Starting phenix.real_space_refine on Fri Sep 19 02:27:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gs2_51537/09_2025/9gs2_51537.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gs2_51537/09_2025/9gs2_51537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gs2_51537/09_2025/9gs2_51537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gs2_51537/09_2025/9gs2_51537.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gs2_51537/09_2025/9gs2_51537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gs2_51537/09_2025/9gs2_51537.map" } resolution = 3.46 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= 0.004 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 2 7.16 5 S 113 5.16 5 C 14245 2.51 5 N 3857 2.21 5 O 4148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22365 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3058 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 365} Chain: "B" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3058 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 365} Chain: "C" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3058 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 365} Chain: "D" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3058 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 365} Chain: "E" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3058 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 365} Chain: "F" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3058 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 365} Chain: "G" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3058 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 365} Chain: "H" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 955 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 113} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 21940 SG CYS H 159 70.171 88.502 30.050 1.00182.29 S ATOM 22077 SG CYS H 178 67.940 86.071 30.549 1.00164.72 S Time building chain proxies: 5.92, per 1000 atoms: 0.26 Number of scatterers: 22365 At special positions: 0 Unit cell: (151.943, 149.035, 111.231, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 2 26.01 S 113 16.00 O 4148 8.00 N 3857 7.00 C 14245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS H 164 " - pdb=" SG CYS H 180 " distance=2.03 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: 1.97 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES H 301 " pdb="FE1 FES H 301 " - pdb=" ND1 HIS H 181 " pdb="FE1 FES H 301 " - pdb=" ND1 HIS H 161 " pdb="FE2 FES H 301 " - pdb=" SG CYS H 159 " pdb="FE2 FES H 301 " - pdb=" SG CYS H 178 " pdb="FE2 FES H 301 " - pdb=" SG CYS H 164 " Number of angles added : 6 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5220 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 24 sheets defined 43.7% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 75 through 83 Processing helix chain 'A' and resid 93 through 106 removed outlier: 4.181A pdb=" N ALA A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 197 removed outlier: 3.771A pdb=" N ILE A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 201 removed outlier: 4.256A pdb=" N GLY A 201 " --> pdb=" O THR A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 201' Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 233 through 248 Processing helix chain 'A' and resid 248 through 256 removed outlier: 3.787A pdb=" N TYR A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 285 Processing helix chain 'A' and resid 299 through 307 Processing helix chain 'A' and resid 321 through 328 removed outlier: 3.617A pdb=" N PHE A 325 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 341 through 350 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 390 through 402 Processing helix chain 'A' and resid 407 through 420 Processing helix chain 'A' and resid 424 through 434 Processing helix chain 'A' and resid 438 through 445 removed outlier: 3.735A pdb=" N MET A 445 " --> pdb=" O ASP A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 450 removed outlier: 3.989A pdb=" N ARG A 450 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 4.146A pdb=" N ILE A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 83 Processing helix chain 'B' and resid 93 through 105 removed outlier: 4.336A pdb=" N ALA B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 248 through 255 removed outlier: 3.997A pdb=" N TYR B 252 " --> pdb=" O ASN B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 321 through 330 removed outlier: 3.812A pdb=" N PHE B 325 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER B 329 " --> pdb=" O PHE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 351 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 405 through 420 Processing helix chain 'B' and resid 424 through 434 removed outlier: 3.574A pdb=" N LEU B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 430 " --> pdb=" O ALA B 426 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU B 431 " --> pdb=" O GLN B 427 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 433 " --> pdb=" O GLN B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 446 through 452 removed outlier: 3.740A pdb=" N ARG B 450 " --> pdb=" O SER B 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 82 Processing helix chain 'C' and resid 94 through 106 removed outlier: 3.867A pdb=" N PHE C 99 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 removed outlier: 4.443A pdb=" N ILE C 194 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA C 195 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR C 199 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 234 through 248 removed outlier: 3.863A pdb=" N ASP C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 254 Processing helix chain 'C' and resid 272 through 285 Processing helix chain 'C' and resid 299 through 308 Processing helix chain 'C' and resid 321 through 327 removed outlier: 3.961A pdb=" N PHE C 325 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 350 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 390 through 402 Processing helix chain 'C' and resid 405 through 420 removed outlier: 3.898A pdb=" N LYS C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 436 removed outlier: 3.818A pdb=" N LEU C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 444 through 452 removed outlier: 4.158A pdb=" N SER C 447 " --> pdb=" O LYS C 444 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG C 450 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA C 452 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 83 removed outlier: 3.707A pdb=" N GLN D 82 " --> pdb=" O VAL D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 removed outlier: 4.493A pdb=" N LEU D 100 " --> pdb=" O TYR D 96 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 105 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.609A pdb=" N ILE D 194 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA D 195 " --> pdb=" O ALA D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.792A pdb=" N ASP D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 284 Processing helix chain 'D' and resid 299 through 307 Processing helix chain 'D' and resid 321 through 330 removed outlier: 4.009A pdb=" N PHE D 325 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 350 removed outlier: 3.752A pdb=" N ASP D 350 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 370 Processing helix chain 'D' and resid 390 through 402 Processing helix chain 'D' and resid 405 through 420 Processing helix chain 'D' and resid 424 through 435 removed outlier: 3.773A pdb=" N LEU D 428 " --> pdb=" O SER D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 446 removed outlier: 3.935A pdb=" N LYS D 444 " --> pdb=" O HIS D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 450 Processing helix chain 'D' and resid 451 through 456 Processing helix chain 'E' and resid 76 through 83 Processing helix chain 'E' and