Starting phenix.real_space_refine on Sat May 17 19:07:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v2h_42914/05_2025/8v2h_42914.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v2h_42914/05_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_42914/05_2025/8v2h_42914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v2h_42914/05_2025/8v2h_42914.map" model { file = "/net/cci-nas-00/data/ceres_data/8v2h_42914/05_2025/8v2h_42914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v2h_42914/05_2025/8v2h_42914.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.64, per 1000 atoms: 0.66 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: 4.28 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.54 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: 4.52 Time building geometry restraints manager: 4.89 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: 13.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.130 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 34.900 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.410 ------------------------------------------------------------------------------- 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 : 4.40 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (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 TRP 0.006 0.001 TRP C 158 HIS 0.003 0.000 HIS B 124 PHE 0.011 0.001 PHE C 318 TYR 0.005 0.001 TYR A 435 ARG 0.003 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.19106 ( 1028) hydrogen bonds : angle 4.92871 ( 3009) SS BOND : bond 0.00575 ( 4) SS BOND : angle 3.34689 ( 8) covalent geometry : bond 0.00187 (16428) covalent geometry : angle 0.45511 (22176) *********************** 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 : 1.911 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: 0.3716 (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: 0.5171 (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: 0.3294 time to fit residues: 174.8361 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 : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 181 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 B 415 GLN C 408 HIS C 415 GLN C 452 HIS C 458 GLN G 143 GLN D 415 GLN D 458 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.154291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.109310 restraints weight = 26146.027| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.95 r_work: 0.2990 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16432 Z= 0.186 Angle : 0.580 9.832 22184 Z= 0.315 Chirality : 0.041 0.138 2564 Planarity : 0.005 0.059 2784 Dihedral : 4.020 32.297 2192 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 1.60 % Allowed : 7.09 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.19), residues: 2012 helix: 1.64 (0.14), residues: 1420 sheet: -0.27 (0.60), residues: 64 loop : -2.50 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 432 HIS 0.004 0.001 HIS A 190 PHE 0.018 0.002 PHE C 318 TYR 0.011 0.001 TYR F 99 ARG 0.008 0.000 ARG G 86 Details of bonding type rmsd hydrogen bonds : bond 0.07428 ( 1028) hydrogen bonds : angle 3.97772 ( 3009) SS BOND : bond 0.00622 ( 4) SS BOND : angle 2.12236 ( 8) covalent geometry : bond 0.00420 (16428) covalent geometry : angle 0.57876 (22176) *********************** 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: 28 poor density : 336 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8720 (t0) cc_final: 0.8422 (t0) REVERT: A 471 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7634 (ttp-170) REVERT: B 283 ASP cc_start: 0.6031 (t0) cc_final: 0.5637 (p0) REVERT: G 72 MET cc_start: 0.7775 (mmm) cc_final: 0.7568 (mmm) REVERT: G 86 ARG cc_start: 0.8224 (mmm160) cc_final: 0.7644 (ttm110) outliers start: 28 outliers final: 12 residues processed: 343 average time/residue: 0.3569 time to fit residues: 169.5652 Evaluate side-chains 332 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 319 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain C residue 211 THR 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 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 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 124 optimal weight: 0.0070 chunk 65 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 overall best weight: 0.9604 ------------------------------------------------------------------------------- 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 B 415 GLN C 415 GLN C 458 GLN G 3 GLN G 8 GLN D 415 GLN D 458 