Starting phenix.real_space_refine on Wed Jun 11 06:09:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5aey_2850/06_2025/5aey_2850.cif Found real_map, /net/cci-nas-00/data/ceres_data/5aey_2850/06_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_2850/06_2025/5aey_2850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5aey_2850/06_2025/5aey_2850.map" model { file = "/net/cci-nas-00/data/ceres_data/5aey_2850/06_2025/5aey_2850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5aey_2850/06_2025/5aey_2850.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.91, per 1000 atoms: 0.62 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: 2.83 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.46 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: 3.80 Time building geometry restraints manager: 3.37 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.150 Process input model: 30.550 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.920 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.029 0.004 TRP A 72 HIS 0.007 0.002 HIS E 293 PHE 0.028 0.004 PHE A 138 TYR 0.047 0.007 TYR E 107 ARG 0.004 0.001 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.20531 ( 545) hydrogen bonds : angle 7.74110 ( 1545) covalent geometry : bond 0.01143 (12890) covalent geometry : angle 1.71384 (17495) *********************** 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 : 1.524 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: 0.2896 time to fit residues: 225.8229 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 : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 40 optimal weight: 50.0000 chunk 79 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.087318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.079653 restraints weight = 48253.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.081268 restraints weight = 29492.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.082366 restraints weight = 20047.711| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12890 Z= 0.185 Angle : 0.812 8.094 17495 Z= 0.424 Chirality : 0.047 0.203 2020 Planarity : 0.005 0.072 2220 Dihedral : 13.580 168.401 1860 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.30 % Favored : 89.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.19), residues: 1580 helix: -0.69 (0.20), residues: 595 sheet: -0.27 (0.27), residues: 355 loop : -2.18 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 72 HIS 0.006 0.001 HIS C 275 PHE 0.023 0.002 PHE A 4 TYR 0.027 0.002 TYR B 107 ARG 0.008 0.001 ARG B 229 Details of bonding type rmsd hydrogen bonds : bond 0.05186 ( 545) hydrogen bonds : angle 5.75304 ( 1545) covalent geometry : bond 0.00411 (12890) covalent geometry : angle 0.81235 (17495) *********************** 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 353 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 352 time to evaluate : 1.514 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: A 74 TYR cc_start: 0.7525 (m-80) cc_final: 0.7034 (m-10) REVERT: A 126 PHE cc_start: 0.7665 (m-10) cc_final: 0.7341 (m-80) REVERT: A 146 MET cc_start: 0.7253 (mtp) cc_final: 0.6909 (mtp) REVERT: A 148 GLU cc_start: 0.4348 (tt0) cc_final: 0.4046 (tt0) REVERT: A 176 LEU cc_start: 0.8773 (tt) cc_final: 0.7031 (tt) REVERT: A 208 ASP cc_start: 0.7069 (m-30) cc_final: 0.6851 (p0) REVERT: B 74 TYR cc_start: 0.6728 (m-80) cc_final: 0.6337 (m-10) REVERT: B 126 PHE cc_start: 0.7426 (m-10) cc_final: 0.6852 (m-80) REVERT: B 142 ASP cc_start: 0.7084 (t70) cc_final: 0.6641 (t0) REVERT: B 148 GLU cc_start: 0.3931 (tt0) cc_final: 0.3644 (tt0) REVERT: B 176 LEU cc_start: 0.8863 (tt) cc_final: 0.6974 (tt) REVERT: B 234 TYR cc_start: 0.8682 (t80) cc_final: 0.8373 (t80) REVERT: B 261 GLN cc_start: 0.7866 (tp40) cc_final: 0.7552 (tp-100) REVERT: B 265 ASN cc_start: 0.7572 (m110) cc_final: 0.7346 (m-40) REVERT: C 74 TYR cc_start: 0.7255 (m-80) cc_final: 0.6784 (m-10) REVERT: C 126 PHE cc_start: 0.7755 (m-10) cc_final: 0.7302 (m-80) REVERT: C 142 ASP cc_start: 0.6840 (t70) cc_final: 0.6371 (t0) REVERT: C 