resid 93 through 106 removed outlier: 4.056A pdb=" N ALA E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 182 through 192 removed outlier: 3.598A pdb=" N ASP E 186 " --> pdb=" O HIS E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 198 removed outlier: 3.743A pdb=" N LYS E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 193 through 198' Processing helix chain 'E' and resid 199 through 202 removed outlier: 4.052A pdb=" N LYS E 202 " --> pdb=" O THR E 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 202' Processing helix chain 'E' and resid 233 through 248 Processing helix chain 'E' and resid 249 through 254 removed outlier: 3.795A pdb=" N ASP E 254 " --> pdb=" O LYS E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 285 Processing helix chain 'E' and resid 299 through 308 Processing helix chain 'E' and resid 321 through 328 removed outlier: 3.854A pdb=" N PHE E 325 " --> pdb=" O ILE E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 350 Processing helix chain 'E' and resid 390 through 402 Processing helix chain 'E' and resid 405 through 420 Processing helix chain 'E' and resid 424 through 435 removed outlier: 3.679A pdb=" N LEU E 428 " --> pdb=" O SER E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 Processing helix chain 'E' and resid 446 through 454 removed outlier: 3.520A pdb=" N ARG E 450 " --> pdb=" O SER E 447 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN E 453 " --> pdb=" O ARG E 450 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS E 454 " --> pdb=" O ASN E 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 82 Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.754A pdb=" N LEU F 100 " --> pdb=" O TYR F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 191 removed outlier: 3.975A pdb=" N ASP F 186 " --> pdb=" O HIS F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 198 removed outlier: 3.951A pdb=" N THR F 198 " --> pdb=" O ILE F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 233 through 248 Processing helix chain 'F' and resid 248 through 255 Processing helix chain 'F' and resid 272 through 285 Processing helix chain 'F' and resid 299 through 309 Processing helix chain 'F' and resid 320 through 332 removed outlier: 3.568A pdb=" N GLY F 332 " --> pdb=" O ARG F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 351 Processing helix chain 'F' and resid 366 through 370 Processing helix chain 'F' and resid 390 through 402 Processing helix chain 'F' and resid 405 through 420 Processing helix chain 'F' and resid 424 through 435 Processing helix chain 'F' and resid 438 through 445 Processing helix chain 'F' and resid 446 through 450 removed outlier: 3.582A pdb=" N ARG F 450 " --> pdb=" O SER F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 456 Processing helix chain 'G' and resid 76 through 83 Processing helix chain 'G' and resid 94 through 106 removed outlier: 3.781A pdb=" N TRP G 98 " --> pdb=" O LYS G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 196 Processing helix chain 'G' and resid 224 through 228 Processing helix chain 'G' and resid 233 through 248 Processing helix chain 'G' and resid 248 through 254 Processing helix chain 'G' and resid 272 through 285 Processing helix chain 'G' and resid 299 through 307 Processing helix chain 'G' and resid 320 through 334 Processing helix chain 'G' and resid 341 through 350 Processing helix chain 'G' and resid 351 through 354 Processing helix chain 'G' and resid 366 through 370 Processing helix chain 'G' and resid 371 through 375 Processing helix chain 'G' and resid 390 through 402 Processing helix chain 'G' and resid 405 through 420 Processing helix chain 'G' and resid 424 through 434 removed outlier: 3.565A pdb=" N LEU G 428 " --> pdb=" O SER G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 445 Processing helix chain 'G' and resid 446 through 452 removed outlier: 3.838A pdb=" N LEU G 449 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG G 450 " --> pdb=" O SER G 447 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 131 Processing helix chain 'H' and resid 142 through 147 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 110 removed outlier: 12.507A pdb=" N ILE A 152 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 12.569A pdb=" N LEU A 177 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 11.353A pdb=" N ARG A 154 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 12.008A pdb=" N THR A 175 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 10.864A pdb=" N ARG A 156 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 11.536A pdb=" N THR A 173 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 10.531A pdb=" N ALA A 158 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 12.716A pdb=" N THR A 171 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N MET A 160 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 169 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 116 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLN A 90 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N THR B 118 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 135 removed outlier: 3.669A pdb=" N ILE A 121 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 131 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 114 " --> pdb=" O GLU G 88 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLN G 90 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL A 116 " --> pdb=" O GLN G 90 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET G 160 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 12.361A pdb=" N THR G 171 " --> pdb=" O ALA G 158 " (cutoff:3.500A) removed outlier: 10.387A pdb=" N ALA G 158 " --> pdb=" O THR G 171 " (cutoff:3.500A) removed outlier: 11.572A pdb=" N THR G 173 " --> pdb=" O ARG G 156 " (cutoff:3.500A) removed outlier: 11.255A pdb=" N ARG G 156 " --> pdb=" O THR G 173 " (cutoff:3.500A) removed outlier: 11.761A pdb=" N THR G 175 " --> pdb=" O ARG G 154 " (cutoff:3.500A) removed outlier: 10.996A pdb=" N ARG G 154 " --> pdb=" O THR G 175 " (cutoff:3.500A) removed outlier: 12.379A pdb=" N LEU G 177 " --> pdb=" O ILE G 152 " (cutoff:3.500A) removed outlier: 12.234A pdb=" N ILE G 152 " --> pdb=" O LEU G 177 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 214 through 215 removed outlier: 6.438A pdb=" N ASN A 287 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU A 317 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N CYS A 289 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLU A 319 " --> pdb=" O CYS A 289 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 291 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER A 314 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N PHE A 361 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 316 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N THR A 363 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 318 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ARG A 261 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N MET A 362 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR A 263 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THR A 364 " --> pdb=" O TYR A 263 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 265 " --> pdb=" O THR A 364 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 109 through 110 removed outlier: 8.546A pdb=" N PHE B 149 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU B 177 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 116 " --> pdb=" O GLU B 88 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLN B 90 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR C 118 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 203 removed outlier: 3.621A pdb=" N LYS B 220 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 212 through 215 removed outlier: 4.386A pdb=" N SER B 208 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N ASN B 292 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASN B 287 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU B 317 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N CYS B 289 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLU B 319 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU B 291 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N SER B 314 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N PHE B 361 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 316 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N THR B 363 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU B 318 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ARG B 261 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N MET B 362 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR B 263 " --> pdb=" O MET B 362 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N THR B 364 " --> pdb=" O TYR B 263 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU B 265 " --> pdb=" O THR B 364 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N TYR B 382 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLY B 262 " --> pdb=" O TYR B 382 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N VAL B 384 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU B 264 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 109 through 110 removed outlier: 3.766A pdb=" N GLY C 139 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N PHE C 149 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LEU C 177 " --> pdb=" O PHE C 149 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLN C 90 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 9.153A pdb=" N THR D 118 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 212 through 215 removed outlier: 4.244A pdb=" N SER C 208 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N ASN C 292 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASN C 287 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU C 317 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N CYS C 289 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLU C 319 " --> pdb=" O CYS C 289 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU C 291 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ILE C 359 " --> pdb=" O SER C 314 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 109 through 110 removed outlier: 3.579A pdb=" N ARG D 154 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N PHE D 149 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU D 177 " --> pdb=" O PHE D 149 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE D 169 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N LYS D 159 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 11.391A pdb=" N SER D 167 " --> pdb=" O LYS D 159 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL E 116 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 213 through 220 removed outlier: 6.194A pdb=" N PHE D 216 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR D 207 " --> pdb=" O PHE D 216 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLN D 218 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE D 205 " --> pdb=" O GLN D 218 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER D 208 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ASN D 292 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN D 287 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU D 317 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N CYS D 289 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLU D 319 " --> pdb=" O CYS D 289 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU D 291 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N SER D 314 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N PHE D 361 " --> pdb=" O SER D 314 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU D 316 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR D 363 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU D 318 " --> pdb=" O THR D 363 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARG D 261 " --> pdb=" O THR D 360 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N MET D 362 " --> pdb=" O ARG D 261 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TYR D 263 " --> pdb=" O MET D 362 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N VAL D 384 " --> pdb=" O GLY D 262 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU D 264 " --> pdb=" O VAL D 384 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 109 through 110 removed outlier: 5.603A pdb=" N PHE E 169 " --> pdb=" O SER E 157 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLN E 90 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N THR F 118 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 213 through 215 removed outlier: 3.962A pdb=" N SER E 208 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ASN E 292 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU E 319 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYR E 263 " --> pdb=" O MET E 362 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 84 through 89 Processing sheet with id=AB6, first strand: chain 'F' and resid 110 through 111 removed outlier: 3.537A pdb=" N TRP F 142 " --> pdb=" O VAL F 110 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG F 154 " --> pdb=" O GLY F 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 202 through 203 removed outlier: 3.839A pdb=" N LYS F 220 " --> pdb=" O THR F 203 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 205 through 206 removed outlier: 3.575A pdb=" N LEU F 317 " --> pdb=" O CYS F 289 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE F 359 " --> pdb=" O SER F 314 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG F 261 " --> pdb=" O THR F 360 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N MET F 362 " --> pdb=" O ARG F 261 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR F 263 " --> pdb=" O MET F 362 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N THR F 364 " --> pdb=" O TYR F 263 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU F 265 " --> pdb=" O THR F 364 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR F 382 " --> pdb=" O GLY F 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 208 through 209 Processing sheet with id=AC1, first strand: chain 'G' and resid 115 through 118 Processing sheet with id=AC2, first strand: chain 'G' and resid 122 through 123 removed outlier: 3.681A pdb=" N SER G 127 " --> pdb=" O HIS G 123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 212 through 215 removed outlier: 6.380A pdb=" N TYR G 206 " --> pdb=" O ILE G 290 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ASN G 292 " --> pdb=" O TYR G 206 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N SER G 208 " --> pdb=" O ASN G 292 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASN G 287 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU G 317 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N CYS G 289 " --> pdb=" O LEU G 317 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLU G 319 " --> pdb=" O CYS G 289 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU G 291 " --> pdb=" O GLU G 319 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE G 359 " --> pdb=" O SER G 314 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR G 382 " --> pdb=" O GLY G 262 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR G 266 " --> pdb=" O VAL G 384 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 94 through 97 Processing sheet with id=AC5, first strand: chain 'H' and resid 106 through 111 removed outlier: 3.655A pdb=" N ILE H 118 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET H 155 " --> pdb=" O PHE H 117 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 167 through 168 removed outlier: 3.834A pdb=" N LYS H 193 " --> pdb=" O HIS H 184 " (cutoff:3.500A) 1001 hydrogen bonds defined for protein. 