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.155556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.110286 restraints weight = 26187.715| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.85 r_work: 0.3034 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16432 Z= 0.128 Angle : 0.503 9.481 22184 Z= 0.272 Chirality : 0.038 0.179 2564 Planarity : 0.003 0.037 2784 Dihedral : 3.824 31.485 2192 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 1.43 % Allowed : 9.84 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.19), residues: 2012 helix: 1.79 (0.14), residues: 1440 sheet: -0.35 (0.61), residues: 64 loop : -2.52 (0.22), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 432 HIS 0.002 0.001 HIS B 124 PHE 0.022 0.002 PHE H 65 TYR 0.016 0.001 TYR E 138 ARG 0.008 0.000 ARG G 86 Details of bonding type rmsd hydrogen bonds : bond 0.05997 ( 1028) hydrogen bonds : angle 3.71964 ( 3009) SS BOND : bond 0.00381 ( 4) SS BOND : angle 1.24671 ( 8) covalent geometry : bond 0.00258 (16428) covalent geometry : angle 0.50293 (22176) *********************** 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 : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7535 (ttp-170) REVERT: E 68 PHE cc_start: 0.7459 (t80) cc_final: 0.7215 (t80) REVERT: B 124 HIS cc_start: 0.7332 (t-170) cc_final: 0.7006 (t-170) REVERT: B 283 ASP cc_start: 0.6219 (t0) cc_final: 0.5912 (p0) REVERT: F 8 GLN cc_start: 0.6815 (mt0) cc_final: 0.6552 (mt0) REVERT: F 36 MET cc_start: 0.7746 (mtt) cc_final: 0.7454 (mtm) REVERT: F 97 ASN cc_start: 0.5571 (p0) cc_final: 0.5261 (p0) REVERT: G 69 LEU cc_start: 0.8833 (mm) cc_final: 0.8618 (tp) REVERT: G 72 MET cc_start: 0.7743 (mmm) cc_final: 0.7534 (mmm) outliers start: 25 outliers final: 16 residues processed: 340 average time/residue: 0.3435 time to fit residues: 160.7992 Evaluate side-chains 331 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 314 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 8 GLN 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 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 168 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 94 optimal weight: 0.5980 chunk 114 optimal weight: 0.0020 chunk 176 optimal weight: 0.7980 chunk 190 optimal weight: 5.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- 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 B 415 GLN C 415 GLN C 458 GLN D 458 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.155949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109108 restraints weight = 26307.632| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.82 r_work: 0.3024 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16432 Z= 0.123 Angle : 0.502 9.818 22184 Z= 0.269 Chirality : 0.038 0.164 2564 Planarity : 0.003 0.037 2784 Dihedral : 3.768 30.463 2192 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.68 % Favored : 96.27 % Rotamer: Outliers : 1.60 % Allowed : 10.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.19), residues: 2012 helix: 1.87 (0.14), residues: 1440 sheet: -0.40 (0.61), residues: 64 loop : -2.47 (0.23), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 432 HIS 0.002 0.001 HIS B 124 PHE 0.016 0.001 PHE G 65 TYR 0.016 0.001 TYR E 138 ARG 0.005 0.000 ARG C 300 Details of bonding type rmsd hydrogen bonds : bond 0.05670 ( 1028) hydrogen bonds : angle 3.61919 ( 3009) SS BOND : bond 0.00320 ( 4) SS BOND : angle 0.98501 ( 8) covalent geometry : bond 0.00250 (16428) covalent geometry : angle 0.50145 (22176) *********************** 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 356 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 328 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8603 (t0) cc_final: 0.8346 (t0) REVERT: A 471 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7590 (ttp-170) REVERT: E 68 PHE cc_start: 0.7499 (t80) cc_final: 0.7127 (t80) REVERT: E 72 MET cc_start: 0.7414 (mmm) cc_final: 0.7141 (mmm) REVERT: B 283 ASP cc_start: 0.6380 (t0) cc_final: 0.6122 (p0) REVERT: F 8 GLN cc_start: 0.7063 (mt0) cc_final: 0.6801 (mt0) REVERT: F 36 MET cc_start: 0.7598 (mtt) cc_final: 0.7335 (mtm) REVERT: F 97 ASN cc_start: 0.5752 (p0) cc_final: 0.5263 (p0) REVERT: G 13 LYS cc_start: 0.8458 (mmmt) cc_final: 0.8126 (mmtm) REVERT: G 72 MET cc_start: 0.7788 (mmm) cc_final: 0.7580 (mmm) REVERT: H 72 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7992 (ttm) outliers start: 28 outliers final: 22 residues processed: 342 average time/residue: 0.3376 time to fit residues: 160.2799 