201 LEU cc_start: 0.8608 (tt) cc_final: 0.8273 (tt) REVERT: D 142 ASP cc_start: 0.7130 (t70) cc_final: 0.6484 (t70) REVERT: D 176 LEU cc_start: 0.8850 (tt) cc_final: 0.7539 (tt) REVERT: D 261 GLN cc_start: 0.8245 (tp40) cc_final: 0.7957 (tp40) REVERT: E 121 ARG cc_start: 0.7535 (mtp85) cc_final: 0.6735 (mtp85) REVERT: E 176 LEU cc_start: 0.8680 (tt) cc_final: 0.7130 (tt) REVERT: E 194 ASP cc_start: 0.7683 (t0) cc_final: 0.7317 (p0) REVERT: E 315 MET cc_start: 0.7608 (mtm) cc_final: 0.7045 (ptp) outliers start: 1 outliers final: 0 residues processed: 353 average time/residue: 0.3019 time to fit residues: 144.6343 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 : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 103 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 41 optimal weight: 0.0270 chunk 100 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 overall best weight: 5.2046 ------------------------------------------------------------------------------- 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** ** E 15 GLN ** 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 = 0.3320 r_free = 0.3320 target = 0.080855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.073298 restraints weight = 48877.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.074880 restraints weight = 29418.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.076020 restraints weight = 19862.466| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.5316 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= 0.153 Angle : 0.753 8.814 17495 Z= 0.391 Chirality : 0.046 0.271 2020 Planarity : 0.005 0.107 2220 Dihedral : 13.417 178.631 1860 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.68 % Favored : 90.00 % Rotamer: Outliers : 0.21 % Allowed : 2.97 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.20), residues: 1580 helix: -0.16 (0.22), residues: 555 sheet: -0.15 (0.25), residues: 385 loop : -2.09 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 72 HIS 0.009 0.002 HIS C 275 PHE 0.013 0.001 PHE A 4 TYR 0.030 0.002 TYR C 234 ARG 0.007 0.001 ARG C 34 Details of bonding type rmsd hydrogen bonds : bond 0.04674 ( 545) hydrogen bonds : angle 5.21085 ( 1545) covalent geometry : bond 0.00337 (12890) covalent geometry : angle 0.75259 (17495) *********************** 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 316 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 313 time to evaluate : 1.534 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 43 LYS cc_start: 0.7373 (tptt) cc_final: 0.7147 (tptt) REVERT: B 74 TYR cc_start: 0.6413 (m-80) cc_final: 0.6010 (m-10) REVERT: B 106 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6797 (mm-30) REVERT: B 148 GLU cc_start: 0.2920 (tt0) cc_final: 0.2549 (tt0) REVERT: B 154 TYR cc_start: 0.7630 (t80) cc_final: 0.7393 (t80) REVERT: B 197 LEU cc_start: 0.8087 (mp) cc_final: 0.7866 (mp) REVERT: B 266 THR cc_start: 0.8651 (m) cc_final: 0.8432 (m) REVERT: C 98 ILE cc_start: 0.9070 (pt) cc_final: 0.8869 (pt) REVERT: C 118 ASN cc_start: 0.7416 (m110) cc_final: 0.6966 (m110) REVERT: C 208 ASP cc_start: 0.7056 (p0) cc_final: 0.6811 (p0) REVERT: D 146 MET cc_start: 0.7037 (mtp) cc_final: 0.6332 (mtp) REVERT: D 261 GLN cc_start: 0.8415 (tp40) cc_final: 0.8159 (tp40) REVERT: D 315 MET cc_start: 0.7927 (ptp) cc_final: 0.7229 (ptp) REVERT: E 126 PHE cc_start: 0.7795 (m-10) cc_final: 0.7573 (m-80) REVERT: E 146 MET cc_start: 0.8215 (ttp) cc_final: 0.7396 (ttp) REVERT: E 176 LEU cc_start: 0.8941 (tt) cc_final: 0.7469 (tt) REVERT: E 194 ASP cc_start: 0.7589 (t0) cc_final: 0.7211 (p0) REVERT: E 315 MET cc_start: 0.7478 (mtm) cc_final: 0.7221 (mtp) outliers start: 3 outliers final: 0 residues processed: 316 average time/residue: 0.2593 time to fit residues: 117.2055 Evaluate side-chains 203 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 48 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 10 optimal weight: 40.0000 chunk 102 optimal weight: 0.0030 overall best weight: 4.3998 ------------------------------------------------------------------------------- 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** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS ** E 15 GLN ** 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 = 0.3350 r_free = 0.3350 target = 0.088085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.080819 restraints weight = 49501.