Starting phenix.real_space_refine on Sun Aug 24 01:35:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v2h_42914/08_2025/8v2h_42914.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v2h_42914/08_2025/8v2h_42914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v2h_42914/08_2025/8v2h_42914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v2h_42914/08_2025/8v2h_42914.map" model { file = "/net/cci-nas-00/data/ceres_data/8v2h_42914/08_2025/8v2h_42914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v2h_42914/08_2025/8v2h_42914.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 K 4 8.98 5 S 124 5.16 5 C 10324 2.51 5 N 2724 2.21 5 O 2984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16168 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2884 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 6, 'TRANS': 354} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1152 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "B" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2884 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 6, 'TRANS': 354} Chain: "F" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1152 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "C" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2884 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 6, 'TRANS': 354} Chain: "G" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1152 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "D" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2884 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 6, 'TRANS': 354} Chain: "H" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1152 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 3.91, per 1000 atoms: 0.24 Number of scatterers: 16168 At special positions: 0 Unit cell: (121.26, 122.12, 100.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 K 4 19.00 S 124 16.00 O 2984 8.00 N 2724 7.00 C 10324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 371 " distance=2.04 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 371 " distance=2.04 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 371 " distance=2.04 Simple disulfide: pdb=" SG CYS D 333 " - pdb=" SG CYS D 371 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 670.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3824 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 8 sheets defined 74.4% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 122 through 157 removed outlier: 3.522A pdb=" N ARG A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 147 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 202 removed outlier: 3.709A pdb=" N LEU A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU A 177 " --> pdb=" O CYS A 173 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.645A pdb=" N ILE A 208 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 removed outlier: 3.517A pdb=" N PHE A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 261 removed outlier: 3.774A pdb=" N ILE A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 Processing helix chain 'A' and resid 267 through 277 removed outlier: 4.297A pdb=" N ALA A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 285 through 294 removed outlier: 4.299A pdb=" N ILE A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.628A pdb=" N THR A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 335 Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'A' and resid 369 through 397 Processing helix chain 'A' and resid 401 through 439 removed outlier: 3.811A pdb=" N ASN A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 478 removed outlier: 3.630A pdb=" N VAL A 449 " --> pdb=" O ASP A 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 18 Processing helix chain 'E' and resid 31 through 39 removed outlier: 3.589A pdb=" N VAL E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER E 38 " --> pdb=" O THR E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.802A pdb=" N VAL E 55 " --> pdb=" O MET E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 80 through 92 removed outlier: 3.720A pdb=" N GLU E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ARG E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 112 removed outlier: 3.823A pdb=" N ARG E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N HIS E 107 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 removed outlier: 3.631A pdb=" N GLU E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET E 124 " --> pdb=" O GLU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'B' and resid 123 through 157 removed outlier: 3.832A pdb=" N ALA B 127 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER B 136 " --> pdb=" O ARG B 132 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 140 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 201 removed outlier: 3.848A pdb=" N LEU B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU B 177 " --> pdb=" O CYS B 173 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 213 through 226 removed outlier: 3.592A pdb=" N ILE B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 261 removed outlier: 3.777A