Starting phenix.real_space_refine on Fri Aug 7 08:26:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thc_41253/08_2026/8thc_41253.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thc_41253/08_2026/8thc_41253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8thc_41253/08_2026/8thc_41253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thc_41253/08_2026/8thc_41253.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8thc_41253/08_2026/8thc_41253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thc_41253/08_2026/8thc_41253.map" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 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 P 14 5.49 5 Mg 3 5.21 5 S 98 5.16 5 C 12925 2.51 5 N 3442 2.21 5 O 3948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20430 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3897 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 21, 'TRANS': 457} Chain breaks: 4 Chain: "B" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2495 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain: "C" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2571 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "D" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2629 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 12, 'TRANS': 319} Chain: "E" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2675 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain breaks: 1 Chain: "F" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1995 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "G" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2011 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain: "H" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2003 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.60, per 1000 atoms: 0.18 Number of scatterers: 20430 At special positions: 0 Unit cell: (117.576, 122.544, 150.696, 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) S 98 16.00 P 14 15.00 Mg 3 11.99 O 3948 8.00 N 3442 7.00 C 12925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 689.0 milliseconds 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4906 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 17 sheets defined 50.4% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 256 through 276 removed outlier: 3.906A pdb=" N LYS A 276 " --> pdb=" O HIS A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.561A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 387 removed outlier: 6.090A pdb=" N ASP A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 429 Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.808A pdb=" N LEU A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 455 Processing helix chain 'A' and resid 465 through 481 removed outlier: 3.503A pdb=" N VAL A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 496 removed outlier: 3.556A pdb=" N LEU A 489 " --> pdb=" O CYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 510 Processing helix chain 'A' and resid 535 through 557 removed outlier: 3.801A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 581 removed outlier: 3.585A pdb=" N ASP A 581 " --> pdb=" O ASN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 592 Processing helix chain 'A' and resid 616 through 627 removed outlier: 3.537A pdb=" N HIS A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 removed outlier: 3.965A pdb=" N ARG A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 661 Processing helix chain 'A' and resid 700 through 708 removed outlier: 4.044A pdb=" N LEU A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 716 Processing helix chain 'A' and resid 716 through 733 Processing helix chain 'A' and resid 773 through 781 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 4.130A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 4.432A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.685A pdb=" N LYS B 149 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE B 150 " --> pdb=" O SER B 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 150' Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.949A pdb=" N VAL B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.711A pdb=" N GLU B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 217 removed outlier: 3.572A pdb=" N GLY B 217 " --> pdb=" O VAL B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 244 through 255 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 302 removed outlier: 3.514A pdb=" N GLY B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.628A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.574A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 89 through 102 Processing helix chain 'C' and resid 118 through 122 removed outlier: 4.000A pdb=" N ALA C 121 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.683A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 153 " --> pdb=" O ALA C 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 149 through 153' Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 170 through 186 removed outlier: 3.613A pdb=" N VAL C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 202 removed outlier: 4.136A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 237 removed outlier: 3.515A pdb=" N ILE C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.683A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR C 288 " --> pdb=" O ILE C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 313 removed outlier: 4.113A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 334 removed outlier: 3.861A pdb=" N GLN C 319 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 42 through 55 removed outlier: 4.021A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 83 Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 105 through 116 Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 215 through 225 removed outlier: 3.531A pdb=" N ARG D 219 " --> pdb=" O GLY D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.751A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 291 Processing helix chain 'D' and resid 296 through 311 removed outlier: 3.538A pdb=" N VAL D 300 " --> pdb=" O SER