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.082435 restraints weight = 29881.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.083567 restraints weight = 19954.784| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12890 Z= 0.142 Angle : 0.725 8.405 17495 Z= 0.374 Chirality : 0.045 0.205 2020 Planarity : 0.005 0.072 2220 Dihedral : 13.253 178.640 1860 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.92 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.20), residues: 1580 helix: 0.03 (0.23), residues: 535 sheet: 0.44 (0.27), residues: 345 loop : -1.94 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 72 HIS 0.005 0.001 HIS C 275 PHE 0.011 0.001 PHE A 4 TYR 0.030 0.002 TYR D 234 ARG 0.005 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 545) hydrogen bonds : angle 5.03366 ( 1545) covalent geometry : bond 0.00314 (12890) covalent geometry : angle 0.72480 (17495) *********************** 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 273 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.500 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 148 GLU cc_start: 0.5138 (pt0) cc_final: 0.4791 (pt0) REVERT: A 230 LYS cc_start: 0.7963 (mmtm) cc_final: 0.7393 (pttm) REVERT: B 48 TYR cc_start: 0.8810 (m-80) cc_final: 0.8524 (m-80) REVERT: B 74 TYR cc_start: 0.6391 (m-80) cc_final: 0.6144 (m-10) REVERT: B 315 MET cc_start: 0.7646 (ptp) cc_final: 0.6782 (ptp) REVERT: C 98 ILE cc_start: 0.9015 (pt) cc_final: 0.8803 (pt) REVERT: C 126 PHE cc_start: 0.7681 (m-10) cc_final: 0.7379 (m-80) REVERT: D 230 LYS cc_start: 0.7458 (mmtm) cc_final: 0.6813 (mmtm) REVERT: D 261 GLN cc_start: 0.8366 (tp40) cc_final: 0.8074 (tp40) REVERT: D 315 MET cc_start: 0.7766 (ptp) cc_final: 0.7338 (ptp) REVERT: E 176 LEU cc_start: 0.9170 (tt) cc_final: 0.8269 (tt) REVERT: E 194 ASP cc_start: 0.7178 (t70) cc_final: 0.6920 (p0) REVERT: E 315 MET cc_start: 0.7668 (mtm) cc_final: 0.7343 (mtp) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.2558 time to fit residues: 100.6164 Evaluate side-chains 207 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 65 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 77 optimal weight: 30.0000 chunk 140 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 152 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 8 optimal weight: 30.0000 chunk 34 optimal weight: 30.0000 overall best weight: 13.1996 ------------------------------------------------------------------------------- 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 ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN D 78 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 GLN ** E 25 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 = 0.3264 r_free = 0.3264 target = 0.078680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.071687 restraints weight = 49623.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.073168 restraints weight = 29703.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.074257 restraints weight = 19849.999| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 12890 Z= 0.260 Angle : 0.821 9.121 17495 Z= 0.433 Chirality : 0.048 0.255 2020 Planarity : 0.006 0.081 2220 Dihedral : 13.665 179.989 1860 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.51 % Favored : 89.18 % Rotamer: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.20), residues: 1580 helix: -0.64 (0.20), residues: 620 sheet: 0.24 (0.27), residues: 345 loop : -2.35 (0.22), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 72 HIS 0.008 0.002 HIS A 228 PHE 0.017 0.002 PHE D 4 TYR 0.043 0.003 TYR A 107 ARG 0.008 0.001 ARG C 34 Details of bonding type rmsd hydrogen bonds : bond 0.04983 ( 545) hydrogen bonds : angle 5.60091 ( 1545) covalent geometry : bond 0.00581 (12890) covalent geometry : angle 0.82147 (17495) *********************** 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 253 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 252 time to evaluate : 1.361 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: A 230 LYS cc_start: 0.7823 (mmtm) cc_final: 0.7421 (mmtm) REVERT: A 315 MET cc_start: 0.8225 (mtp) cc_final: 0.7819 (mtm) REVERT: B 48 TYR cc_start: 0.8793 (m-80) cc_final: 0.8587 (m-80) REVERT: B 74 TYR cc_start: 0.6639 (m-80) cc_final: 0.6329 (m-10) REVERT: B 178 ILE cc_start: 0.8786 (mm) cc_final: 0.8520 (mm) REVERT: C 106 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7172 (mm-30) REVERT: C 208 ASP cc_start: 0.6905 (p0) cc_final: 0.6697 (p0) REVERT: C 315 MET cc_start: 0.7913 (ptp) cc_final: 0.7549 (ptp) REVERT: D 230 LYS cc_start: 0.7480 (mmtm) cc_final: 0.7231 (mmtm) REVERT: D 265 ASN cc_start: 0.8371 (m-40) cc_final: 0.8090 (m-40) REVERT: D 284 GLU cc_start: 0.7312 (mp0) cc_final: 0.7102 (mm-30) REVERT: D 315 MET cc_start: 0.7873 (ptp) cc_final: 0.7308 (ptp) REVERT: E 176 LEU cc_start: 0.9162 (tt) cc_final: 0.8468 (tt) REVERT: E 194 ASP cc_start: 0.7219 (t70) cc_final: 0.6906 (p0) outliers start: 1 outliers final: 1 residues processed: 253 average time/residue: 0.2389 time to fit residues: 87.2962 Evaluate side-chains 203 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 128 optimal weight: 40.0000 chunk 64 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 68 optimal weight: 50.0000 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 96 optimal weight: 8.9990 chunk 13 optimal weight: 40.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 158 GLN A 265 ASN C 78 ASN D 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.079743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.072526 restraints weight = 50349.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.074090 restraints weight = 30227.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.075165 restraints weight = 20363.371| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.6230 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= 0.169 Angle : 0.735 8.426 17495 Z= 0.386 Chirality : 0.045 0.201 2020 Planarity : 0.006 0.106 2220 Dihedral : 13.374 179.167 1860 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.30 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.20), residues: 1580 helix: -0.41 (0.21), residues: 590 sheet: 0.30 (0.27), residues: 345 loop : -2.06 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 72 HIS 0.005 0.001 HIS A 293 PHE 0.012 0.001 PHE A 4 TYR 0.033 0.002 TYR A 107 ARG 0.007 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 545) hydrogen bonds : angle 5.27450 ( 1545) covalent geometry : bond 0.00374 (12890) covalent geometry : angle 0.73510 (17495) *********************** 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 272 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 1.398 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: A 230 LYS cc_start: 0.7846 (mmtm) cc_final: 0.7301 (pttm) REVERT: B 48 TYR cc_start: 0.8799 (m-80) cc_final: 0.8475 (m-80) REVERT: B 54 GLN cc_start: 0.8627 (pt0) cc_final: 0.8418 (pt0) REVERT: B 178 ILE cc_start: 0.8802 (mm) cc_final: 0.8500 (mm) REVERT: C 106 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7153 (mm-30) REVERT: C 176 LEU cc_start: 0.8333 (tt) cc_final: 0.8044 (tt) REVERT: D 74 TYR cc_start: 0.6714 (m-10) cc_final: 0.6426 (m-10) REVERT: D 106 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6790 (mm-30) REVERT: D 182 MET cc_start: 0.8231 (ptt) cc_final: 0.7805 (ptm) REVERT: D 234 TYR cc_start: 0.7911 (t80) cc_final: 0.7315 (t80) REVERT: D 315 MET cc_start: 0.7918 (ptp) cc_final: 0.7345 (ptp) REVERT: E 176 LEU cc_start: 0.9107 (tt) cc_final: 0.8312 (tt) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.2670 time to fit residues: 102.3999 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 : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 73 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 149 optimal weight: 30.0000 chunk 133 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 137 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 44 optimal weight: 40.