pdb=" N ILE B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 267 through 277 removed outlier: 4.295A pdb=" N ALA B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 300 through 310 removed outlier: 3.787A pdb=" N THR B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 335 Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 369 through 397 Processing helix chain 'B' and resid 401 through 439 removed outlier: 3.808A pdb=" N ASN B 426 " --> pdb=" O ASN B 422 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 428 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS B 439 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 478 removed outlier: 3.548A pdb=" N VAL B 449 " --> pdb=" O ASP B 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 18 removed outlier: 3.719A pdb=" N ALA F 10 " --> pdb=" O GLU F 6 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU F 11 " --> pdb=" O GLU F 7 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU F 18 " --> pdb=" O GLU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 39 removed outlier: 3.668A pdb=" N SER F 38 " --> pdb=" O THR F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 55 removed outlier: 3.927A pdb=" N VAL F 55 " --> pdb=" O MET F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 76 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.847A pdb=" N ARG F 106 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS F 107 " --> pdb=" O ALA F 103 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN F 111 " --> pdb=" O HIS F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 126 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'C' and resid 119 through 157 removed outlier: 3.764A pdb=" N ALA C 127 " --> pdb=" O GLY C 123 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY C 146 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 201 removed outlier: 3.881A pdb=" N LEU C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU C 177 " --> pdb=" O CYS C 173 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 210 removed outlier: 3.512A pdb=" N ILE C 208 " --> pdb=" O ASP C 205 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA C 209 " --> pdb=" O TRP C 206 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET C 210 " --> pdb=" O ARG C 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 205 through 210' Processing helix chain 'C' and resid 213 through 226 removed outlier: 3.578A pdb=" N ILE C 218 " --> pdb=" O ARG C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 261 removed outlier: 3.774A pdb=" N ILE C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'C' and resid 267 through 277 removed outlier: 4.296A pdb=" N ALA C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 284 through 294 removed outlier: 4.351A pdb=" N SER C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 310 removed outlier: 3.764A pdb=" N THR C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 335 Processing helix chain 'C' and resid 345 through 358 Processing helix chain 'C' and resid 369 through 397 removed outlier: 3.523A pdb=" N LYS C 373 " --> pdb=" O THR C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 439 removed outlier: 3.836A pdb=" N ASN C 426 " --> pdb=" O ASN C 422 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 427 " --> pdb=" O ALA C 423 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 439 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 477 removed outlier: 3.692A pdb=" N VAL C 449 " --> pdb=" O ASP C 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 20 removed outlier: 3.733A pdb=" N LEU G 18 " --> pdb=" O GLU G 14 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE G 19 " --> pdb=" O ALA G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 38 removed outlier: 3.505A pdb=" N THR G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER G 38 " --> pdb=" O THR G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 55 removed outlier: 3.728A pdb=" N LEU G 48 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL G 55 " --> pdb=" O MET G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 77 removed outlier: 3.791A pdb=" N THR G 70 " --> pdb=" O PRO G 66 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS G 77 " --> pdb=" O ALA G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 91 Processing helix chain 'G' and resid 102 through 111 removed outlier: 3.729A pdb=" N ARG G 106 " --> pdb=" O ALA G 102 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS G 107 " --> pdb=" O ALA G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 138 through 145 Processing helix chain 'D' and resid 119 through 157 removed outlier: 4.201A pdb=" N HIS D 124 " --> pdb=" O TYR D 120 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA D 127 " --> pdb=" O GLY D 123 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER D 136 " --> pdb=" O ARG D 132 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU D 140 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY D 146 " --> pdb=" O PHE D 142 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 147 " --> pdb=" O GLY D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 201 removed outlier: 