D 296 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN D 311 " --> pdb=" O TYR D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.671A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 353 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 19 through 32 removed outlier: 3.909A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 62 through 67 removed outlier: 3.643A pdb=" N TYR E 66 " --> pdb=" O PRO E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 105 removed outlier: 3.778A pdb=" N ASP E 100 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY E 102 " --> pdb=" O SER E 99 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASN E 104 " --> pdb=" O MET E 101 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP E 105 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 119 removed outlier: 3.729A pdb=" N MET E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 147 through 161 Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 226 Processing helix chain 'E' and resid 229 through 245 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 353 removed outlier: 3.983A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 19 removed outlier: 3.797A pdb=" N PHE F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.805A pdb=" N GLN F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER F 155 " --> pdb=" O LEU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 166 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 221 removed outlier: 4.354A pdb=" N SER F 220 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.902A pdb=" N LYS G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLY G 18 " --> pdb=" O ARG G 14 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASP G 21 " --> pdb=" O ASP G 17 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS G 22 " --> pdb=" O GLY G 18 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL G 23 " --> pdb=" O PHE G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 removed outlier: 3.683A pdb=" N ALA G 56 " --> pdb=" O GLY G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.979A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 Processing helix chain 'G' and resid 209 through 218 removed outlier: 4.223A pdb=" N GLY G 218 " --> pdb=" O ASP G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'H' and resid 9 through 18 removed outlier: 3.745A pdb=" N LYS H 13 " --> pdb=" O ALA H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 141 through 153 removed outlier: 4.230A pdb=" N GLN H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 209 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.439A pdb=" N VAL A 227 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU A 483 " --> pdb=" O VAL A 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 337 through 338 removed outlier: 6.718A pdb=" N HIS A 337 " --> pdb=" O THR A 461 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 366 Processing sheet with id=AA4, first strand: chain 'A' and resid 600 through 601 removed outlier: 6.471A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASN E 141 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE E 96 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU E 40 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 77 removed outlier: 6.094A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET B 45 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 46 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 49 through 52 removed outlier: 6.064A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 79 through 83 removed outlier: 4.161A pdb=" N LEU C 80 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 63 through 64 removed outlier: 3.983A pdb=" N TYR D 64 " --> pdb=" O PHE D 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 135 through 140 removed outlier: 5.716A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 57 through 60 removed outlier: 6.715A pdb=" N LYS F 5 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR F 60 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N GLU F 3 " --> pdb=" O TYR F 60 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU F 88 " --> pdb=" O PHE F 6 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 71 removed outlier: 3.984A pdb=" N VAL F 26 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 179 through 182 Processing sheet with id=AB4, first strand: chain 'G' and resid 60 through 61 removed outlier: 3.714A pdb=" N ARG G 61 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU G 3 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 66 through 71 removed outlier: 3.613A pdb=" N VAL G 26 " --> pdb=" O MET G 70 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU G 137 " --> pdb=" O ILE G 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU G 229 " --> pdb=" O SER G 135 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS G 196 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 206 through 208 removed outlier: 5.904A pdb=" N SER G 157 " --> pdb=" O ASP G 172 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP G 172 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE H 111 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU H 88 " --> pdb=" O PHE H 6 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA H 92 " --> pdb=" O LEU H 2 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLU H 3 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR H 60 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS H 5 " --> pdb=" O GLN H 58 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 68 through 71 removed outlier: 5.505A pdb=" N LEU H 25 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL H 40 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 177 through 182 removed outlier: 3.522A pdb=" N VAL H 180 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) 1035 hydrogen bonds defined for protein. 