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.081550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.074270 restraints weight = 49226.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.075785 restraints weight = 29694.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.076841 restraints weight = 20057.458| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12890 Z= 0.143 Angle : 0.711 8.246 17495 Z= 0.374 Chirality : 0.045 0.215 2020 Planarity : 0.005 0.070 2220 Dihedral : 13.068 176.841 1860 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.56 % Favored : 90.19 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.20), residues: 1580 helix: -0.32 (0.20), residues: 620 sheet: 0.63 (0.27), residues: 325 loop : -2.03 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 72 HIS 0.004 0.001 HIS A 293 PHE 0.014 0.001 PHE A 138 TYR 0.027 0.002 TYR E 107 ARG 0.007 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04249 ( 545) hydrogen bonds : angle 4.97162 ( 1545) covalent geometry : bond 0.00314 (12890) covalent geometry : angle 0.71142 (17495) *********************** 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 278 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.383 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: A 230 LYS cc_start: 0.7805 (mmtm) cc_final: 0.7396 (pttm) REVERT: B 48 TYR cc_start: 0.8767 (m-80) cc_final: 0.8470 (m-80) REVERT: B 121 ARG cc_start: 0.7538 (ptp-170) cc_final: 0.6954 (ptm160) REVERT: B 168 ILE cc_start: 0.8801 (mp) cc_final: 0.8370 (tp) REVERT: B 178 ILE cc_start: 0.8796 (mm) cc_final: 0.8374 (mm) REVERT: B 179 SER cc_start: 0.8578 (p) cc_final: 0.8370 (p) REVERT: C 208 ASP cc_start: 0.6850 (p0) cc_final: 0.6604 (p0) REVERT: D 106 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6942 (mm-30) REVERT: D 284 GLU cc_start: 0.6872 (mp0) cc_final: 0.6603 (mp0) REVERT: D 315 MET cc_start: 0.7836 (ptp) cc_final: 0.7248 (ptp) REVERT: E 194 ASP cc_start: 0.6937 (p0) cc_final: 0.6666 (p0) REVERT: E 230 LYS cc_start: 0.7728 (mmtm) cc_final: 0.7519 (mmtm) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2700 time to fit residues: 105.9776 Evaluate side-chains 204 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 31 optimal weight: 30.0000 chunk 144 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 141 optimal weight: 50.0000 chunk 29 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 39 optimal weight: 30.0000 chunk 16 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN D 78 ASN D 118 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.081406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.074031 restraints weight = 49740.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.075620 restraints weight = 29847.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.076695 restraints weight = 20124.663| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.6713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12890 Z= 0.162 Angle : 0.713 8.279 17495 Z= 0.376 Chirality : 0.046 0.236 2020 Planarity : 0.005 0.062 2220 Dihedral : 12.947 176.940 1860 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.43 % Favored : 90.51 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.20), residues: 1580 helix: -0.30 (0.20), residues: 620 sheet: 0.61 (0.28), residues: 325 loop : -2.07 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 16 HIS 0.006 0.001 HIS A 293 PHE 0.014 0.002 PHE B 138 TYR 0.033 0.003 TYR E 107 ARG 0.008 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 545) hydrogen bonds : angle 5.08575 ( 1545) covalent geometry : bond 0.00364 (12890) covalent geometry : angle 0.71326 (17495) *********************** 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 256 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ILE cc_start: 0.8601 (mm) cc_final: 0.8312 (mm) REVERT: A 230 LYS cc_start: 0.7771 (mmtm) cc_final: 0.7366 (pttm) REVERT: B 