3.852A pdb=" N LEU D 169 " --> pdb=" O SER D 165 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU D 177 " --> pdb=" O CYS D 173 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 210 removed outlier: 3.564A pdb=" N ALA D 209 " --> pdb=" O TRP D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 226 Processing helix chain 'D' and resid 255 through 261 removed outlier: 3.780A pdb=" N ILE D 261 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 266 Processing helix chain 'D' and resid 267 through 277 removed outlier: 4.290A pdb=" N ALA D 271 " --> pdb=" O LEU D 267 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 Processing helix chain 'D' and resid 283 through 294 Processing helix chain 'D' and resid 300 through 310 removed outlier: 3.595A pdb=" N THR D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 335 Processing helix chain 'D' and resid 345 through 358 Processing helix chain 'D' and resid 369 through 398 removed outlier: 3.543A pdb=" N LEU D 398 " --> pdb=" O VAL D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 439 removed outlier: 3.819A pdb=" N ASN D 426 " --> pdb=" O ASN D 422 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU D 428 " --> pdb=" O ALA D 424 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS D 439 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 478 removed outlier: 3.513A pdb=" N VAL D 449 " --> pdb=" O ASP D 445 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 17 Processing helix chain 'H' and resid 18 through 20 No H-bonds generated for 'chain 'H' and resid 18 through 20' Processing helix chain 'H' and resid 28 through 38 removed outlier: 3.600A pdb=" N SER H 38 " --> pdb=" O THR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 55 removed outlier: 3.617A pdb=" N VAL H 55 " --> pdb=" O MET H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 77 removed outlier: 3.575A pdb=" N ARG H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 92 removed outlier: 3.641A pdb=" N PHE H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 111 removed outlier: 4.257A pdb=" N HIS H 107 " --> pdb=" O ALA H 103 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL H 108 " --> pdb=" O GLU H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 138 through 145 removed outlier: 3.754A pdb=" N GLN H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 241 Processing sheet with id=AA2, first strand: chain 'E' and resid 100 through 101 Processing sheet with id=AA3, first strand: chain 'B' and resid 235 through 241 Processing sheet with id=AA4, first strand: chain 'F' and resid 100 through 101 removed outlier: 3.504A pdb=" N VAL F 136 " --> pdb=" O ILE F 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 235 through 241 Processing sheet with id=AA6, first strand: chain 'G' and resid 100 through 101 removed outlier: 3.935A pdb=" N ILE G 100 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL G 136 " --> pdb=" O ILE G 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 235 through 241 Processing sheet with id=AA8, first strand: chain 'H' and resid 100 through 101 1028 hydrogen bonds defined for protein. 3009 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5235 1.34 - 1.46: 3610 1.46 - 1.58: 7367 1.58 - 1.70: 0 1.70 - 1.81: 216 Bond restraints: 16428 Sorted by residual: bond pdb=" C PHE E 65 " pdb=" N PRO E 66 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.33e+00 bond pdb=" C ILE C 261 " pdb=" N PRO C 262 " ideal model delta sigma weight residual 1.335 1.351 -0.017 1.19e-02 7.06e+03 1.96e+00 bond pdb=" C ILE B 261 " pdb=" N PRO B 262 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.19e-02 7.06e+03 1.86e+00 bond pdb=" C ILE A 261 " pdb=" N PRO A 262 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.19e-02 7.06e+03 1.81e+00 bond pdb=" C ILE D 261 " pdb=" N PRO D 262 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.19e-02 7.06e+03 1.79e+00 ... (remaining 16423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 21835 1.42 - 2.84: 275 2.84 - 4.25: 48 4.25 - 5.67: 14 5.67 - 7.09: 4 Bond angle restraints: 22176 Sorted by residual: angle pdb=" C GLY H 23 " pdb=" N ASP H 24 " pdb=" CA ASP H 24 " ideal model delta sigma weight residual 121.54 127.87 -6.33 1.91e+00 2.74e-01 1.10e+01 angle pdb=" C LYS H 94 " pdb=" N ASP H 95 " pdb=" CA ASP H 95 " ideal model delta sigma weight residual 121.54 126.84 -5.30 1.91e+00 2.74e-01 7.69e+00 angle pdb=" N ILE C 175 " pdb=" CA ILE C 175 " pdb=" C ILE C 175 " ideal model delta sigma weight residual 111.81 109.44 2.37 8.60e-01 1.35e+00 7.59e+00 angle pdb=" N ILE D 175 " pdb=" CA ILE D 175 " pdb=" C ILE D 175 " ideal model delta sigma weight residual 111.81 109.44 2.37 8.60e-01 1.35e+00 7.57e+00 angle pdb=" N ILE B 175 " pdb=" CA ILE B 175 " pdb=" C ILE B 175 " ideal model delta sigma weight residual 111.81 109.47 2.34 8.60e-01 1.35e+00 7.41e+00 ... (remaining 22171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 8792 15.04 - 30.08: 797 30.08 - 45.11: 196 45.11 - 60.15: 63 60.15 - 75.19: 44 Dihedral angle restraints: 9892 sinusoidal: 3988 harmonic: 5904 Sorted by residual: dihedral pdb=" CB CYS B 333 " pdb=" SG CYS B 333 " pdb=" SG CYS