2988 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 6761 1.36 - 1.51: 5018 1.51 - 1.65: 8826 1.65 - 1.80: 77 1.80 - 1.95: 75 Bond restraints: 20757 Sorted by residual: bond pdb=" O3B AGS A 801 " pdb=" PB AGS A 801 " ideal model delta sigma weight residual 1.673 1.585 0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" O3B AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sigma weight residual 1.673 1.585 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" O3B AGS B 401 " pdb=" PB AGS B 401 " ideal model delta sigma weight residual 1.673 1.585 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" O3B AGS C 401 " pdb=" PB AGS C 401 " ideal model delta sigma weight residual 1.673 1.588 0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" O3A AGS B 401 " pdb=" PA AGS B 401 " ideal model delta sigma weight residual 1.664 1.586 0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 20752 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 27439 2.04 - 4.07: 506 4.07 - 6.11: 95 6.11 - 8.14: 25 8.14 - 10.18: 18 Bond angle restraints: 28083 Sorted by residual: angle pdb=" N GLU F 129 " pdb=" CA GLU F 129 " pdb=" C GLU F 129 " ideal model delta sigma weight residual 113.18 107.24 5.94 1.21e+00 6.83e-01 2.41e+01 angle pdb=" CA LEU F 131 " pdb=" C LEU F 131 " pdb=" O LEU F 131 " ideal model delta sigma weight residual 121.58 117.13 4.45 1.16e+00 7.43e-01 1.47e+01 angle pdb=" CB ARG G 80 " pdb=" CG ARG G 80 " pdb=" CD ARG G 80 " ideal model delta sigma weight residual 111.30 119.81 -8.51 2.30e+00 1.89e-01 1.37e+01 angle pdb=" CA MET C 78 " pdb=" CB MET C 78 " pdb=" CG MET C 78 " ideal model delta sigma weight residual 114.10 121.50 -7.40 2.00e+00 2.50e-01 1.37e+01 angle pdb=" O3A AGS D 401 " pdb=" PB AGS D 401 " pdb=" O3B AGS D 401 " ideal model delta sigma weight residual 100.38 110.56 -10.18 3.00e+00 1.11e-01 1.15e+01 ... (remaining 28078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 12579 35.52 - 71.04: 260 71.04 - 106.57: 40 106.57 - 142.09: 3 142.09 - 177.61: 5 Dihedral angle restraints: 12887 sinusoidal: 5372 harmonic: 7515 Sorted by residual: dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 179.97 120.03 1 2.00e+01 2.50e-03 3.60e+01 dihedral pdb=" O2B AGS A 801 " pdb=" O3B AGS A 801 " pdb=" PB AGS A 801 " pdb=" PG AGS A 801 " ideal model delta sinusoidal sigma weight residual 7.37 -170.24 177.61 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2B AGS B 401 " pdb=" O3B AGS B 401 " pdb=" PB AGS B 401 " pdb=" PG AGS B 401 " ideal model delta sinusoidal sigma weight residual 7.37 -177.57 -175.06 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2819 0.059 - 0.119: 410 0.119 - 0.178: 46 0.178 - 0.237: 6 0.237 - 0.297: 7 Chirality restraints: 3288 Sorted by residual: chirality pdb=" CB ILE C 106 " pdb=" CA ILE C 106 " pdb=" CG1 ILE C 106 " pdb=" CG2 ILE C 106 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB ILE G 128 " pdb=" CA ILE G 128 " pdb=" CG1 ILE G 128 " pdb=" CG2 ILE G 128 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C3' AGS D 401 " pdb=" C2' AGS D 401 " pdb=" C4' AGS D 401 " pdb=" O3' AGS D 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 3285 not shown) Planarity restraints: 3557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 224 " 0.253 9.50e-02 1.11e+02 1.13e-01 7.92e+00 pdb=" NE ARG H 224 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG H 224 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG H 224 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG H 224 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS F 190 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO F 191 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO F 191 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 191 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 97 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO E 98 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 98 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 98 " 0.038 5.00e-02 4.00e+02 ... (remaining 3554 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 406 2.69 - 3.25: 20090 3.25 - 3.80: 32085 3.80 - 4.35: 41577 4.35 - 4.90: 68369 Nonbonded interactions: 162527 Sorted by model distance: nonbonded pdb=" OG1 THR C 60 " pdb="MG MG C 402 " model vdw 2.142 2.170 nonbonded pdb=" O2B AGS D 401 " pdb="MG MG D 402 " model vdw 2.163 2.170 nonbonded pdb=" OG1 THR B 56 " pdb="MG MG B 402 " model vdw 2.179 2.170 nonbonded pdb=" OH TYR C 71 " pdb=" O PHE C 111 " model vdw 2.244 3.040 nonbonded pdb=" OG SER E 99 " pdb=" OE2 GLU E 142 " model vdw 2.262 3.040 ... (remaining 162522 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 'F' selection = (chain 'G' and resid 1 through 254) selection = (chain 'H' and resid 1 through 254) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.780 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 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 : 0.004 0.088 20757 Z= 0.204 Angle : 0.713 10.176 28083 Z= 0.358 Chirality : 0.045 0.297 3288 Planarity : 0.005 0.113 3557 Dihedral : 16.112 177.610 7981 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.09 % Allowed : 0.52 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.17), residues: 2532 helix: 1.13 (0.15), residues: 1152 sheet: 0.38 (0.25), residues: 486 loop : -1.00 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 69 TYR 0.015 0.001 TYR H 133 PHE 0.028 0.001 PHE E 305 TRP 0.036 0.002 TRP A 780 HIS 0.011 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.20 (20757) covalent geometry : angle 0.71340 / 0.36 (28083) hydrogen bonds : bond 0.18600 / 12.19 ( 1035) hydrogen bonds : angle 6.69558 / 4.70 ( 2988) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 367 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8648 (mm) cc_final: 0.8403 (mm) REVERT: B 73 ASP cc_start: 0.8028 (p0) cc_final: 0.7772 (p0) REVERT: C 212 LEU cc_start: 0.9416 (mm) cc_final: 0.9156 (mm) REVERT: C 276 ASP cc_start: 0.7101 (m-30) cc_final: 0.6856 (m-30) REVERT: D 145 MET cc_start: 0.2913 (mmm) cc_final: 0.2654 (tpt) REVERT: E 174 MET cc_start: 0.8073 (ppp) cc_final: 0.7819 (tmm) REVERT: F 125 PHE cc_start: 0.5475 (m-80) cc_final: 0.5265 (p90) REVERT: F 126 LEU cc_start: 0.1063 (OUTLIER) cc_final: 0.0501 (tp) REVERT: F 239 PHE cc_start: 0.2416 (m-10) cc_final: 0.2197 (m-10) REVERT: G 1 MET cc_start: 0.2991 (tmm) cc_final: 0.2624 (tpt) REVERT: G 14 ARG cc_start: 0.7128 (ptm-80) cc_final: 0.6715 (ptm-80) REVERT: G 70 MET cc_start: 0.5866 (pmm) cc_final: 0.5516 (pmm) REVERT: G 120 ASP cc_start: 0.5891 (t0) cc_final: 0.4874 (p0) REVERT: G 249 PHE cc_start: 0.8334 (m-10) cc_final: 0.7997 (m-80) outliers start: 2 outliers final: 0 residues processed: 368 average time/residue: 0.1120 time to fit residues: 67.8312 Evaluate side-chains 268 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 126 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 194 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.5612 > 50:) chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 460 HIS A 620 HIS ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 HIS D 60 HIS D 128 ASN D 338 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.147514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.113914 restraints weight = 54876.