2766 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.63 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 9415 1.41 - 1.61: 13251 1.61 - 1.81: 176 1.81 - 2.01: 28 2.01 - 2.20: 4 Bond restraints: 22874 Sorted by residual: bond pdb=" N MET E 445 " pdb=" CA MET E 445 " ideal model delta sigma weight residual 1.455 1.480 -0.024 1.25e-02 6.40e+03 3.84e+00 bond pdb=" CA GLY D 351 " pdb=" C GLY D 351 " ideal model delta sigma weight residual 1.530 1.514 0.017 1.04e-02 9.25e+03 2.66e+00 bond pdb=" CA HIS D 366 " pdb=" CB HIS D 366 " ideal model delta sigma weight residual 1.522 1.533 -0.011 7.00e-03 2.04e+04 2.46e+00 bond pdb=" CB ASP H 210 " pdb=" CG ASP H 210 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.41e+00 bond pdb=" CB PHE A 184 " pdb=" CG PHE A 184 " ideal model delta sigma weight residual 1.502 1.468 0.034 2.30e-02 1.89e+03 2.24e+00 ... (remaining 22869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 30099 1.97 - 3.94: 669 3.94 - 5.90: 119 5.90 - 7.87: 22 7.87 - 9.84: 4 Bond angle restraints: 30913 Sorted by residual: angle pdb=" C LYS E 444 " pdb=" N MET E 445 " pdb=" CA MET E 445 " ideal model delta sigma weight residual 122.65 116.86 5.79 1.66e+00 3.63e-01 1.21e+01 angle pdb=" C VAL G 433 " pdb=" N MET G 434 " pdb=" CA MET G 434 " ideal model delta sigma weight residual 121.58 115.03 6.55 1.95e+00 2.63e-01 1.13e+01 angle pdb=" CB LYS A 410 " pdb=" CG LYS A 410 " pdb=" CD LYS A 410 " ideal model delta sigma weight residual 111.30 119.01 -7.71 2.30e+00 1.89e-01 1.12e+01 angle pdb=" CB MET E 310 " pdb=" CG MET E 310 " pdb=" SD MET E 310 " ideal model delta sigma weight residual 112.70 122.54 -9.84 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C PHE F 398 " pdb=" N MET F 399 " pdb=" CA MET F 399 " ideal model delta sigma weight residual 121.58 115.28 6.30 1.95e+00 2.63e-01 1.04e+01 ... (remaining 30908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 12148 17.87 - 35.74: 1291 35.74 - 53.61: 265 53.61 - 71.48: 46 71.48 - 89.35: 21 Dihedral angle restraints: 13771 sinusoidal: 5654 harmonic: 8117 Sorted by residual: dihedral pdb=" CA VAL E 85 " pdb=" C VAL E 85 " pdb=" N ASP E 86 " pdb=" CA ASP E 86 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ASP A 437 " pdb=" C ASP A 437 " pdb=" N ALA A 438 " pdb=" CA ALA A 438 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA SER B 338 " pdb=" C SER B 338 " pdb=" N SER B 339 " pdb=" CA SER B 339 " ideal model delta harmonic sigma weight residual -180.00 -157.14 -22.86 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 13768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2403 0.038 - 0.076: 659 0.076 - 0.114: 243 0.114 - 0.152: 63 0.152 - 0.190: 9 Chirality restraints: 3377 Sorted by residual: chirality pdb=" CB VAL B 340 " pdb=" CA VAL B 340 " pdb=" CG1 VAL B 340 " pdb=" CG2 VAL B 340 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CB VAL E 85 " pdb=" CA VAL E 85 " pdb=" CG1 VAL E 85 " pdb=" CG2 VAL E 85 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.74e-01 chirality pdb=" CA VAL E 85 " pdb=" N VAL E 85 " pdb=" C VAL E 85 " pdb=" CB VAL E 85 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 3374 not shown) Planarity restraints: 3970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 412 " -0.013 2.00e-02 2.50e+03 2.15e-02 8.07e+00 pdb=" CG PHE G 412 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE G 412 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE G 412 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE G 412 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE G 412 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE G 412 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 407 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C ASP A 407 " -0.043 2.00e-02 2.50e+03 pdb=" O ASP A 407 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE A 408 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 285 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ASP B 285 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP B 285 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR B 286 " 0.013 2.00e-02 2.50e+03 ... (remaining 3967 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 413 2.63 - 3.20: 22794 3.20 - 3.77: 35366 3.77 - 4.33: 48187 4.33 - 4.90: 76817 Nonbonded interactions: 183577 Sorted by model distance: nonbonded pdb=" OD2 ASP C 93 " pdb=" OG SER C 95 " model vdw 2.066 3.040 nonbonded pdb=" O PHE C 412 " pdb=" OG SER C 415 " model vdw 2.103 3.040 nonbonded pdb=" OG1 THR D 299 " pdb=" OD1 ASP D 301 " model vdw 2.105 3.040 nonbonded pdb=" OD2 ASP D 300 " pdb=" OG1 THR D 341 " model vdw 2.108 3.040 nonbonded pdb=" OD1 ASN B 304 " pdb=" ND2 ASN B 308 " model vdw 2.128 3.120 ... (remaining 183572 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.760 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 26.240 Find NCS groups from input model: 0.400 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: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 : 0.008 0.969 22880 Z= 0.245 Angle : 0.807 38.907 30921 Z= 0.394 Chirality : 0.043 0.190 3377 Planarity : 0.004 0.047 3970 Dihedral : 15.281 89.355 8548 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.67 % Favored : 95.22 % Rotamer: Outliers : 0.08 % Allowed : 17.77 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.16), residues: 2782 helix: 0.43 (0.16), residues: 1041 sheet: -0.89 (0.21), residues: 620 loop : -0.53 (0.20), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 81 TYR 0.025 0.001 TYR A 120 PHE 0.048 0.002 PHE G 412 TRP 0.029 0.002 TRP G 98 HIS 0.004 0.001 HIS D 305 Details of bonding type rmsd covalent geometry : bond 0.00430 (22874) covalent geometry : angle 0.73703 (30913) SS BOND : bond 0.00248 ( 1) SS BOND : angle 0.33511 ( 2) hydrogen bonds : bond 0.18817 ( 995) hydrogen bonds : angle 7.42050 ( 2766) metal coordination : bond 0.43366 ( 5) metal coordination : angle 23.58137 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 238 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 HIS cc_start: 0.9142 (p-80) cc_final: 0.8794 (p90) REVERT: B 153 LYS cc_start: 0.9436 (tmtt) cc_final: 0.9070 (tmtt) REVERT: B 375 MET cc_start: 0.7141 (tmm) cc_final: 0.6606 (tmm) REVERT: B 408 ILE cc_start: 0.9616 (mm) cc_final: 0.9350 (tt) REVERT: C 155 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8227 (mp0) REVERT: C 224 MET cc_start: 0.9192 (mpp) cc_final: 0.8780 (tpp) REVERT: C 445 MET cc_start: 0.9218 (pmm) cc_final: 0.8957 (pmm) REVERT: D 224 MET cc_start: 0.9410 (ptp) cc_final: 0.9084 (ppp) REVERT: E 178 TYR cc_start: 0.8796 (t80) cc_final: 0.8589 (t80) REVERT: E 246 MET cc_start: 0.9230 (pmm) cc_final: 0.8996 (pmm) REVERT: F 98 TRP cc_start: 0.8675 (m-10) cc_final: 0.8435 (m-10) REVERT: F 362 MET cc_start: 0.8825 (mpp) cc_final: 0.8423 (mpp) REVERT: F 370 LEU cc_start: 0.8699 (mt) cc_final: 0.8352 (pp) REVERT: G 246 MET cc_start: 0.9365 (mmm) cc_final: 0.9139 (mmm) REVERT: G 278 GLN cc_start: 0.9456 (mt0) cc_final: 0.9205 (mt0) REVERT: H 114 LYS cc_start: 0.9320 (tppt) cc_final: 0.9097 (mmmm) REVERT: H 148 LYS cc_start: 0.7380 (mmtp) cc_final: 0.6914 (mmtm) outliers start: 2 outliers final: 1 residues processed: 238 average time/residue: 0.1658 time to fit residues: 62.1610 Evaluate side-chains 212 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 30.0000 chunk 111 optimal weight: 2.