B 371 " pdb=" CB CYS B 371 " ideal model delta sinusoidal sigma weight residual -86.00 -147.04 61.04 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CB CYS A 333 " pdb=" SG CYS A 333 " pdb=" SG CYS A 371 " pdb=" CB CYS A 371 " ideal model delta sinusoidal sigma weight residual -86.00 -146.12 60.12 1 1.00e+01 1.00e-02 4.82e+01 dihedral pdb=" CB CYS D 333 " pdb=" SG CYS D 333 " pdb=" SG CYS D 371 " pdb=" CB CYS D 371 " ideal model delta sinusoidal sigma weight residual 93.00 50.09 42.91 1 1.00e+01 1.00e-02 2.57e+01 ... (remaining 9889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1486 0.025 - 0.051: 687 0.051 - 0.076: 306 0.076 - 0.102: 64 0.102 - 0.127: 21 Chirality restraints: 2564 Sorted by residual: chirality pdb=" CA ASP H 95 " pdb=" N ASP H 95 " pdb=" C ASP H 95 " pdb=" CB ASP H 95 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE G 27 " pdb=" N ILE G 27 " pdb=" C ILE G 27 " pdb=" CB ILE G 27 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA ASP F 95 " pdb=" N ASP F 95 " pdb=" C ASP F 95 " pdb=" CB ASP F 95 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.54e-01 ... (remaining 2561 not shown) Planarity restraints: 2784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 261 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO D 262 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 262 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 262 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 261 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.35e+00 pdb=" N PRO B 262 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 262 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 262 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 261 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO C 262 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 262 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 262 " -0.022 5.00e-02 4.00e+02 ... (remaining 2781 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 4935 2.83 - 3.41: 18559 3.41 - 3.99: 28212 3.99 - 4.56: 40186 4.56 - 5.14: 56752 Nonbonded interactions: 148644 Sorted by model distance: nonbonded pdb=" O HOH C 502 " pdb=" O HOH D 501 " model vdw 2.253 3.040 nonbonded pdb=" O HOH A1102 " pdb=" O HOH B 501 " model vdw 2.254 3.040 nonbonded pdb=" O HOH B 502 " pdb=" O HOH C 501 " model vdw 2.254 3.040 nonbonded pdb=" O HOH A1101 " pdb=" O HOH D 502 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP B 283 " pdb=" OG SER B 285 " model vdw 2.256 3.040 ... (remaining 148639 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 118 through 478) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.450 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 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 : 0.002 0.023 16432 Z= 0.107 Angle : 0.459 7.090 22184 Z= 0.271 Chirality : 0.035 0.127 2564 Planarity : 0.003 0.038 2784 Dihedral : 13.743 75.188 6056 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.43 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.19), residues: 2012 helix: 1.83 (0.14), residues: 1416 sheet: -0.29 (0.59), residues: 64 loop : -2.26 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 134 TYR 0.005 0.001 TYR A 435 PHE 0.011 0.001 PHE C 318 TRP 0.006 0.001 TRP C 158 HIS 0.003 0.000 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00187 (16428) covalent geometry : angle 0.45511 (22176) SS BOND : bond 0.00575 ( 4) SS BOND : angle 3.34689 ( 8) hydrogen bonds : bond 0.19106 ( 1028) hydrogen bonds : angle 4.92871 ( 3009) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 63 ILE cc_start: 0.6884 (mm) cc_final: 0.6536 (mt) REVERT: F 97 ASN cc_start: 0.4152 (p0) cc_final: 0.3717 (p0) REVERT: C 210 MET cc_start: 0.7969 (mmm) cc_final: 0.7762 (mmm) REVERT: G 99 TYR cc_start: 0.5626 (m-80) cc_final: 0.5374 (m-80) REVERT: H 141 PHE cc_start: 0.7279 (t80) cc_final: 0.7051 (t80) outliers start: 0 outliers final: 0 residues processed: 381 average time/residue: 0.1426 time to fit residues: 75.7724 Evaluate side-chains 315 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.0770 chunk 91 optimal weight: 7.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN C 408 HIS C 415 GLN C 452 HIS C 458 GLN G 3 GLN G 143 GLN D 293 ASN D 415 GLN D 458 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.156799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.111434 restraints weight = 26322.279| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.80 r_work: 0.3068 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16432 Z= 0.126 Angle : 0.509 9.375 22184 Z= 0.276 Chirality : 0.038 0.133 2564 Planarity : 0.004 0.039 2784 Dihedral : 3.631 25.610 2192 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 1.20 % Allowed : 6.98 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.19), residues: 2012 helix: 1.78 (0.14), residues: 1448 sheet: None (None), residues: 0 loop : -2.18 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 86 TYR 0.011 0.001 TYR F 99 PHE 0.016 0.001 PHE H 65 TRP 0.013 0.001 TRP C 432 HIS 0.002 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00249 (16428) covalent geometry : angle 0.50783 (22176) SS