Evaluate side-chains 334 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 310 time to evaluate : 1.887 ------------------------------------------------------------------------------- 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 293 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 333 CYS 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 322 LEU Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain G residue 8 GLN 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 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 99 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 28 optimal weight: 0.0970 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 B 415 GLN C 458 GLN D 293 ASN D 458 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.155516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114296 restraints weight = 26690.853| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.40 r_work: 0.3025 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16432 Z= 0.134 Angle : 0.524 10.798 22184 Z= 0.279 Chirality : 0.038 0.132 2564 Planarity : 0.004 0.041 2784 Dihedral : 3.804 31.440 2192 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 2.06 % Allowed : 11.84 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.19), residues: 2012 helix: 1.87 (0.14), residues: 1440 sheet: -0.39 (0.61), residues: 64 loop : -2.46 (0.23), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 158 HIS 0.003 0.001 HIS D 452 PHE 0.018 0.002 PHE G 68 TYR 0.015 0.001 TYR E 138 ARG 0.005 0.000 ARG F 126 Details of bonding type rmsd hydrogen bonds : bond 0.05976 ( 1028) hydrogen bonds : angle 3.63270 ( 3009) SS BOND : bond 0.00417 ( 4) SS BOND : angle 1.70226 ( 8) covalent geometry : bond 0.00285 (16428) covalent geometry : angle 0.52338 (22176) *********************** 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 356 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 320 time to evaluate : 1.797 Fit side-chains revert: symmetry clash REVERT: A 471 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7533 (ttp-170) REVERT: E 68 PHE cc_start: 0.7331 (t80) cc_final: 0.6934 (t80) REVERT: E 72 MET cc_start: 0.7560 (mmm) cc_final: 0.7333 (mmm) REVERT: E 111 ASN cc_start: 0.6880 (p0) cc_final: 0.6124 (p0) REVERT: B 210 MET cc_start: 0.8125 (mmm) cc_final: 0.7881 (mmm) REVERT: F 13 LYS cc_start: 0.8247 (mmmt) cc_final: 0.8004 (mmtm) REVERT: F 97 ASN cc_start: 0.5617 (p0) cc_final: 0.5110 (p0) REVERT: G 69 LEU cc_start: 0.8827 (mm) cc_final: 0.8428 (tp) REVERT: G 89 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.6833 (m-10) outliers start: 36 outliers final: 27 residues processed: 342 average time/residue: 0.3312 time to fit residues: 157.1685 Evaluate side-chains 341 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 312 time to evaluate : 1.854 ------------------------------------------------------------------------------- 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 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 322 LEU Chi-restraints excluded: chain B residue 333 CYS 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 462 GLN 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 130 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 B 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 = 0.4098 r_free = 0.4098 target = 0.155131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112176 restraints weight = 26506.215| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.17 r_work: 0.3028 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16432 Z= 0.137 Angle : 0.539 10.118 22184 Z= 0.286 Chirality : 0.039 0.129 2564 Planarity : 0.004 0.042 2784 Dihedral : 3.873 32.508 2192 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.78 % Favored : 96.17 % Rotamer: Outliers : 2.23 % Allowed : 12.41 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.19), residues: 2012 helix: 1.83 (0.14), residues: 1440 sheet: -0.41 (0.61), residues: 64 loop : -2.47 (0.23), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 158 HIS 0.003 0.001 HIS D 452 PHE 0.025 0.002 PHE H 68 TYR 0.016 0.001 TYR E 138 ARG 0.007 0.000 ARG C 300 Details of bonding type rmsd hydrogen bonds : bond 0.06063 ( 1028) hydrogen bonds : angle 3.61291 ( 3009) SS BOND : bond 0.00386 ( 4) SS BOND : angle 1.45228 ( 8) covalent geometry : bond 0.00295 (16428) covalent geometry : angle 0.53871 (22176) *********************** 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 364 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 