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.115928 restraints weight = 30783.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.117067 restraints weight = 21004.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.117254 restraints weight = 17314.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.117471 restraints weight = 15405.582| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20757 Z= 0.147 Angle : 0.621 13.318 28083 Z= 0.308 Chirality : 0.043 0.180 3288 Planarity : 0.004 0.064 3557 Dihedral : 12.044 171.517 2893 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.04 % Allowed : 8.93 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.17), residues: 2532 helix: 1.47 (0.16), residues: 1172 sheet: 0.37 (0.25), residues: 480 loop : -0.73 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 69 TYR 0.027 0.001 TYR B 306 PHE 0.025 0.002 PHE C 100 TRP 0.017 0.001 TRP A 266 HIS 0.005 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (20757) covalent geometry : angle 0.62083 / 0.31 (28083) hydrogen bonds : bond 0.03915 / 2.58 ( 1035) hydrogen bonds : angle 4.86061 / 3.42 ( 2988) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 293 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 THR cc_start: 0.8039 (m) cc_final: 0.7593 (p) REVERT: B 11 TRP cc_start: 0.6984 (m-10) cc_final: 0.6767 (m-10) REVERT: B 115 GLU cc_start: 0.8441 (pm20) cc_final: 0.8003 (pm20) REVERT: B 297 MET cc_start: 0.8675 (ttt) cc_final: 0.8334 (ttt) REVERT: D 145 MET cc_start: 0.2926 (mmm) cc_final: 0.2648 (tpt) REVERT: D 172 TYR cc_start: 0.8155 (m-80) cc_final: 0.7935 (m-80) REVERT: E 249 LYS cc_start: 0.8759 (mptt) cc_final: 0.8296 (mmtt) REVERT: F 125 PHE cc_start: 0.5442 (m-80) cc_final: 0.5240 (p90) REVERT: F 126 LEU cc_start: 0.1652 (OUTLIER) cc_final: 0.0912 (tp) REVERT: G 1 MET cc_start: 0.3266 (tmm) cc_final: 0.2962 (tpt) REVERT: G 14 ARG cc_start: 0.7481 (ptm-80) cc_final: 0.7135 (ptm-80) REVERT: G 120 ASP cc_start: 0.5988 (t0) cc_final: 0.5272 (p0) REVERT: G 199 MET cc_start: 0.6518 (tmm) cc_final: 0.6106 (tpp) REVERT: G 248 PHE cc_start: 0.8054 (m-80) cc_final: 0.7519 (m-80) REVERT: H 64 HIS cc_start: 0.7205 (t70) cc_final: 0.6919 (t70) outliers start: 24 outliers final: 13 residues processed: 307 average time/residue: 0.1106 time to fit residues: 55.8508 Evaluate side-chains 275 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 261 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 144 CYS Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 245 PHE Chi-restraints excluded: chain G residue 6 PHE Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 225 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 192 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 chunk 183 optimal weight: 20.0000 chunk 235 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 199 optimal weight: 20.0000 chunk 145 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN A 712 GLN C 184 HIS C 213 GLN C 260 HIS D 60 HIS ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.146503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.112395 restraints weight = 55529.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.113125 restraints weight = 34882.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.113528 restraints weight = 26138.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.114146 restraints weight = 22203.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.114324 restraints weight = 20067.707| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20757 Z= 0.168 Angle : 0.612 11.030 28083 Z= 0.300 Chirality : 0.042 0.196 3288 Planarity : 0.004 0.071 3557 Dihedral : 10.931 173.524 2893 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.78 % Allowed : 12.48 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.17), residues: 2532 helix: 1.57 (0.16), residues: 1176 sheet: 0.40 (0.25), residues: 489 loop : -0.64 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 228 TYR 0.024 0.002 TYR B 306 PHE 0.029 0.002 PHE D 187 TRP 0.017 0.002 TRP A 780 HIS 0.005 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (20757) covalent geometry : angle 0.61168 / 0.30 (28083) hydrogen bonds : bond 0.03882 / 2.55 ( 1035) hydrogen bonds : angle 4.69948 / 3.32 ( 2988) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 256 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8341 (tt) REVERT: A 709 THR cc_start: 0.8108 (m) cc_final: 0.7628 (p) REVERT: B 297 MET cc_start: 0.8686 (ttt) cc_final: 0.8254 (ttt) REVERT: D 106 VAL cc_start: 0.8751 (t) cc_final: 0.7842 (t) REVERT: D 145 MET cc_start: 0.3038 (mmm) cc_final: 0.2821 (tpt) REVERT: D 168 LEU cc_start: 0.9098 (mm) cc_final: 0.8875 (mm) REVERT: E 135 TYR cc_start: 0.8601 (p90) cc_final: 0.7984 (p90) REVERT: E 236 MET cc_start: 0.8208 (mtt) cc_final: 0.7963 (tpt) REVERT: E 249 LYS cc_start: 0.8681 (mptt) cc_final: 0.8289 (mmtt) REVERT: F 126 LEU cc_start: 0.1815 (OUTLIER) cc_final: 0.1144 (tp) REVERT: G 14 ARG cc_start: 0.7519 (ptm-80) cc_final: 0.7096 (ptm-80) REVERT: H 42 ASP cc_start: 0.7478 (p0) cc_final: 0.6921 (p0) outliers start: 41 outliers final: 24 residues processed: 284 average time/residue: 0.1105 time to fit residues: 50.9391 Evaluate side-chains 261 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 245 PHE Chi-restraints excluded: chain G residue 6 PHE Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 225 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 34 optimal weight: 0.7980 chunk 238 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 209 optimal weight: 9.9990 chunk 198 optimal weight: 30.0000 chunk 172 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 41 optimal weight: 0.0870 chunk 108 optimal weight: 0.7980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 HIS C 264 ASN D 60 HIS ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.145165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.111015 restraints weight = 54745.