BOND : bond 0.00428 ( 4) SS BOND : angle 1.90527 ( 8) hydrogen bonds : bond 0.05735 ( 1028) hydrogen bonds : angle 3.78180 ( 3009) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 343 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 65 PHE cc_start: 0.7108 (t80) cc_final: 0.6900 (t80) REVERT: E 72 MET cc_start: 0.7702 (mmm) cc_final: 0.7460 (mmm) REVERT: B 283 ASP cc_start: 0.5987 (t0) cc_final: 0.5597 (p0) REVERT: F 97 ASN cc_start: 0.5377 (p0) cc_final: 0.4842 (p0) REVERT: F 126 ARG cc_start: 0.8191 (mtm180) cc_final: 0.7936 (mtt-85) REVERT: G 72 MET cc_start: 0.7761 (mmm) cc_final: 0.7533 (mmm) outliers start: 21 outliers final: 11 residues processed: 350 average time/residue: 0.1503 time to fit residues: 72.6551 Evaluate side-chains 335 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 324 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 81 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 83 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 8 optimal weight: 0.3980 chunk 63 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN E 111 ASN B 293 ASN C 408 HIS C 415 GLN C 458 GLN D 293 ASN D 458 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.154176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.111423 restraints weight = 26451.234| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.14 r_work: 0.2991 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16432 Z= 0.178 Angle : 0.558 9.546 22184 Z= 0.301 Chirality : 0.040 0.125 2564 Planarity : 0.004 0.056 2784 Dihedral : 3.998 32.024 2192 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.58 % Favored : 96.37 % Rotamer: Outliers : 1.43 % Allowed : 9.38 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.19), residues: 2012 helix: 1.59 (0.14), residues: 1448 sheet: -0.32 (0.61), residues: 64 loop : -2.63 (0.23), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 86 TYR 0.014 0.001 TYR E 138 PHE 0.019 0.002 PHE H 65 TRP 0.008 0.002 TRP A 158 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00403 (16428) covalent geometry : angle 0.55746 (22176) SS BOND : bond 0.00481 ( 4) SS BOND : angle 1.47775 ( 8) hydrogen bonds : bond 0.07263 ( 1028) hydrogen bonds : angle 3.83756 ( 3009) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 330 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8705 (t0) cc_final: 0.8458 (t0) REVERT: A 471 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7601 (ttp-170) REVERT: E 68 PHE cc_start: 0.7559 (t80) cc_final: 0.7213 (t80) REVERT: E 72 MET cc_start: 0.7617 (mmm) cc_final: 0.7336 (mmm) REVERT: B 124 HIS cc_start: 0.7499 (t-170) cc_final: 0.7229 (t-170) REVERT: B 283 ASP cc_start: 0.6273 (t0) cc_final: 0.5916 (p0) REVERT: F 6 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7474 (mp0) REVERT: F 12 PHE cc_start: 0.7899 (m-80) cc_final: 0.7400 (m-80) REVERT: F 74 ARG cc_start: 0.8095 (mmp80) cc_final: 0.7803 (mmm-85) REVERT: F 97 ASN cc_start: 0.5632 (p0) cc_final: 0.5349 (p0) REVERT: G 69 LEU cc_start: 0.8787 (mm) cc_final: 0.8568 (tp) outliers start: 25 outliers final: 18 residues processed: 340 average time/residue: 0.1422 time to fit residues: 66.9053 Evaluate side-chains 338 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 319 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 72 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 54 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN B 293 ASN C 415 GLN C 458 GLN D 458 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.156134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108723 restraints weight = 26412.785| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.22 r_work: 0.3006 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16432 Z= 0.119 Angle : 0.493 8.190 22184 Z= 0.265 Chirality : 0.037 0.196 2564 Planarity : 0.003 0.036 2784 Dihedral : 3.744 30.447 2192 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 1.43 % Allowed : 11.16 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.19), residues: 2012 helix: 1.90 (0.14), residues: 1436 sheet: -0.38 (0.62), residues: 64 loop : -2.48 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 37 TYR 0.016 0.001 TYR E 138 PHE 0.017 0.001 PHE G 68 TRP 0.009 0.001 TRP B 432 HIS 0.002 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00235 (16428) covalent geometry : angle 0.49296 (22176) SS BOND : bond 0.00353 ( 4) SS BOND : angle 0.94979 ( 8) hydrogen bonds : bond 0.05567 ( 1028) hydrogen bonds : angle 3.60063 ( 3009) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 329 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8659 (t0) cc_final: 0.8421 (t0) REVERT: A 419 ARG cc_start: 0.8814 (mtp180) cc_final: 0.8596 (mtp180) REVERT: E 68 PHE cc_start: 0.7522 (t80) cc_final: 0.7027 (t80) REVERT: E 72 MET cc_start: 0.7638 (mmm) cc_final: 0.7303 (mmm) REVERT: B 124 HIS cc_start: 0.7273 (t-170) cc_final: 0.7001 (t-170) REVERT: B 283 ASP cc_start: 0.6462 (t0) cc_final: 0.6150 (p0) REVERT: F 74 ARG cc_start: 0.8122 (mmp80) cc_final: 0.7837 (mmm-85) REVERT: F 97 ASN cc_start: 0.5792 (p0) cc_final: 0.5310 (p0) REVERT: F 138 TYR cc_start: 0.8624 (p90) cc_final: 0.8399 (p90) REVERT: G 13 