325 time to evaluate : 1.811 Fit side-chains revert: symmetry clash REVERT: A 471 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7672 (ttp-170) REVERT: E 68 PHE cc_start: 0.7529 (t80) cc_final: 0.7174 (t80) REVERT: E 111 ASN cc_start: 0.7088 (p0) cc_final: 0.6387 (p0) REVERT: F 13 LYS cc_start: 0.8359 (mmmt) cc_final: 0.8130 (mmtm) REVERT: F 97 ASN cc_start: 0.5768 (p0) cc_final: 0.5271 (p0) REVERT: G 69 LEU cc_start: 0.8882 (mm) cc_final: 0.8675 (tp) outliers start: 39 outliers final: 32 residues processed: 347 average time/residue: 0.4099 time to fit residues: 197.3507 Evaluate side-chains 347 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 314 time to evaluate : 2.070 ------------------------------------------------------------------------------- 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 433 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 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 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 462 GLN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 78 optimal weight: 4.9990 chunk 140 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 chunk 178 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN G 8 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 = 0.4098 r_free = 0.4098 target = 0.155158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.110113 restraints weight = 26495.888| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.67 r_work: 0.3021 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16432 Z= 0.137 Angle : 0.551 10.736 22184 Z= 0.290 Chirality : 0.038 0.126 2564 Planarity : 0.004 0.041 2784 Dihedral : 3.879 33.264 2192 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 2.23 % Allowed : 13.27 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.19), residues: 2012 helix: 1.82 (0.14), residues: 1440 sheet: -0.41 (0.61), residues: 64 loop : -2.45 (0.23), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 158 HIS 0.003 0.001 HIS D 452 PHE 0.025 0.002 PHE H 68 TYR 0.016 0.001 TYR E 138 ARG 0.008 0.000 ARG F 86 Details of bonding type rmsd hydrogen bonds : bond 0.06041 ( 1028) hydrogen bonds : angle 3.61400 ( 3009) SS BOND : bond 0.00438 ( 4) SS BOND : angle 1.31007 ( 8) covalent geometry : bond 0.00295 (16428) covalent geometry : angle 0.55028 (22176) *********************** 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 359 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 320 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7621 (ttp-170) REVERT: E 68 PHE cc_start: 0.7440 (t80) cc_final: 0.7200 (t80) REVERT: E 72 MET cc_start: 0.7414 (mmm) cc_final: 0.7213 (mmm) REVERT: E 111 ASN cc_start: 0.7194 (p0) cc_final: 0.6471 (p0) REVERT: E 126 ARG cc_start: 0.8299 (ptp-170) cc_final: 0.8058 (ptt-90) REVERT: B 471 ARG cc_start: 0.7983 (ttp-110) cc_final: 0.7782 (ptp-170) REVERT: F 74 ARG cc_start: 0.8048 (mmp80) cc_final: 0.7835 (mmm-85) REVERT: F 97 ASN cc_start: 0.5710 (p0) cc_final: 0.5245 (p0) REVERT: G 69 LEU cc_start: 0.8874 (mm) cc_final: 0.8566 (tp) REVERT: G 89 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.6723 (m-10) outliers start: 39 outliers final: 31 residues processed: 343 average time/residue: 0.3258 time to fit residues: 155.7114 Evaluate side-chains 347 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 314 time to evaluate : 1.758 ------------------------------------------------------------------------------- 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 26 THR 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 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 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 462 GLN Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 89 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 33 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.155714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.115574 restraints weight = 26313.159| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.56 r_work: 0.3039 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2244 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= 0.128 Angle : 0.553 12.010 22184 Z= 0.289 Chirality : 0.038 0.136 2564 Planarity : 0.003 0.036 2784 Dihedral : 3.848 32.450 2192 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 2.12 % Allowed : 13.56 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.19), residues: 2012 helix: 2.06 (0.14), residues: 1408 sheet: -0.44 (0.61), residues: 64 loop : -2.32 