48 TYR cc_start: 0.8746 (m-80) cc_final: 0.8451 (m-80) REVERT: B 168 ILE cc_start: 0.8782 (mp) cc_final: 0.8352 (tp) REVERT: B 178 ILE cc_start: 0.8778 (mm) cc_final: 0.8426 (mm) REVERT: B 179 SER cc_start: 0.8610 (p) cc_final: 0.8404 (p) REVERT: C 74 TYR cc_start: 0.6348 (m-10) cc_final: 0.5869 (m-10) REVERT: C 106 GLU cc_start: 0.7171 (tp30) cc_final: 0.6310 (tp30) REVERT: C 178 ILE cc_start: 0.9135 (mm) cc_final: 0.8910 (mm) REVERT: C 223 ASP cc_start: 0.7802 (m-30) cc_final: 0.7516 (t0) REVERT: D 1 MET cc_start: 0.5826 (ttt) cc_final: 0.5596 (mtp) REVERT: D 284 GLU cc_start: 0.6836 (mp0) cc_final: 0.6548 (mp0) REVERT: D 315 MET cc_start: 0.7902 (ptp) cc_final: 0.7329 (ptp) REVERT: E 120 GLU cc_start: 0.6965 (tp30) cc_final: 0.5835 (tp30) REVERT: E 252 MET cc_start: 0.6369 (ttt) cc_final: 0.6165 (ttt) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.2242 time to fit residues: 84.4356 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 : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 4 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 154 optimal weight: 8.9990 chunk 122 optimal weight: 0.0870 chunk 49 optimal weight: 0.0870 chunk 30 optimal weight: 30.0000 chunk 34 optimal weight: 50.0000 chunk 0 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 overall best weight: 2.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 GLN ** C 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 118 ASN E 228 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.091226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.083905 restraints weight = 49017.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.085500 restraints weight = 29819.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.086605 restraints weight = 20056.223| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.7083 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= 0.119 Angle : 0.675 8.215 17495 Z= 0.348 Chirality : 0.045 0.249 2020 Planarity : 0.005 0.058 2220 Dihedral : 12.694 174.543 1860 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.73 % Favored : 91.20 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.20), residues: 1580 helix: -0.02 (0.22), residues: 590 sheet: 0.74 (0.28), residues: 325 loop : -1.91 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 72 HIS 0.004 0.001 HIS D 228 PHE 0.013 0.001 PHE D 270 TYR 0.031 0.002 TYR C 154 ARG 0.008 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 545) hydrogen bonds : angle 4.73865 ( 1545) covalent geometry : bond 0.00255 (12890) covalent geometry : angle 0.67512 (17495) *********************** 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 268 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ILE cc_start: 0.8677 (mm) cc_final: 0.8384 (mm) REVERT: A 208 ASP cc_start: 0.6906 (p0) cc_final: 0.6692 (p0) REVERT: A 230 LYS cc_start: 0.7825 (mmtm) cc_final: 0.7431 (pttm) REVERT: B 1 MET cc_start: 0.6189 (ttt) cc_final: 0.5946 (mtm) REVERT: B 48 TYR cc_start: 0.8684 (m-80) cc_final: 0.8473 (m-80) REVERT: B 178 ILE cc_start: 0.8718 (mm) cc_final: 0.8280 (mm) REVERT: C 106 GLU cc_start: 0.7269 (tp30) cc_final: 0.6715 (tp30) REVERT: C 178 ILE cc_start: 0.9156 (mm) cc_final: 0.8891 (mm) REVERT: C 208 ASP cc_start: 0.6678 (p0) cc_final: 0.6455 (p0) REVERT: C 223 ASP cc_start: 0.7842 (m-30) cc_final: 0.7458 (t0) REVERT: D 120 GLU cc_start: 0.7255 (tp30) cc_final: 0.6631 (tp30) REVERT: D 182 MET cc_start: 0.7811 (ptt) cc_final: 0.7327 (ptm) REVERT: D 315 MET cc_start: 0.7874 (ptp) cc_final: 0.7328 (ptp) REVERT: E 162 GLU cc_start: 0.7938 (pp20) cc_final: 0.7575 (tp30) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2274 time to fit residues: 91.2077 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 : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 148 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 18 optimal weight: 30.0000 chunk 151 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 73 optimal weight: 0.1980 chunk 118 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 overall best weight: 5.