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8178 (mmtm) REVERT: G 69 LEU cc_start: 0.8829 (mm) cc_final: 0.8564 (tp) REVERT: H 13 LYS cc_start: 0.8294 (mmmt) cc_final: 0.7961 (mmtm) REVERT: H 72 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7979 (ttm) outliers start: 25 outliers final: 15 residues processed: 339 average time/residue: 0.1438 time to fit residues: 68.2024 Evaluate side-chains 332 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 316 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 462 GLN Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 130 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 181 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 111 ASN B 293 ASN F 8 GLN C 458 GLN D 458 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.155214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.114520 restraints weight = 26435.487| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.59 r_work: 0.3004 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16432 Z= 0.137 Angle : 0.522 10.860 22184 Z= 0.278 Chirality : 0.038 0.157 2564 Planarity : 0.004 0.043 2784 Dihedral : 3.807 31.549 2192 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 2.23 % Allowed : 11.16 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.19), residues: 2012 helix: 1.85 (0.14), residues: 1440 sheet: -0.36 (0.62), residues: 64 loop : -2.48 (0.22), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 300 TYR 0.015 0.001 TYR E 138 PHE 0.013 0.001 PHE C 318 TRP 0.007 0.001 TRP A 158 HIS 0.003 0.001 HIS D 452 Details of bonding type rmsd covalent geometry : bond 0.00291 (16428) covalent geometry : angle 0.52143 (22176) SS BOND : bond 0.00387 ( 4) SS BOND : angle 1.04271 ( 8) hydrogen bonds : bond 0.06084 ( 1028) hydrogen bonds : angle 3.61334 ( 3009) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 321 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: E 68 PHE cc_start: 0.7372 (t80) cc_final: 0.6934 (t80) REVERT: E 72 MET cc_start: 0.7721 (mmm) cc_final: 0.7472 (mmm) REVERT: E 86 ARG cc_start: 0.8115 (mmm160) cc_final: 0.7848 (mmt180) REVERT: E 111 ASN cc_start: 0.6839 (p0) cc_final: 0.6074 (p0) REVERT: B 124 HIS cc_start: 0.7152 (t-170) cc_final: 0.6916 (t-170) REVERT: F 97 ASN cc_start: 0.5688 (p0) cc_final: 0.5187 (p0) REVERT: G 7 GLU cc_start: 0.7889 (pm20) cc_final: 0.7671 (pm20) REVERT: G 69 LEU cc_start: 0.8869 (mm) cc_final: 0.8610 (tp) REVERT: G 86 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7485 (mmm-85) outliers start: 39 outliers final: 27 residues processed: 339 average time/residue: 0.1366 time to fit residues: 64.7204 Evaluate side-chains 342 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 315 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 462 GLN Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 130 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 126 optimal weight: 0.5980 chunk 170 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 198 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 172 optimal weight: 0.0870 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN C 458 GLN D 458 GLN H 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.156495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.110310 restraints weight = 26500.589| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.89 r_work: 0.3031 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16432 Z= 0.115 Angle : 0.512 10.052 22184 Z= 0.269 Chirality : 0.037 0.150 2564 Planarity : 0.003 0.037 2784 Dihedral : 3.682 29.299 2192 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.68 % Favored : 96.27 % Rotamer: Outliers : 1.83 % Allowed : 12.24 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.19), residues: 2012 helix: 2.01 (0.14), residues: 1436 sheet: None (None), residues: 0 loop : -2.32 (0.21), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 37 TYR 0.017 0.001 TYR E 138 PHE 0.026 0.001 PHE H 68 TRP 0.007 0.001 TRP A 432 HIS 0.002 0.000 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00229 (16428) covalent geometry : angle 0.51083 (22176) SS BOND : bond 0.00366 ( 4) SS BOND : angle 1.65876 ( 8) hydrogen bonds : bond 0.05241 ( 1028) hydrogen bonds : angle 3.51348 ( 3009) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 326 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7586 (ttp-170) REVERT: E 68 PHE cc_start: 0.7553 (t80) cc_final: 0.7032 (t80) REVERT: E 72 MET cc_start: 0.7501 (mmm) cc_final: 0.7219 (mmm) REVERT: E 111 ASN cc_start: 0.7146 (p0) cc_final: 0.6430 (p0) REVERT: F 13 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8060 (mmtm) REVERT: F 97 ASN cc_start: 0.5771 (p0) cc_final: 0.5284 (p0) REVERT: G 7 GLU cc_start: 0.8018 (pm20) cc_final: 0.7731 (pm20) REVERT: G 68 PHE cc_start: 0.7818 (t80) cc_final: 0.7599 (t80) REVERT: G 69 LEU cc_start: 0.8853 (mm) cc_final: 0.8557 (tp) REVERT: G 72 MET cc_start: 0.7713 (mmm) cc_final: 0.7496 (mmm) REVERT: H 145 MET cc_start: 0.6666 (ppp) cc_final: 0.6448 (ppp) outliers start: 32 outliers final: 22 residues processed: 338 average time/residue: 0.1495 time to fit residues: 70.3523 Evaluate side-chains 340 