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 158 HIS 0.002 0.001 HIS D 452 PHE 0.022 0.001 PHE G 141 TYR 0.015 0.001 TYR E 138 ARG 0.006 0.000 ARG F 37 Details of bonding type rmsd hydrogen bonds : bond 0.05694 ( 1028) hydrogen bonds : angle 3.56002 ( 3009) SS BOND : bond 0.00376 ( 4) SS BOND : angle 1.19064 ( 8) covalent geometry : bond 0.00270 (16428) covalent geometry : angle 0.55225 (22176) *********************** 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 357 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 320 time to evaluate : 1.796 Fit side-chains revert: symmetry clash REVERT: A 471 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7596 (ttp-170) REVERT: E 13 LYS cc_start: 0.7839 (mmmt) cc_final: 0.7517 (mmtt) REVERT: E 68 PHE cc_start: 0.7174 (t80) cc_final: 0.6895 (t80) REVERT: E 72 MET cc_start: 0.7581 (mmm) cc_final: 0.7250 (mmm) REVERT: E 111 ASN cc_start: 0.6771 (p0) cc_final: 0.5971 (p0) REVERT: F 97 ASN cc_start: 0.5459 (p0) cc_final: 0.4983 (p0) REVERT: G 69 LEU cc_start: 0.8808 (mm) cc_final: 0.8419 (tp) REVERT: G 89 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.6545 (m-10) outliers start: 37 outliers final: 32 residues processed: 341 average time/residue: 0.3376 time to fit residues: 160.4492 Evaluate side-chains 351 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 317 time to evaluate : 1.907 ------------------------------------------------------------------------------- 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 A residue 471 ARG Chi-restraints excluded: chain E residue 26 THR 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 223 LEU Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 322 LEU 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 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 462 GLN 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 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 119 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 169 optimal weight: 0.0980 chunk 113 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 182 optimal weight: 8.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 41 GLN B 293 ASN C 458 GLN D 458 GLN H 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.156624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.109760 restraints weight = 26354.655| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.84 r_work: 0.3043 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16432 Z= 0.122 Angle : 0.554 12.036 22184 Z= 0.288 Chirality : 0.038 0.155 2564 Planarity : 0.003 0.037 2784 Dihedral : 3.799 30.933 2192 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 1.72 % Allowed : 14.19 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.19), residues: 2012 helix: 1.96 (0.14), residues: 1432 sheet: -0.44 (0.61), residues: 64 loop : -2.45 (0.23), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 432 HIS 0.002 0.000 HIS D 452 PHE 0.028 0.001 PHE G 141 TYR 0.017 0.001 TYR H 138 ARG 0.006 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.05305 ( 1028) hydrogen bonds : angle 3.55097 ( 3009) SS BOND : bond 0.00319 ( 4) SS BOND : angle 1.10819 ( 8) covalent geometry : bond 0.00247 (16428) covalent geometry : angle 0.55401 (22176) *********************** 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 355 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 325 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8195 (mmmt) cc_final: 0.7880 (mmtt) REVERT: E 68 PHE cc_start: 0.7458 (t80) cc_final: 0.7094 (t80) REVERT: E 71 MET cc_start: 0.8786 (ttt) cc_final: 0.8510 (ptm) REVERT: E 111 ASN cc_start: 0.7167 (p0) cc_final: 0.6420 (p0) REVERT: F 66 PRO cc_start: 0.8178 (Cg_exo) cc_final: 0.7946 (Cg_endo) REVERT: F 97 ASN cc_start: 0.5788 (p0) cc_final: 0.5329 (p0) REVERT: C 294 LYS cc_start: 0.7749 (mmtm) cc_final: 0.7449 (mmtm) REVERT: C 301 PHE cc_start: 0.8025 (t80) cc_final: 0.7734 (t80) REVERT: G 69 LEU cc_start: 0.8846 (mm) cc_final: 0.8595 (tp) REVERT: G 89 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.6683 (m-10) REVERT: D 300 ARG cc_start: 0.7156 (ttp80) cc_final: 0.6780 (ttp80) REVERT: H 68 PHE cc_start: 0.7597 (t80) cc_final: 0.7250 (t80) outliers start: 30 outliers final: 25 residues processed: 342 average time/residue: 0.3814 time to fit residues: 182.7734 Evaluate side-chains 345 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 319 time to evaluate : 1.805 ------------------------------------------------------------------------------- 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 