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 HIS D 305 HIS E 435 ASN F 123 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.065944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.046553 restraints weight = 112740.788| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 6.12 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22880 Z= 0.174 Angle : 0.711 34.147 30921 Z= 0.337 Chirality : 0.045 0.176 3377 Planarity : 0.005 0.071 3970 Dihedral : 5.227 46.044 3057 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.13 % Favored : 95.76 % Rotamer: Outliers : 2.04 % Allowed : 16.34 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.16), residues: 2782 helix: 0.56 (0.16), residues: 1061 sheet: -0.67 (0.21), residues: 608 loop : -0.47 (0.20), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 214 TYR 0.031 0.002 TYR C 96 PHE 0.023 0.002 PHE G 398 TRP 0.026 0.002 TRP F 142 HIS 0.005 0.001 HIS G 141 Details of bonding type rmsd covalent geometry : bond 0.00376 (22874) covalent geometry : angle 0.64344 (30913) SS BOND : bond 0.00547 ( 1) SS BOND : angle 1.68934 ( 2) hydrogen bonds : bond 0.04196 ( 995) hydrogen bonds : angle 5.63951 ( 2766) metal coordination : bond 0.03123 ( 5) metal coordination : angle 21.73860 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 244 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ILE cc_start: 0.9682 (mt) cc_final: 0.9478 (mm) REVERT: A 362 MET cc_start: 0.8579 (mpp) cc_final: 0.8343 (mpp) REVERT: A 397 MET cc_start: 0.9494 (ptm) cc_final: 0.9183 (ptp) REVERT: A 440 HIS cc_start: 0.9311 (p-80) cc_final: 0.9038 (p90) REVERT: B 153 LYS cc_start: 0.9472 (tmtt) cc_final: 0.9032 (tmtt) REVERT: B 375 MET cc_start: 0.7413 (tmm) cc_final: 0.7055 (tmm) REVERT: B 413 VAL cc_start: 0.9296 (OUTLIER) cc_final: 0.9089 (m) REVERT: C 155 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8304 (mp0) REVERT: C 224 MET cc_start: 0.9109 (mpp) cc_final: 0.8814 (tpp) REVERT: C 362 MET cc_start: 0.8763 (mpp) cc_final: 0.8053 (mpp) REVERT: D 96 TYR cc_start: 0.5640 (m-10) cc_final: 0.5385 (m-80) REVERT: D 362 MET cc_start: 0.9540 (mmm) cc_final: 0.9293 (tpp) REVERT: D 445 MET cc_start: 0.8859 (mtp) cc_final: 0.8659 (mtp) REVERT: E 132 PHE cc_start: 0.8237 (p90) cc_final: 0.7925 (p90) REVERT: E 170 GLU cc_start: 0.9078 (pt0) cc_final: 0.8360 (pt0) REVERT: E 178 TYR cc_start: 0.9049 (t80) cc_final: 0.8719 (t80) REVERT: F 362 MET cc_start: 0.8760 (mpp) cc_final: 0.8442 (mpp) REVERT: G 434 MET cc_start: 0.9363 (ppp) cc_final: 0.9059 (ppp) REVERT: H 114 LYS cc_start: 0.9375 (tppt) cc_final: 0.9036 (mmmm) REVERT: H 148 LYS cc_start: 0.7075 (mmtp) cc_final: 0.6623 (mtmm) REVERT: H 201 GLU cc_start: 0.9108 (pm20) cc_final: 0.8842 (pm20) REVERT: H 207 PHE cc_start: 0.8884 (m-10) cc_final: 0.8661 (m-10) outliers start: 50 outliers final: 20 residues processed: 280 average time/residue: 0.1387 time to fit residues: 62.1905 Evaluate side-chains 235 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 440 HIS Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 454 HIS Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 412 PHE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 144 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 200 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 GLN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.061797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.043238 restraints weight = 116953.450| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 6.10 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22880 Z= 0.185 Angle : 0.680 32.307 30921 Z= 0.325 Chirality : 0.044 0.221 3377 Planarity : 0.004 0.063 3970 Dihedral : 5.094 46.645 3054 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.39 % Favored : 95.51 % Rotamer: Outliers : 2.36 % Allowed : 17.93 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.16), residues: 2782 helix: 0.51 (0.16), residues: 1075 sheet: -0.61 (0.20), residues: 644 loop : -0.41 (0.20), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 214 TYR 0.022 0.001 TYR C 96 PHE 0.020 0.002 PHE C 132 TRP 0.015 0.001 TRP B 251 HIS 0.004 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00401 (22874) covalent geometry : angle 0.62164 (30913) SS BOND : bond 0.00353 ( 1) SS BOND : angle 1.67222 ( 2) hydrogen bonds : bond 0.03831 ( 995) hydrogen bonds : angle 5.37546 ( 2766) metal coordination : bond 0.03093 ( 5) metal coordination : angle 19.72731 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 215 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ILE cc_start: 0.9681 (mt) cc_final: 0.9465 (mm) REVERT: A 362 MET cc_start: 0.8756 (mpp) cc_final: 0.8386 (mpp) REVERT: A 440 HIS cc_start: 0.9279 (p-80) cc_final: 0.8980 (p90) REVERT: B 153 LYS cc_start: 0.9468 (tmtt) cc_final: 0.8989 (tmtt) REVERT: B 375 MET cc_start: 0.7522 (tmm) cc_final: 0.6974 (tmm) REVERT: B 413 VAL cc_start: 0.9273 (OUTLIER) cc_final: 0.9058 (m) REVERT: B 434 MET cc_start: 0.9065 (ptm) cc_final: 0.8836 (ptm) REVERT: C 109 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8640 (ptp-170) REVERT: C 155 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8426 (mp0) REVERT: C 224 MET cc_start: 0.9161 (mpp) cc_final: 0.8836 (tpp) REVERT: C 362 MET cc_start: 0.8852 (mpp) cc_final: 0.8224 (mpp) REVERT: D 214 ARG cc_start: 0.8552 (mmm160) cc_final: 0.8115 (mmm160) REVERT: E 170 GLU cc_start: 0.9061 (pt0) cc_final: 0.8279 (pt0) REVERT: E 178 TYR cc_start: 0.9108 (t80) cc_final: 0.8748 (t80) REVERT: F 88 GLU cc_start: 0.8221 (mp0) cc_final: 0.7770 (tm-30) REVERT: F 310 MET cc_start: 0.8221 (tpp) cc_final: 0.7736 (tpp) REVERT: F 362 MET cc_start: 0.8825 (mpp) cc_final: 0.8465 (mpp) REVERT: F 407 ASP cc_start: 0.9524 (p0) cc_final: 0.9119 (p0) REVERT: G 246 MET cc_start: 0.9476 (mmm) cc_final: 0.9199 (mmm) REVERT: G 307 MET cc_start: 0.9507 (mtp) cc_final: 0.9229 (mtt) REVERT: G 388 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.8054 (t0) REVERT: G 434 MET cc_start: 0.9401 (ppp) cc_final: 0.9059 (ppp) REVERT: H 114 LYS cc_start: 0.9360 (tppt) cc_final: 0.9030 (mmmt) outliers start: 58 outliers final: 34 residues processed: 254 average time/residue: 0.1529 time to fit residues: 62.0500 Evaluate side-chains 244 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 440 HIS Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 454 HIS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 412 PHE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 388 ASN Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 3 optimal weight: 0.0980 chunk 193 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 chunk 263 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 256 optimal weight: 0.0570 chunk 140 optimal weight: 7.9990 chunk 171 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 90 GLN E 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.063180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.044495 restraints weight = 117611.660| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 6.26 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22880 Z= 0.113 Angle : 0.656 26.592 30921 Z= 0.310 Chirality : 0.044 0.194 3377 Planarity : 0.004 0.062 3970 Dihedral : 4.868 46.039 3054 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.95 % Favored : 95.94 % Rotamer: Outliers : 2.04 % Allowed : 19.15 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.16), residues: 2782 helix: 0.47 (0.16), residues: 1083 sheet: -0.34 (0.21), residues: 641 loop : -0.40 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 328 TYR 0.019 0.001 TYR D 266 PHE 0.022 0.001 PHE C 132 TRP 0.016 0.001 TRP B 251 HIS 0.005 0.000 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00244 (22874) covalent geometry : angle 0.60859 (30913) SS BOND : bond 0.00183 ( 1) SS BOND : angle 1.43072 ( 2) hydrogen bonds : bond 0.03347 ( 995) hydrogen bonds : angle 5.13831 ( 2766) metal coordination : bond 0.02379 ( 5) metal coordination : angle 17.66284 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 236 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ILE cc_start: 0.9674 (mt) cc_final: 0.9438 (mm) REVERT: A 440 HIS cc_start: 0.9295 (p-80) cc_final: 0.8993 (p90) REVERT: B 153 LYS cc_start: 0.9459 (tmtt) cc_final: 0.8983 (tmtt) REVERT: B 375 MET cc_start: 0.7531 (tmm) cc_final: 0.6934 (tmm) REVERT: B 407 ASP cc_start: 0.9743 (t0) cc_final: 0.9508 (p0) REVERT: B 413 VAL cc_start: 0.9259 (OUTLIER) cc_final: 0.9037 (m) REVERT: B 434 MET cc_start: 0.9021 (ptm) cc_final: 0.8782 (ptm) REVERT: C 103 MET cc_start: 0.9543 (ttm) cc_final: 0.9328 (ttt) REVERT: C 109 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8624 (ptp-170) REVERT: C 155 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8501 (mp0) REVERT: C 160 MET cc_start: 0.8805 (mmm) cc_final: 0.8564 (mmt) REVERT: C 188 LEU cc_start: 0.9601 (tp) cc_final: 0.9196 (pp) REVERT: C 224 MET cc_start: 0.9148 (mpp) cc_final: 0.8869 (tpp) REVERT: C 278 GLN cc_start: 0.9440 (pt0) cc_final: 0.8953 (pp30) REVERT: C 362 MET cc_start: 0.8789 (mpp) cc_final: 0.8185 (mpp) REVERT: D 160 MET cc_start: 0.8740 (mmt) cc_final: 0.8540 (mmt) REVERT: D 214 ARG cc_start: 0.8560 (mmm160) cc_final: 0.8161 (mmm160) REVERT: D 310 MET cc_start: 0.9244 (pmm) cc_final: 0.8716 (pmm) REVERT: E 178 TYR cc_start: 0.9057 (t80) cc_final: 0.8702 (t80) REVERT: E 260 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7844 (ptt180) REVERT: E 315 ILE cc_start: 0.9000 (mt) cc_final: 0.8774 (tp) REVERT: F 88 GLU cc_start: 0.8167 (mp0) cc_final: 0.7749 (tm-30) REVERT: F 291 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8780 (mt) REVERT: F 310 MET cc_start: 0.8187 (tpp) cc_final: 0.7789 (tpp) REVERT: F 362 MET cc_start: 0.8803 (mpp) cc_final: 0.8377 (mpp) REVERT: G 155 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8023 (tm-30) REVERT: G 246 MET cc_start: 0.9464 (mmm) cc_final: 0.9187 (mmm) REVERT: G 388 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.8001 (t0) REVERT: G 434 MET cc_start: 0.9441 (ppp) cc_final: 0.9101 (ppp) REVERT: H 110 LYS cc_start: 0.9444 (mmmm) cc_final: 0.9194 (mmmm) outliers start: 50 outliers final: 30 residues processed: 274 average time/residue: 0.1443 time to fit residues: 63.4630 Evaluate side-chains 251 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 454 HIS Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 260 ARG Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 388 ASN Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 40 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 201 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 271 optimal weight: 0.9990 chunk 166 optimal weight: 8.9990 chunk 227 optimal weight: 3.9990 chunk 243 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 278 GLN ** F 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.065772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.046308 restraints weight = 113187.250| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 6.19 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22880 Z= 0.144 Angle : 0.649 26.395 30921 Z= 0.309 Chirality : 0.043 0.233 3377 Planarity : 0.004 0.057 3970 Dihedral : 4.789 46.978 3054 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 2.57 % Allowed : 19.11 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.16), residues: 2782 helix: 0.56 (0.16), residues: 1084 sheet: -0.24 (0.21), residues: 635 loop : -0.41 (0.20), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 112 TYR 0.019 0.001 TYR E 259 PHE 0.022 0.001 PHE C 132 TRP 0.031 0.001 TRP F 142 HIS 0.004 0.001 HIS G 141 Details of bonding type rmsd covalent geometry : bond 0.00314 (22874) covalent geometry : angle 0.60330 (30913) SS BOND : bond 0.00257 ( 1) SS BOND : angle 1.43636 ( 2) hydrogen bonds : bond 0.03259 ( 995) hydrogen bonds : angle 5.03912 ( 2766) metal coordination : bond 0.02575 ( 5) metal coordination : angle 17.17105 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 214 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ILE cc_start: 0.9679 (mt) cc_final: 0.9430 (mm) REVERT: A 362 MET cc_start: 0.8847 (mpp) cc_final: 0.8290 (mpp) REVERT: A 395 GLU cc_start: 0.9304 (OUTLIER) cc_final: 0.9104 (pp20) REVERT: A 434 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.5964 (pmt) REVERT: A 440 HIS cc_start: 0.9301 (p-80) cc_final: 0.9039 (p90) REVERT: B 153 LYS cc_start: 0.9459 (tmtt) cc_final: 0.8966 (tmtt) REVERT: B 375 MET cc_start: 0.7621 (tmm) cc_final: 0.7100 (tmm) REVERT: B 407 ASP cc_start: 0.9745 (t0) cc_final: 0.9511 (p0) REVERT: B 413 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.9036 (m) REVERT: B 434 MET cc_start: 0.9007 (ptm) cc_final: 0.8773 (ptm) REVERT: C 103 MET cc_start: 0.9549 (ttm) cc_final: 0.9302 (ttt) REVERT: C 109 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8536 (ptp-170) REVERT: C 155 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8728 (mm-30) REVERT: C 224 MET cc_start: 0.9154 (mpp) cc_final: 0.8852 (tpp) REVERT: C 362 MET cc_start: 0.8830 (mpp) cc_final: 0.8298 (mpp) REVERT: D 83 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8300 (pmm) REVERT: D 214 ARG cc_start: 0.8581 (mmm160) cc_final: 0.8159 (mmm160) REVERT: D 310 MET cc_start: 0.9236 (pmm) cc_final: 0.8629 (pmm) REVERT: E 83 MET cc_start: 0.9037 (mtm) cc_final: 0.8827 (mtm) REVERT: E 260 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7717 (ptt180) REVERT: E 397 MET cc_start: 0.9325 (tpt) cc_final: 0.9018 (ttm) REVERT: F 88 GLU cc_start: 0.8219 (mp0) cc_final: 0.7793 (tm-30) REVERT: F 103 MET cc_start: 0.9356 (tmm) cc_final: 0.8661 (tmm) REVERT: F 109 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8049 (ttp-170) REVERT: F 112 ARG cc_start: 0.6146 (OUTLIER) cc_final: 0.4831 (tpt90) REVERT: F 310 MET cc_start: 0.8188 (tpp) cc_final: 0.7898 (tpp) REVERT: F 362 MET cc_start: 0.8731 (mpp) cc_final: 0.8495 (mpp) REVERT: F 445 MET cc_start: 0.9048 (ppp) cc_final: 0.8821 (ppp) REVERT: G 155 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8066 (tm-30) REVERT: G 246 MET cc_start: 0.9453 (mmm) cc_final: 0.9204 (mmm) REVERT: G 388 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.8049 (t0) REVERT: G 434 MET cc_start: 0.9436 (ppp) cc_final: 0.9111 (ppp) outliers start: 63 outliers final: 39 residues processed: 260 average time/residue: 0.1436 time to fit residues: 59.0211 Evaluate side-chains 250 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 202 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 440 HIS Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 454 HIS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 260 ARG Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 388 ASN Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 128 optimal weight: 8.9990 chunk 270 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 252 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 180 optimal weight: 0.0020 chunk 86 optimal weight: 2.9990 chunk 204 optimal weight: 20.0000 chunk 153 optimal weight: 0.9980 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 414 ASN E 278 GLN ** F 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 427 GLN H 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.062855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.044321 restraints weight = 118216.475| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 6.24 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22880 Z= 0.124 Angle : 0.653 25.324 30921 Z= 0.308 Chirality : 0.043 0.212 3377 Planarity : 0.004 0.052 3970 Dihedral : 4.686 46.278 3054 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.42 % Favored : 95.51 % Rotamer: Outliers : 2.85 % Allowed : 19.48 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.16), residues: 2782 helix: 0.57 (0.16), residues: 1081 sheet: -0.19 (0.21), residues: 639 loop : -0.39 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 328 TYR 0.017 0.001 TYR D 266 PHE 0.022 0.001 PHE C 132 TRP 0.020 0.001 TRP F 142 HIS 0.004 0.001 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00271 (22874) covalent geometry : angle 0.60725 (30913) SS BOND : bond 0.00226 ( 1) SS BOND : angle 1.36226 ( 2) hydrogen bonds : bond 0.03108 ( 995) hydrogen bonds : angle 4.95688 ( 2766) metal coordination : bond 0.02403 ( 5) metal coordination : angle 17.24317 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 216 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ILE cc_start: 0.9693 (mt) cc_final: 0.9428 (mm) REVERT: A 160 MET cc_start: 0.8830 (mmm) cc_final: 0.8143 (mmt) REVERT: A 362 MET cc_start: 0.8835 (mpp) cc_final: 0.8234 (mpp) REVERT: A 434 MET cc_start: 0.6526 (OUTLIER) cc_final: 0.5776 (pmt) REVERT: A 440 HIS cc_start: 0.9288 (p-80) cc_final: 0.8997 (p90) REVERT: B 153 LYS cc_start: 0.9457 (tmtt) cc_final: 0.8958 (tmtt) REVERT: B 250 LYS cc_start: 0.9474 (OUTLIER) cc_final: 0.9212 (tppt) REVERT: B 375 MET cc_start: 0.7619 (tmm) cc_final: 0.7167 (tmm) REVERT: B 407 ASP cc_start: 0.9722 (t0) cc_final: 0.9458 (p0) REVERT: B 413 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.9014 (m) REVERT: C 103 MET cc_start: 0.9537 (ttm) cc_final: 0.9289 (ttt) REVERT: C 109 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8515 (ptp-170) REVERT: C 155 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8784 (mm-30) REVERT: C 188 LEU cc_start: 0.9586 (tp) cc_final: 0.9165 (pp) REVERT: C 224 MET cc_start: 0.9126 (mpp) cc_final: 0.8851 (tpp) REVERT: C 362 MET cc_start: 0.8784 (mpp) cc_final: 0.8289 (mpp) REVERT: D 83 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8256 (pmm) REVERT: D 214 ARG cc_start: 0.8585 (mmm160) cc_final: 0.8215 (mmm160) REVERT: D 310 MET cc_start: 0.9228 (pmm) cc_final: 0.8637 (pmm) REVERT: D 434 MET cc_start: 0.9100 (tmm) cc_final: 0.8709 (ppp) REVERT: E 260 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7768 (ptt180) REVERT: E 397 MET cc_start: 0.9315 (tpt) cc_final: 0.9035 (ttm) REVERT: F 88 GLU cc_start: 0.8167 (mp0) cc_final: 0.7750 (tm-30) REVERT: F 103 MET cc_start: 0.9388 (tmm) cc_final: 0.8853 (tmm) REVERT: F 109 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8161 (ttp-170) REVERT: F 291 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8692 (mt) REVERT: F 310 MET cc_start: 0.8193 (tpp) cc_final: 0.7863 (tpp) REVERT: F 362 MET cc_start: 0.8776 (mpp) cc_final: 0.8518 (mpp) REVERT: G 155 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8050 (tm-30) REVERT: G 388 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.8142 (t0) REVERT: G 427 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8684 (pt0) REVERT: G 434 MET cc_start: 0.9507 (ppp) cc_final: 0.9181 (ppp) outliers start: 70 outliers final: 42 residues processed: 263 average time/residue: 0.1545 time to fit residues: 64.5560 Evaluate side-chains 262 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 210 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 440 HIS Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 454 HIS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 260 ARG Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 388 ASN Chi-restraints excluded: chain G residue 427 GLN Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 72 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 108 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 273 optimal weight: 2.9990 chunk 262 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 GLN D 165 ASN D 429 GLN ** F 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 427 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.061090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.042507 restraints weight = 120771.795| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 6.20 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22880 Z= 0.226 Angle : 0.693 28.024 30921 Z= 0.331 Chirality : 0.044 0.213 3377 Planarity : 0.004 0.048 3970 Dihedral : 4.793 43.959 3054 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.89 % Favored : 95.04 % Rotamer: Outliers : 2.81 % Allowed : 20.33 % Favored : 76.85 % 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 aren not related in a simple way. whole: -0.03 (0.16), residues: 2782 helix: 0.59 (0.16), residues: 1080 sheet: -0.20 (0.21), residues: 638 loop : -0.36 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 117 TYR 0.020 0.002 TYR C 96 PHE 0.022 0.002 PHE D 209 TRP 0.030 0.002 TRP F 142 HIS 0.007 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00485 (22874) covalent geometry : angle 0.64529 (30913) SS BOND : bond 0.00454 ( 1) SS BOND : angle 1.52601 ( 2) hydrogen bonds : bond 0.03342 ( 995) hydrogen bonds : angle 5.05563 ( 2766) metal coordination : bond 0.02977 ( 5) metal coordination : angle 18.14610 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 212 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9166 (mm) REVERT: A 160 MET cc_start: 0.8629 (mmm) cc_final: 0.8065 (mmt) REVERT: A 362 MET cc_start: 0.8848 (mpp) cc_final: 0.8277 (mpp) REVERT: A 434 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.6044 (pmt) REVERT: A 440 HIS cc_start: 0.9274 (p-80) cc_final: 0.9012 (p90) REVERT: B 250 LYS cc_start: 0.9476 (OUTLIER) cc_final: 0.9250 (tppt) REVERT: B 375 MET cc_start: 0.7633 (tmm) cc_final: 0.7275 (tmm) REVERT: B 407 ASP cc_start: 0.9737 (t0) cc_final: 0.9470 (p0) REVERT: B 413 VAL cc_start: 0.9241 (OUTLIER) cc_final: 0.9012 (m) REVERT: B 434 MET cc_start: 0.8909 (ptm) cc_final: 0.8690 (ptm) REVERT: C 109 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8626 (ptp-170) REVERT: C 155 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8789 (mm-30) REVERT: C 224 MET cc_start: 0.9100 (mpp) cc_final: 0.8838 (tpp) REVERT: C 362 MET cc_start: 0.8894 (mpp) cc_final: 0.8425 (mpp) REVERT: C 375 MET cc_start: 0.8816 (mmm) cc_final: 0.8587 (mmm) REVERT: D 214 ARG cc_start: 0.8617 (mmm160) cc_final: 0.8315 (mmt-90) REVERT: D 310 MET cc_start: 0.9274 (pmm) cc_final: 0.8698 (pmm) REVERT: D 434 MET cc_start: 0.9187 (tmm) cc_final: 0.8874 (ppp) REVERT: D 445 MET cc_start: 0.8778 (mtp) cc_final: 0.8528 (ptp) REVERT: D 451 ASN cc_start: 0.9462 (m-40) cc_final: 0.9212 (t0) REVERT: E 260 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7759 (ptt180) REVERT: E 397 MET cc_start: 0.9386 (tpt) cc_final: 0.9081 (ttm) REVERT: E 428 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9346 (pp) REVERT: F 88 GLU cc_start: 0.8234 (mp0) cc_final: 0.7773 (tm-30) REVERT: F 109 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8135 (ttp-170) REVERT: F 112 ARG cc_start: 0.8548 (tpp-160) cc_final: 0.8290 (tpp-160) REVERT: F 310 MET cc_start: 0.8243 (tpp) cc_final: 0.7938 (tpp) REVERT: F 362 MET cc_start: 0.8805 (mpp) cc_final: 0.8546 (mpp) REVERT: G 155 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8139 (tm-30) REVERT: G 246 MET cc_start: 0.9439 (mtp) cc_final: 0.9217 (mtp) REVERT: G 397 MET cc_start: 0.9047 (ppp) cc_final: 0.8604 (ppp) REVERT: G 434 MET cc_start: 0.9507 (ppp) cc_final: 0.9193 (ppp) outliers start: 69 outliers final: 47 residues processed: 257 average time/residue: 0.1446 time to fit residues: 59.6243 Evaluate side-chains 259 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 204 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 454 HIS Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 260 ARG Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 328 ARG Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 62 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 84 optimal weight: 0.0770 chunk 216 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 267 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 overall best weight: 2.