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.113381 restraints weight = 30491.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.113484 restraints weight = 20870.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.114827 restraints weight = 18453.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.114502 restraints weight = 16220.467| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20757 Z= 0.117 Angle : 0.575 11.795 28083 Z= 0.278 Chirality : 0.042 0.324 3288 Planarity : 0.004 0.061 3557 Dihedral : 10.449 175.392 2893 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.04 % Allowed : 13.96 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2532 helix: 1.63 (0.16), residues: 1177 sheet: 0.37 (0.25), residues: 494 loop : -0.55 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 44 TYR 0.023 0.001 TYR A 361 PHE 0.020 0.001 PHE A 722 TRP 0.014 0.001 TRP A 780 HIS 0.005 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (20757) covalent geometry : angle 0.57483 / 0.28 (28083) hydrogen bonds : bond 0.03314 / 2.19 ( 1035) hydrogen bonds : angle 4.48815 / 3.18 ( 2988) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 266 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8355 (tt) REVERT: A 709 THR cc_start: 0.8054 (m) cc_final: 0.7563 (p) REVERT: B 247 ASP cc_start: 0.8126 (t70) cc_final: 0.7855 (t70) REVERT: B 297 MET cc_start: 0.8712 (ttt) cc_final: 0.8328 (ttt) REVERT: D 61 MET cc_start: 0.6774 (tmm) cc_final: 0.6468 (tmm) REVERT: D 81 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8229 (mm-30) REVERT: D 145 MET cc_start: 0.2698 (mmm) cc_final: 0.2420 (tpt) REVERT: E 135 TYR cc_start: 0.8538 (p90) cc_final: 0.7917 (p90) REVERT: E 249 LYS cc_start: 0.8722 (mptt) cc_final: 0.8313 (mmtt) REVERT: G 14 ARG cc_start: 0.7647 (ptm-80) cc_final: 0.7067 (ptm-80) REVERT: G 199 MET cc_start: 0.6724 (tmm) cc_final: 0.6322 (tpp) REVERT: G 249 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7961 (m-80) REVERT: H 104 GLU cc_start: 0.5909 (mt-10) cc_final: 0.5553 (mt-10) outliers start: 47 outliers final: 27 residues processed: 292 average time/residue: 0.1121 time to fit residues: 53.9001 Evaluate side-chains 275 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 246 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 245 PHE Chi-restraints excluded: chain G residue 6 PHE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 225 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 126 optimal weight: 10.0000 chunk 210 optimal weight: 30.0000 chunk 49 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 237 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN D 342 GLN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 GLN H 38 GLN ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.138413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.103196 restraints weight = 54880.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.103449 restraints weight = 32123.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.104767 restraints weight = 22609.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.104765 restraints weight = 19859.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.104851 restraints weight = 17982.110| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 20757 Z= 0.283 Angle : 0.756 13.341 28083 Z= 0.371 Chirality : 0.046 0.252 3288 Planarity : 0.005 0.060 3557 Dihedral : 10.631 172.146 2891 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.73 % Allowed : 14.74 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.17), residues: 2532 helix: 1.15 (0.15), residues: 1167 sheet: 0.08 (0.24), residues: 489 loop : -0.68 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 44 TYR 0.034 0.002 TYR D 286 PHE 0.019 0.002 PHE D 280 TRP 0.017 0.003 TRP B 11 HIS 0.009 0.002 HIS D 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.28 (20757) covalent geometry : angle 0.75560 / 0.37 (28083) hydrogen bonds : bond 0.04399 / 2.85 ( 1035) hydrogen bonds : angle 4.91040 / 3.51 ( 2988) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 251 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8533 (tt) REVERT: A 709 THR cc_start: 0.8207 (m) cc_final: 0.7663 (p) REVERT: B 186 TYR cc_start: 0.8270 (p90) cc_final: 0.7934 (p90) REVERT: B 247 ASP cc_start: 0.8377 (t70) cc_final: 0.8159 (t70) REVERT: B 297 MET cc_start: 0.8734 (ttt) cc_final: 0.8212 (ttt) REVERT: C 99 ASP cc_start: 0.9035 (m-30) cc_final: 0.7971 (t0) REVERT: D 61 MET cc_start: 0.7441 (tmm) cc_final: 0.7179 (tmm) REVERT: D 342 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8457 (mp-120) REVERT: E 135 TYR cc_start: 0.8650 (p90) cc_final: 0.8166 (p90) REVERT: E 243 ASN cc_start: 0.9032 (m-40) cc_final: 0.8698 (t0) REVERT: E 249 LYS cc_start: 0.8691 (mptt) cc_final: 0.8451 (tptp) REVERT: G 11 LEU cc_start: 0.7771 (tp) cc_final: 0.7248 (tp) REVERT: G 14 ARG cc_start: 0.7305 (ptm-80) cc_final: 0.6997 (ptm-80) REVERT: G 99 ILE cc_start: 0.9120 (tp) cc_final: 0.8649 (mt) REVERT: G 249 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.8030 (m-10) REVERT: H 104 GLU cc_start: 0.6245 (mt-10) cc_final: 0.5822 (mt-10) outliers start: 63 outliers final: 42 residues processed: 298 average time/residue: 0.1214 time to fit residues: 58.9893 Evaluate side-chains 281 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 236 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 342 GLN Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 245 PHE Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 225 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 82 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 180 optimal weight: 40.0000 chunk 184 optimal weight: 20.0000 chunk 226 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 224 optimal weight: 9.9990 chunk 148 optimal weight: 0.7980 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 GLN H 83 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.137859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.094900 restraints weight = 55045.