4.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** C 118 ASN ** 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 = 0.3394 r_free = 0.3394 target = 0.089878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.082477 restraints weight = 49681.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.084080 restraints weight = 30294.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.085192 restraints weight = 20450.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.085957 restraints weight = 14830.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.086550 restraints weight = 11422.962| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.7183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12890 Z= 0.140 Angle : 0.704 8.380 17495 Z= 0.362 Chirality : 0.045 0.258 2020 Planarity : 0.005 0.053 2220 Dihedral : 12.636 171.010 1860 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.20), residues: 1580 helix: 0.05 (0.21), residues: 590 sheet: 0.89 (0.28), residues: 325 loop : -1.93 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 297 TYR 0.040 0.002 TYR C 154 PHE 0.014 0.001 PHE A 302 TRP 0.018 0.002 TRP B 72 HIS 0.005 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00313 (12890) covalent geometry : angle 0.70413 (17495) hydrogen bonds : bond 0.03986 ( 545) hydrogen bonds : angle 4.86839 ( 1545) =============================================================================== Job complete usr+sys time: 1907.73 seconds wall clock time: 34 minutes 11.05 seconds (2051.05 seconds total)