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 293 HIS B 228 HIS ** C 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN E 118 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.083599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.075980 restraints weight = 48931.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.077580 restraints weight = 29599.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.078699 restraints weight = 20088.834| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.7081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12890 Z= 0.146 Angle : 0.694 8.659 17495 Z= 0.362 Chirality : 0.046 0.265 2020 Planarity : 0.005 0.056 2220 Dihedral : 12.677 174.903 1860 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.99 % Favored : 90.95 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.21), residues: 1580 helix: -0.02 (0.21), residues: 590 sheet: 0.68 (0.28), residues: 325 loop : -1.83 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 72 HIS 0.005 0.001 HIS A 293 PHE 0.013 0.001 PHE B 138 TYR 0.029 0.002 TYR B 107 ARG 0.007 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 545) hydrogen bonds : angle 4.89690 ( 1545) covalent geometry : bond 0.00329 (12890) covalent geometry : angle 0.69429 (17495) ********************** 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 255 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 253 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ILE cc_start: 0.8572 (mm) cc_final: 0.8328 (mm) REVERT: A 230 LYS cc_start: 0.7781 (mmtm) cc_final: 0.7351 (pttm) REVERT: A 261 GLN cc_start: 0.7715 (mt0) cc_final: 0.7161 (mt0) REVERT: B 1 MET cc_start: 0.6131 (ttt) cc_final: 0.5833 (mtp) REVERT: B 48 TYR cc_start: 0.8794 (m-80) cc_final: 0.8477 (m-80) REVERT: B 116 THR cc_start: 0.8883 (p) cc_final: 0.8648 (p) REVERT: C 106 GLU cc_start: 0.7291 (tp30) cc_final: 0.6823 (tp30) REVERT: C 208 ASP cc_start: 0.6778 (p0) cc_final: 0.6568 (p0) REVERT: C 223 ASP cc_start: 0.7736 (m-30) cc_final: 0.7406 (t0) REVERT: D 120 GLU cc_start: 0.7275 (tp30) cc_final: 0.6645 (tp30) REVERT: D 182 MET cc_start: 0.7914 (ptt) cc_final: 0.7424 (ptm) REVERT: D 315 MET cc_start: 0.7920 (ptp) cc_final: 0.7345 (ptp) REVERT: E 178 ILE cc_start: 0.8741 (mm) cc_final: 0.8536 (mm) REVERT: E 315 MET cc_start: 0.7613 (ptp) cc_final: 0.7339 (ptm) outliers start: 2 outliers final: 0 residues processed: 254 average time/residue: 0.2086 time to fit residues: 79.8627 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 : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 1 optimal weight: 5.9990 chunk 71 optimal weight: 0.0020 chunk 83 optimal weight: 40.0000 chunk 49 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 66 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 overall best weight: 5.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3371 r_free = 0.3371 target = 0.084069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.076451 restraints weight = 49052.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.078051 restraints weight = 29781.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.079158 restraints weight = 20181.230| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.7199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12890 Z= 0.144 Angle : 0.690 8.495 17495 Z= 0.359 Chirality : 0.046 0.249 2020 Planarity : 0.005 0.053 2220 Dihedral : 12.598 170.786 1860 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.21), residues: 1580 helix: -0.03 (0.21), residues: 590 sheet: 0.68 (0.29), residues: 325 loop : -1.82 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 72 HIS 0.006 0.001 HIS A 293 PHE 0.024 0.002 PHE D 270 TYR 0.033 0.002 TYR C 154 ARG 0.007 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 545) hydrogen bonds : angle 4.92614 ( 1545) covalent geometry : bond 0.00326 (12890) covalent geometry : angle 0.69007 (17495) =============================================================================== Job complete usr+sys time: 3723.89 seconds wall clock time: 67 minutes 6.38 seconds (4026.38 seconds total)