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.097977 restraints weight = 28544.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.099877 restraints weight = 19013.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.101035 restraints weight = 14892.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.101595 restraints weight = 12901.914| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.087 20757 Z= 0.423 Angle : 0.900 17.666 28083 Z= 0.444 Chirality : 0.050 0.231 3288 Planarity : 0.006 0.070 3557 Dihedral : 10.789 179.786 2891 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.34 % Allowed : 16.08 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2532 helix: 0.52 (0.15), residues: 1172 sheet: -0.27 (0.24), residues: 481 loop : -0.96 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 228 TYR 0.034 0.003 TYR D 286 PHE 0.026 0.003 PHE A 245 TRP 0.026 0.003 TRP B 11 HIS 0.012 0.002 HIS D 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00958 / 0.42 (20757) covalent geometry : angle 0.90015 / 0.44 (28083) hydrogen bonds : bond 0.04959 / 3.22 ( 1035) hydrogen bonds : angle 5.33281 / 3.80 ( 2988) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 242 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8469 (tt) REVERT: B 103 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8580 (mm) REVERT: B 248 SER cc_start: 0.9205 (m) cc_final: 0.8959 (t) REVERT: B 297 MET cc_start: 0.8734 (ttt) cc_final: 0.8294 (ttt) REVERT: C 279 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: D 61 MET cc_start: 0.7581 (tmm) cc_final: 0.7208 (tmm) REVERT: E 135 TYR cc_start: 0.8660 (p90) cc_final: 0.8307 (p90) REVERT: E 224 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.8847 (mp10) REVERT: E 243 ASN cc_start: 0.8859 (m-40) cc_final: 0.8617 (t0) REVERT: E 249 LYS cc_start: 0.8752 (mptt) cc_final: 0.8268 (mmtt) REVERT: G 6 PHE cc_start: 0.6797 (OUTLIER) cc_final: 0.6561 (t80) REVERT: G 42 ASP cc_start: 0.8199 (p0) cc_final: 0.7341 (t0) REVERT: G 249 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.8006 (m-80) REVERT: H 104 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6086 (mt-10) outliers start: 77 outliers final: 56 residues processed: 299 average time/residue: 0.1178 time to fit residues: 57.5428 Evaluate side-chains 276 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 214 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 245 PHE Chi-restraints excluded: chain G residue 6 PHE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 225 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 186 optimal weight: 3.9990 chunk 195 optimal weight: 20.0000 chunk 219 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 231 optimal weight: 0.9980 chunk 233 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 183 optimal weight: 20.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN A 603 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.139191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.103725 restraints weight = 54726.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.104818 restraints weight = 29868.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.106402 restraints weight = 23577.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.107038 restraints weight = 16852.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.107091 restraints weight = 15710.914| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20757 Z= 0.147 Angle : 0.654 16.323 28083 Z= 0.320 Chirality : 0.043 0.193 3288 Planarity : 0.004 0.060 3557 Dihedral : 10.462 173.360 2891 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.69 % Allowed : 18.42 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.17), residues: 2532 helix: 1.15 (0.15), residues: 1171 sheet: -0.18 (0.24), residues: 476 loop : -0.80 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 44 TYR 0.025 0.002 TYR B 306 PHE 0.020 0.001 PHE A 509 TRP 0.016 0.002 TRP A 420 HIS 0.008 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (20757) covalent geometry : angle 0.65450 / 0.32 (28083) hydrogen bonds : bond 0.03759 / 2.45 ( 1035) hydrogen bonds : angle 4.74136 / 3.38 ( 2988) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 259 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8601 (pt0) REVERT: A 776 VAL cc_start: 0.7914 (t) cc_final: 0.7634 (m) REVERT: B 128 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8147 (ptt180) REVERT: B 186 TYR cc_start: 0.8208 (p90) cc_final: 0.8003 (p90) REVERT: B 297 MET cc_start: 0.8794 (ttt) cc_final: 0.8437 (ttt) REVERT: C 99 ASP cc_start: 0.9036 (m-30) cc_final: 0.8499 (p0) REVERT: C 120 ASP cc_start: 0.7867 (p0) cc_final: 0.7648 (p0) REVERT: C 202 ASN cc_start: 0.8915 (m-40) cc_final: 0.8645 (p0) REVERT: C 279 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: D 61 MET cc_start: 0.7737 (tmm) cc_final: 0.7322 (tmm) REVERT: E 84 GLU cc_start: 0.8047 (pp20) cc_final: 0.7831 (pp20) REVERT: E 135 TYR cc_start: 0.8474 (p90) cc_final: 0.8083 (p90) REVERT: E 243 ASN cc_start: 0.9049 (m-40) cc_final: 0.8762 (t0) REVERT: E 249 LYS cc_start: 0.8728 (mptt) cc_final: 0.8440 (tptp) REVERT: G 6 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.6266 (t80) REVERT: G 42 ASP cc_start: 0.8166 (p0) cc_final: 0.7325 (t0) REVERT: G 95 THR cc_start: 0.5915 (p) cc_final: 0.5707 (t) REVERT: G 188 MET cc_start: 0.7467 (pmm) cc_final: 0.6066 (tmm) REVERT: G 213 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8109 (mm) REVERT: G 221 LEU cc_start: 0.6100 (tp) cc_final: 0.5809 (tp) REVERT: G 249 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.8040 (m-80) REVERT: H 7 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.5840 (pm20) REVERT: H 104 GLU cc_start: 0.6326 (mt-10) cc_final: 0.5939 (mt-10) outliers start: 62 outliers final: 39 residues processed: 303 average time/residue: 0.1183 time to fit residues: 58.3310 Evaluate side-chains 286 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 245 PHE Chi-restraints excluded: chain G residue 6 PHE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 200 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 148 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 603 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.139638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.103112 restraints weight = 55029.