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 317 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 462 GLN Chi-restraints excluded: chain H residue 32 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN C 458 GLN D 458 GLN H 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.154938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.113972 restraints weight = 26322.787| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.54 r_work: 0.3006 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16432 Z= 0.143 Angle : 0.545 10.658 22184 Z= 0.288 Chirality : 0.039 0.135 2564 Planarity : 0.004 0.048 2784 Dihedral : 3.852 31.288 2192 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 1.66 % Allowed : 12.47 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.19), residues: 2012 helix: 1.87 (0.14), residues: 1440 sheet: -0.38 (0.61), residues: 64 loop : -2.38 (0.23), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 37 TYR 0.014 0.001 TYR H 138 PHE 0.025 0.002 PHE H 68 TRP 0.007 0.001 TRP A 158 HIS 0.003 0.001 HIS D 452 Details of bonding type rmsd covalent geometry : bond 0.00313 (16428) covalent geometry : angle 0.54403 (22176) SS BOND : bond 0.00443 ( 4) SS BOND : angle 1.58083 ( 8) hydrogen bonds : bond 0.06189 ( 1028) hydrogen bonds : angle 3.58986 ( 3009) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 323 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: E 68 PHE cc_start: 0.7362 (t80) cc_final: 0.6856 (t80) REVERT: E 111 ASN cc_start: 0.6864 (p0) cc_final: 0.6045 (p0) REVERT: B 124 HIS cc_start: 0.7182 (t-170) cc_final: 0.6974 (t-170) REVERT: F 97 ASN cc_start: 0.5621 (p0) cc_final: 0.5145 (p0) REVERT: F 143 GLN cc_start: 0.7517 (tm-30) cc_final: 0.7294 (tm-30) REVERT: G 69 LEU cc_start: 0.8873 (mm) cc_final: 0.8530 (tp) outliers start: 29 outliers final: 25 residues processed: 337 average time/residue: 0.1528 time to fit residues: 71.9848 Evaluate side-chains 341 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 316 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 462 GLN Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 130 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 63 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 154 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN D 458 GLN H 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.155599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.109200 restraints weight = 26390.670| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.70 r_work: 0.3026 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16432 Z= 0.132 Angle : 0.550 10.537 22184 Z= 0.290 Chirality : 0.038 0.165 2564 Planarity : 0.003 0.037 2784 Dihedral : 3.852 31.609 2192 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.68 % Favored : 96.27 % Rotamer: Outliers : 2.06 % Allowed : 13.10 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.19), residues: 2012 helix: 1.91 (0.14), residues: 1440 sheet: -0.40 (0.61), residues: 64 loop : -2.39 (0.23), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 37 TYR 0.015 0.001 TYR E 138 PHE 0.017 0.001 PHE G 141 TRP 0.007 0.001 TRP A 432 HIS 0.002 0.001 HIS D 452 Details of bonding type rmsd covalent geometry : bond 0.00281 (16428) covalent geometry : angle 0.54969 (22176) SS BOND : bond 0.00400 ( 4) SS BOND : angle 1.38486 ( 8) hydrogen bonds : bond 0.05782 ( 1028) hydrogen bonds : angle 3.53931 ( 3009) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 320 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 433 LEU cc_start: 0.9108 (mm) cc_final: 0.8897 (mm) REVERT: A 471 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7620 (ttp-170) REVERT: E 68 PHE cc_start: 0.7366 (t80) cc_final: 0.7098 (t80) REVERT: F 97 ASN cc_start: 0.5787 (p0) cc_final: 0.5316 (p0) REVERT: F 143 GLN cc_start: 0.7485 (tm-30) cc_final: 0.7208 (tm-30) REVERT: G 69 LEU cc_start: 0.8864 (mm) cc_final: 0.8620 (tp) REVERT: H 74 ARG cc_start: 0.8105 (ttp-110) cc_final: 0.7821 (ttm110) outliers start: 36 outliers final: 33 residues processed: 340 average time/residue: 0.1484 time to fit residues: 70.3834 Evaluate side-chains 346 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 312 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 462 GLN Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 130 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 85 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 165 optimal weight: 0.0870 chunk 146 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 111 ASN B 293 ASN C 458 GLN G 97 ASN D 458 GLN H 41 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.154992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.113623 restraints weight = 26213.467| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.36 r_work: 0.3011 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16432 Z= 0.154 Angle : 0.582 10.973 22184 Z= 0.307 Chirality : 0.040 0.163 2564 Planarity : 0.004 0.049 2784 Dihedral : 4.044 33.171 2192 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.68 % Favored : 96.27 % Rotamer: Outliers : 2.12 % Allowed : 13.27 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.19), residues: 2012 