343 THR Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 69 LEU 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 223 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 462 GLN 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 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 130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 149 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 102 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 41 GLN B 293 ASN C 458 GLN D 458 GLN H 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.157184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.113638 restraints weight = 26636.872| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.15 r_work: 0.3048 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16432 Z= 0.117 Angle : 0.562 12.386 22184 Z= 0.290 Chirality : 0.037 0.129 2564 Planarity : 0.003 0.050 2784 Dihedral : 3.738 27.669 2192 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.68 % Favored : 96.27 % Rotamer: Outliers : 1.72 % Allowed : 14.36 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.19), residues: 2012 helix: 1.94 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -2.23 (0.21), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 432 HIS 0.003 0.000 HIS D 452 PHE 0.028 0.001 PHE H 68 TYR 0.018 0.001 TYR H 138 ARG 0.014 0.000 ARG F 74 Details of bonding type rmsd hydrogen bonds : bond 0.05019 ( 1028) hydrogen bonds : angle 3.52985 ( 3009) SS BOND : bond 0.00297 ( 4) SS BOND : angle 1.12801 ( 8) covalent geometry : bond 0.00237 (16428) covalent geometry : angle 0.56129 (22176) ********************** 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 350 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 320 time to evaluate : 1.793 Fit side-chains revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8081 (mmmt) cc_final: 0.7823 (mmtt) REVERT: E 68 PHE cc_start: 0.7539 (t80) cc_final: 0.7256 (t80) REVERT: F 66 PRO cc_start: 0.8102 (Cg_exo) cc_final: 0.7875 (Cg_endo) REVERT: F 97 ASN cc_start: 0.5699 (p0) cc_final: 0.5239 (p0) REVERT: C 301 PHE cc_start: 0.8013 (t80) cc_final: 0.7720 (t80) REVERT: G 69 LEU cc_start: 0.8872 (mm) cc_final: 0.8600 (tp) REVERT: G 89 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.6594 (m-10) REVERT: D 300 ARG cc_start: 0.7165 (ttp80) cc_final: 0.6961 (ttp-170) REVERT: H 74 ARG cc_start: 0.8064 (ttp-110) cc_final: 0.7698 (ttm110) REVERT: H 86 ARG cc_start: 0.8252 (mmt180) cc_final: 0.7725 (mmt180) REVERT: H 87 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8234 (mm-30) outliers start: 30 outliers final: 23 residues processed: 336 average time/residue: 0.3352 time to fit residues: 156.3429 Evaluate side-chains 339 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 315 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 69 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 333 CYS Chi-restraints excluded: chain C residue 462 GLN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 160 optimal weight: 1.9990 chunk 172 optimal weight: 0.0470 chunk 161 optimal weight: 0.9990 chunk 82 optimal weight: 0.0060 chunk 65 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 overall best weight: 0.8098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 41 GLN E 111 ASN B 293 ASN C 458 GLN H 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.156498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.109485 restraints weight = 26138.250| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.70 r_work: 0.3058 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16432 Z= 0.124 Angle : 0.579 12.277 22184 Z= 0.298 Chirality : 0.038 0.166 2564 Planarity : 0.003 0.036 2784 Dihedral : 3.776 27.266 2192 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 1.66 % Allowed : 14.53 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.19), residues: 2012 helix: 1.92 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -2.21 (0.22), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 432 HIS 0.003 0.001 HIS D 452 PHE 0.026 0.001 PHE H 68 TYR 0.017 0.001 TYR H 138 ARG 0.011 0.000 ARG E 126 Details of bonding type rmsd hydrogen bonds : bond 0.05304 ( 1028) hydrogen bonds : angle 3.53795 ( 3009) SS BOND : bond 0.00365 ( 4) SS BOND : angle 1.25109 ( 8) covalent geometry : bond 0.00261 (16428) covalent geometry : angle 0.57910 (22176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10328.01 seconds wall clock time: 179 minutes 54.02 seconds (10794.02 seconds total)