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.105655 restraints weight = 29927.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.106548 restraints weight = 21261.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.107032 restraints weight = 16437.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.107128 restraints weight = 15389.966| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20757 Z= 0.140 Angle : 0.646 17.520 28083 Z= 0.315 Chirality : 0.043 0.184 3288 Planarity : 0.004 0.060 3557 Dihedral : 10.304 170.328 2891 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.60 % Allowed : 19.12 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.17), residues: 2532 helix: 1.32 (0.15), residues: 1167 sheet: -0.12 (0.24), residues: 482 loop : -0.76 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 14 TYR 0.024 0.002 TYR B 306 PHE 0.018 0.001 PHE A 509 TRP 0.016 0.002 TRP A 780 HIS 0.007 0.001 HIS A 601 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (20757) covalent geometry : angle 0.64583 / 0.31 (28083) hydrogen bonds : bond 0.03582 / 2.33 ( 1035) hydrogen bonds : angle 4.65264 / 3.31 ( 2988) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 253 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 MET cc_start: 0.8314 (mmm) cc_final: 0.8048 (mmm) REVERT: A 504 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8540 (tp) REVERT: A 580 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8621 (pt0) REVERT: B 103 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8587 (mm) REVERT: B 128 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7703 (ptm160) REVERT: B 186 TYR cc_start: 0.8241 (p90) cc_final: 0.8035 (p90) REVERT: B 297 MET cc_start: 0.8755 (ttt) cc_final: 0.8394 (ttt) REVERT: C 99 ASP cc_start: 0.9086 (m-30) cc_final: 0.8527 (p0) REVERT: C 202 ASN cc_start: 0.8912 (m-40) cc_final: 0.8654 (p0) REVERT: C 279 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: D 61 MET cc_start: 0.7751 (tmm) cc_final: 0.7410 (tmm) REVERT: E 84 GLU cc_start: 0.7998 (pp20) cc_final: 0.7759 (pp20) REVERT: E 135 TYR cc_start: 0.8481 (p90) cc_final: 0.8069 (p90) REVERT: E 224 GLN cc_start: 0.9267 (mp10) cc_final: 0.8734 (mp10) REVERT: E 243 ASN cc_start: 0.9060 (m-40) cc_final: 0.8749 (t0) REVERT: E 249 LYS cc_start: 0.8724 (mptt) cc_final: 0.8471 (tptp) REVERT: G 1 MET cc_start: 0.3598 (tmm) cc_final: 0.2476 (ptm) REVERT: G 6 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.6317 (t80) REVERT: G 11 LEU cc_start: 0.6821 (mt) cc_final: 0.6275 (mt) REVERT: G 181 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8198 (tp) REVERT: G 188 MET cc_start: 0.7450 (pmm) cc_final: 0.6039 (tmm) REVERT: G 199 MET cc_start: 0.7152 (tmm) cc_final: 0.6749 (tmm) REVERT: G 249 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.8075 (m-80) REVERT: H 7 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5800 (pm20) REVERT: H 104 GLU cc_start: 0.6388 (mt-10) cc_final: 0.5979 (mt-10) outliers start: 60 outliers final: 37 residues processed: 299 average time/residue: 0.1089 time to fit residues: 53.1366 Evaluate side-chains 286 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 245 PHE Chi-restraints excluded: chain G residue 6 PHE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 210 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 178 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 211 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN C 127 GLN ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.138175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.104826 restraints weight = 55476.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.104253 restraints weight = 33220.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.104118 restraints weight = 25154.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.104626 restraints weight = 25071.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.105268 restraints weight = 20517.468| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 20757 Z= 0.274 Angle : 0.742 18.834 28083 Z= 0.364 Chirality : 0.045 0.190 3288 Planarity : 0.005 0.063 3557 Dihedral : 10.483 172.436 2891 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.73 % Allowed : 19.42 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.17), residues: 2532 helix: 1.07 (0.15), residues: 1169 sheet: -0.27 (0.24), residues: 481 loop : -0.80 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 44 TYR 0.026 0.002 TYR D 286 PHE 0.018 0.002 PHE G 239 TRP 0.018 0.002 TRP B 11 HIS 0.007 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.27 (20757) covalent geometry : angle 0.74196 / 0.36 (28083) hydrogen bonds : bond 0.04168 / 2.70 ( 1035) hydrogen bonds : angle 4.91087 / 3.50 ( 2988) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 233 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 MET cc_start: 0.8452 (mmm) cc_final: 0.8238 (mmm) REVERT: A 451 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8462 (tt) REVERT: A 580 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8567 (pt0) REVERT: B 103 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8632 (mm) REVERT: B 128 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8068 (ptt180) REVERT: B 297 MET cc_start: 0.8746 (ttt) cc_final: 0.8323 (ttt) REVERT: C 99 ASP cc_start: 0.9136 (m-30) cc_final: 0.8597 (p0) REVERT: C 279 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: D 61 MET cc_start: 0.7772 (tmm) cc_final: 0.7432 (tmm) REVERT: D 168 LEU cc_start: 0.9058 (mm) cc_final: 0.8792 (mm) REVERT: E 84 GLU cc_start: 0.8038 (pp20) cc_final: 0.7811 (pp20) REVERT: E 135 TYR cc_start: 0.8510 (p90) cc_final: 0.8124 (p90) REVERT: E 243 ASN cc_start: 0.8962 (m-40) cc_final: 0.8719 (t0) REVERT: E 249 LYS cc_start: 0.8739 (mptt) cc_final: 0.8475 (tptp) REVERT: G 1 MET cc_start: 0.3393 (tmm) cc_final: 0.2819 (tmm) REVERT: G 6 PHE cc_start: 0.6672 (OUTLIER) cc_final: 0.6319 (t80) REVERT: G 42 ASP cc_start: 0.8272 (p0) cc_final: 0.7418 (t0) REVERT: G 249 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: H 104 GLU cc_start: 0.6399 (mt-10) cc_final: 0.5993 (mt-10) outliers start: 63 outliers final: 45 residues processed: 280 average time/residue: 0.1071 time to fit residues: 49.2870 Evaluate side-chains 278 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 226 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 245 PHE Chi-restraints excluded: chain G residue 6 PHE Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 225 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 137 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 0.0270 chunk 59 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 chunk 186 optimal weight: 9.9990 chunk 242 optimal weight: 8.9990 chunk 197 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 ASN H 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.140429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.105671 restraints weight = 54779.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.108240 restraints weight = 30999.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.108057 restraints weight = 20153.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.108589 restraints weight = 19914.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.108685 restraints weight = 17685.082| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20757 Z= 0.122 Angle : 0.645 13.327 28083 Z= 0.317 Chirality : 0.043 0.175 3288 Planarity : 0.004 0.061 3557 Dihedral : 10.253 174.714 2891 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.78 % Allowed : 20.42 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.17), residues: 2532 helix: 1.37 (0.15), residues: 1168 sheet: -0.07 (0.24), residues: 482 loop : -0.72 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 69 TYR 0.024 0.001 TYR B 306 PHE 0.021 0.001 PHE A 509 TRP 0.023 0.002 TRP A 420 HIS 0.007 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (20757) covalent geometry : angle 0.64539 / 0.32 (28083) hydrogen bonds : bond 0.03437 / 2.25 ( 1035) hydrogen bonds : angle 4.56120 / 3.24 ( 2988) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 252 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 MET cc_start: 0.8304 (mmm) cc_final: 0.8096 (mmm) REVERT: A 451 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8398 (tt) REVERT: A 580 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8491 (pt0) REVERT: A 604 ASP cc_start: 0.8398 (t0) cc_final: 0.8175 (t0) REVERT: B 128 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7810 (ptm160) REVERT: B 297 MET cc_start: 0.8748 (ttt) cc_final: 0.8421 (ttt) REVERT: C 30 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7988 (mm-40) REVERT: C 99 ASP cc_start: 0.9178 (m-30) cc_final: 0.8648 (p0) REVERT: C 279 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: D 61 MET cc_start: 0.7936 (tmm) cc_final: 0.7515 (tmm) REVERT: E 84 GLU cc_start: 0.7977 (pp20) cc_final: 0.7717 (pp20) REVERT: E 135 TYR cc_start: 0.8405 (p90) cc_final: 0.8029 (p90) REVERT: E 224 GLN cc_start: 0.9283 (mp10) cc_final: 0.8744 (mp10) REVERT: E 243 ASN cc_start: 0.9011 (m-40) cc_final: 0.8745 (t0) REVERT: E 249 LYS cc_start: 0.8668 (mptt) cc_final: 0.8430 (tptp) REVERT: G 1 MET cc_start: 0.3593 (tmm) cc_final: 0.3094 (tmm) REVERT: G 6 PHE cc_start: 0.6705 (OUTLIER) cc_final: 0.6396 (t80) REVERT: G 42 ASP cc_start: 0.8214 (p0) cc_final: 0.7417 (t0) REVERT: G 181 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8212 (tp) REVERT: G 188 MET cc_start: 0.7467 (pmm) cc_final: 0.6104 (tmm) REVERT: G 249 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: H 8 GLU cc_start: 0.7876 (pt0) cc_final: 0.7412 (tp30) REVERT: H 104 GLU cc_start: 0.6354 (mt-10) cc_final: 0.5976 (mt-10) outliers start: 41 outliers final: 27 residues processed: 284 average time/residue: 0.1038 time to fit residues: 48.1594 Evaluate side-chains 276 residues out of total 2307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 245 PHE Chi-restraints excluded: chain G residue 6 PHE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 249 PHE Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 38 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 210 optimal weight: 20.0000 chunk 233 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 193 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 ASN H 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.138285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.103934 restraints weight = 55392.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.103845 restraints weight = 34738.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.104407 restraints weight = 24984.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.104716 restraints weight = 22286.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.105030 restraints weight = 20907.969| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20757 Z= 0.183 Angle : 0.670 12.788 28083 Z= 0.328 Chirality : 0.043 0.183 3288 Planarity : 0.004 0.058 3557 Dihedral : 10.267 174.129 2891 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.95 % Allowed : 20.46 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.17), residues: 2532 helix: 1.40 (0.15), residues: 1163 sheet: -0.09 (0.24), residues: 479 loop : -0.75 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 228 TYR 0.024 0.002 TYR B 306 PHE 0.016 0.001 PHE A 509 TRP 0.016 0.002 TRP A 780 HIS 0.007 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (20757) covalent geometry : angle 0.67037 / 0.33 (28083) hydrogen bonds : bond 0.03706 / 2.41 ( 1035) hydrogen bonds : angle 4.63661 / 3.30 ( 2988) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2996.40 seconds wall clock time: 52 minutes 49.56 seconds (3169.56 seconds total)