helix: 1.80 (0.14), residues: 1440 sheet: -0.39 (0.62), residues: 64 loop : -2.43 (0.23), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 37 TYR 0.015 0.001 TYR E 138 PHE 0.027 0.002 PHE H 68 TRP 0.009 0.001 TRP D 432 HIS 0.003 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00341 (16428) covalent geometry : angle 0.58115 (22176) SS BOND : bond 0.00435 ( 4) SS BOND : angle 1.41211 ( 8) hydrogen bonds : bond 0.06373 ( 1028) hydrogen bonds : angle 3.62510 ( 3009) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 314 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.7972 (mp0) cc_final: 0.7649 (pt0) REVERT: A 471 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7740 (ttp-170) REVERT: B 124 HIS cc_start: 0.7362 (t-170) cc_final: 0.7155 (t-170) REVERT: F 97 ASN cc_start: 0.5805 (p0) cc_final: 0.5334 (p0) REVERT: G 69 LEU cc_start: 0.8871 (mm) cc_final: 0.8630 (tp) REVERT: G 89 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: D 469 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8318 (tm-30) outliers start: 37 outliers final: 31 residues processed: 337 average time/residue: 0.1363 time to fit residues: 64.3766 Evaluate side-chains 344 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 311 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 462 GLN Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 161 optimal weight: 0.5980 chunk 192 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 9 optimal weight: 0.0370 chunk 53 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 41 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN D 458 GLN H 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.157355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.112493 restraints weight = 26590.569| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.54 r_work: 0.3106 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16432 Z= 0.116 Angle : 0.555 12.083 22184 Z= 0.288 Chirality : 0.038 0.214 2564 Planarity : 0.003 0.036 2784 Dihedral : 3.782 28.697 2192 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.18 % Favored : 96.77 % Rotamer: Outliers : 1.14 % Allowed : 14.47 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.19), residues: 2012 helix: 2.01 (0.14), residues: 1436 sheet: -0.51 (0.61), residues: 64 loop : -2.34 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 37 TYR 0.016 0.001 TYR E 138 PHE 0.024 0.001 PHE G 141 TRP 0.014 0.001 TRP B 432 HIS 0.003 0.000 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00232 (16428) covalent geometry : angle 0.55468 (22176) SS BOND : bond 0.00325 ( 4) SS BOND : angle 1.17333 ( 8) hydrogen bonds : bond 0.04850 ( 1028) hydrogen bonds : angle 3.45196 ( 3009) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 321 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.7764 (mp0) cc_final: 0.7560 (pt0) REVERT: A 433 LEU cc_start: 0.9086 (mm) cc_final: 0.8859 (mm) REVERT: A 471 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7678 (ttp-170) REVERT: F 86 ARG cc_start: 0.8450 (mtt-85) cc_final: 0.8208 (ttm-80) REVERT: F 97 ASN cc_start: 0.5704 (p0) cc_final: 0.5232 (p0) REVERT: C 294 LYS cc_start: 0.7654 (mmtm) cc_final: 0.7403 (mmtm) REVERT: G 69 LEU cc_start: 0.8868 (mm) cc_final: 0.8643 (tp) REVERT: D 300 ARG cc_start: 0.7093 (ttp80) cc_final: 0.6830 (ttp-170) REVERT: D 433 LEU cc_start: 0.8894 (mm) cc_final: 0.8583 (mm) REVERT: H 68 PHE cc_start: 0.7510 (t80) cc_final: 0.7189 (t80) REVERT: H 86 ARG cc_start: 0.8231 (mmm160) cc_final: 0.7915 (mmt180) outliers start: 20 outliers final: 14 residues processed: 332 average time/residue: 0.1426 time to fit residues: 65.9151 Evaluate side-chains 324 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 309 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 462 GLN Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 160 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 107 HIS ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN G 137 ASN H 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.155273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.113954 restraints weight = 26340.461| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.35 r_work: 0.3026 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16432 Z= 0.147 Angle : 0.604 12.050 22184 Z= 0.313 Chirality : 0.040 0.196 2564 Planarity : 0.004 0.053 2784 Dihedral : 3.985 31.369 2192 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 1.14 % Allowed : 14.59 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.19), residues: 2012 helix: 1.81 (0.14), residues: 1448 sheet: -0.34 (0.62), residues: 64 loop : -2.27 (0.23), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 126 TYR 0.015 0.001 TYR H 138 PHE 0.031 0.002 PHE G 141 TRP 0.009 0.001 TRP C 432 HIS 0.003 0.001 HIS D 452 Details of bonding type rmsd covalent geometry : bond 0.00324 (16428) covalent geometry : angle 0.60305 (22176) SS BOND : bond 0.00386 ( 4) SS BOND : angle 1.63194 ( 8) hydrogen bonds : bond 0.06081 ( 1028) hydrogen bonds : angle 3.57522 ( 3009) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4478.39 seconds wall clock time: 77 minutes 8.55 seconds (4628.55 seconds total)