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 GLN C 414 ASN ** F 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 278 GLN G 427 GLN G 429 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.061691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.043229 restraints weight = 118385.768| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 6.18 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22880 Z= 0.146 Angle : 0.682 26.461 30921 Z= 0.322 Chirality : 0.044 0.200 3377 Planarity : 0.004 0.048 3970 Dihedral : 4.743 45.328 3054 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 2.73 % Allowed : 20.90 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.16), residues: 2782 helix: 0.59 (0.16), residues: 1086 sheet: -0.13 (0.21), residues: 640 loop : -0.37 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 81 TYR 0.018 0.001 TYR D 266 PHE 0.015 0.001 PHE D 209 TRP 0.025 0.001 TRP F 142 HIS 0.004 0.001 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00319 (22874) covalent geometry : angle 0.63465 (30913) SS BOND : bond 0.00400 ( 1) SS BOND : angle 1.45869 ( 2) hydrogen bonds : bond 0.03152 ( 995) hydrogen bonds : angle 5.01193 ( 2766) metal coordination : bond 0.02564 ( 5) metal coordination : angle 17.87400 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 216 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ILE cc_start: 0.9713 (mt) cc_final: 0.9500 (mm) REVERT: A 160 MET cc_start: 0.8518 (mmm) cc_final: 0.7912 (mmt) REVERT: A 362 MET cc_start: 0.8893 (mpp) cc_final: 0.8228 (mpp) REVERT: A 434 MET cc_start: 0.6605 (OUTLIER) cc_final: 0.5843 (pmt) REVERT: A 440 HIS cc_start: 0.9284 (p-80) cc_final: 0.9011 (p90) REVERT: B 153 LYS cc_start: 0.9430 (tmtt) cc_final: 0.9033 (tmtt) REVERT: B 250 LYS cc_start: 0.9488 (OUTLIER) cc_final: 0.9205 (tppt) REVERT: B 375 MET cc_start: 0.7607 (tmm) cc_final: 0.7182 (tmm) REVERT: B 407 ASP cc_start: 0.9724 (t0) cc_final: 0.9442 (p0) REVERT: B 413 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.9018 (m) REVERT: B 434 MET cc_start: 0.8863 (ptm) cc_final: 0.8627 (ptm) REVERT: C 103 MET cc_start: 0.9514 (ttm) cc_final: 0.9275 (ttt) REVERT: C 109 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8596 (ptp-170) REVERT: C 155 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8835 (mm-30) REVERT: C 224 MET cc_start: 0.9091 (mpp) cc_final: 0.8832 (tpp) REVERT: C 278 GLN cc_start: 0.9463 (pt0) cc_final: 0.8935 (pp30) REVERT: C 362 MET cc_start: 0.8804 (mpp) cc_final: 0.8339 (mpp) REVERT: C 375 MET cc_start: 0.8802 (mmm) cc_final: 0.8567 (mmm) REVERT: D 160 MET cc_start: 0.8579 (mmt) cc_final: 0.8255 (mmm) REVERT: D 310 MET cc_start: 0.9245 (pmm) cc_final: 0.8672 (pmm) REVERT: D 434 MET cc_start: 0.9144 (tmm) cc_final: 0.8731 (ppp) REVERT: D 451 ASN cc_start: 0.9464 (m-40) cc_final: 0.9208 (t0) REVERT: E 260 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7809 (ptt180) REVERT: E 310 MET cc_start: 0.8222 (tpp) cc_final: 0.7961 (tpp) REVERT: F 88 GLU cc_start: 0.8209 (mp0) cc_final: 0.7762 (tm-30) REVERT: F 103 MET cc_start: 0.9362 (tmm) cc_final: 0.8773 (tmm) REVERT: F 109 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8019 (ttp-170) REVERT: F 120 TYR cc_start: 0.8528 (t80) cc_final: 0.8277 (t80) REVERT: F 310 MET cc_start: 0.8198 (tpp) cc_final: 0.7913 (tpp) REVERT: F 362 MET cc_start: 0.8824 (mpp) cc_final: 0.8550 (mpp) REVERT: G 155 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8141 (tm-30) REVERT: G 246 MET cc_start: 0.9437 (mtp) cc_final: 0.9191 (mtp) REVERT: G 397 MET cc_start: 0.9000 (ppp) cc_final: 0.8669 (ppp) REVERT: G 434 MET cc_start: 0.9525 (ppp) cc_final: 0.9213 (ppp) outliers start: 67 outliers final: 49 residues processed: 259 average time/residue: 0.1426 time to fit residues: 58.7223 Evaluate side-chains 261 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 454 HIS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 260 ARG Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 328 ARG Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 278 GLN Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 266 optimal weight: 5.9990 chunk 260 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 246 optimal weight: 8.9990 chunk 206 optimal weight: 9.9990 chunk 218 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.060542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.042046 restraints weight = 120941.762| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 6.17 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22880 Z= 0.234 Angle : 0.725 27.520 30921 Z= 0.346 Chirality : 0.044 0.338 3377 Planarity : 0.004 0.048 3970 Dihedral : 4.860 43.032 3054 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.25 % Favored : 94.68 % Rotamer: Outliers : 2.73 % Allowed : 21.48 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.16), residues: 2782 helix: 0.54 (0.16), residues: 1083 sheet: -0.21 (0.21), residues: 635 loop : -0.40 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 81 TYR 0.018 0.002 TYR C 96 PHE 0.022 0.002 PHE D 209 TRP 0.023 0.002 TRP F 142 HIS 0.006 0.001 HIS G 141 Details of bonding type rmsd covalent geometry : bond 0.00504 (22874) covalent geometry : angle 0.67844 (30913) SS BOND : bond 0.00506 ( 1) SS BOND : angle 1.59814 ( 2) hydrogen bonds : bond 0.03388 ( 995) hydrogen bonds : angle 5.14936 ( 2766) metal coordination : bond 0.03024 ( 5) metal coordination : angle 18.28764 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 207 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8462 (m-30) cc_final: 0.8062 (m-30) REVERT: A 160 MET cc_start: 0.8533 (mmm) cc_final: 0.8210 (tpp) REVERT: A 362 MET cc_start: 0.9118 (mpp) cc_final: 0.8447 (mpp) REVERT: A 434 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6079 (pmt) REVERT: A 440 HIS cc_start: 0.9272 (p-80) cc_final: 0.9001 (p90) REVERT: B 153 LYS cc_start: 0.9433 (tmtt) cc_final: 0.9012 (tmtt) REVERT: B 250 LYS cc_start: 0.9488 (OUTLIER) cc_final: 0.9218 (tppt) REVERT: B 375 MET cc_start: 0.7605 (tmm) cc_final: 0.7151 (tmm) REVERT: B 407 ASP cc_start: 0.9727 (t0) cc_final: 0.9446 (p0) REVERT: C 155 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8832 (mm-30) REVERT: C 224 MET cc_start: 0.9084 (mpp) cc_final: 0.8827 (tpp) REVERT: C 362 MET cc_start: 0.8892 (mpp) cc_final: 0.8435 (mpp) REVERT: C 375 MET cc_start: 0.8841 (mmm) cc_final: 0.8598 (tpt) REVERT: D 310 MET cc_start: 0.9278 (pmm) cc_final: 0.8694 (pmm) REVERT: D 434 MET cc_start: 0.9157 (tmm) cc_final: 0.8900 (ppp) REVERT: D 445 MET cc_start: 0.9204 (ttm) cc_final: 0.8665 (ptm) REVERT: D 451 ASN cc_start: 0.9471 (m-40) cc_final: 0.9215 (t0) REVERT: E 103 MET cc_start: 0.9633 (OUTLIER) cc_final: 0.9377 (tmm) REVERT: E 260 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7755 (ptt180) REVERT: E 397 MET cc_start: 0.9436 (tpp) cc_final: 0.9057 (ttm) REVERT: E 428 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9266 (pp) REVERT: F 88 GLU cc_start: 0.8293 (mp0) cc_final: 0.7778 (tm-30) REVERT: F 103 MET cc_start: 0.9391 (tmm) cc_final: 0.8816 (tmm) REVERT: F 109 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8001 (ttp-170) REVERT: F 120 TYR cc_start: 0.8542 (t80) cc_final: 0.8294 (t80) REVERT: F 310 MET cc_start: 0.8192 (tpp) cc_final: 0.7894 (tpp) REVERT: F 362 MET cc_start: 0.8835 (mpp) cc_final: 0.8549 (mpp) REVERT: G 155 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8167 (tm-30) REVERT: G 246 MET cc_start: 0.9436 (mtp) cc_final: 0.9186 (mtp) REVERT: G 397 MET cc_start: 0.9041 (ppp) cc_final: 0.8640 (ppp) REVERT: G 434 MET cc_start: 0.9547 (ppp) cc_final: 0.9267 (ppp) outliers start: 67 outliers final: 57 residues processed: 252 average time/residue: 0.1568 time to fit residues: 63.0757 Evaluate side-chains 263 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 200 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 454 HIS Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 260 ARG Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 328 ARG Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 278 GLN Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 120 optimal weight: 3.9990 chunk 227 optimal weight: 0.6980 chunk 156 optimal weight: 6.9990 chunk 265 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 253 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 GLN ** F 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.060521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.042101 restraints weight = 120820.313| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 6.16 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22880 Z= 0.211 Angle : 0.728 28.158 30921 Z= 0.347 Chirality : 0.045 0.284 3377 Planarity : 0.004 0.047 3970 Dihedral : 4.883 44.284 3054 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.96 % Favored : 94.97 % Rotamer: Outliers : 2.53 % Allowed : 21.84 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.16), residues: 2782 helix: 0.47 (0.16), residues: 1090 sheet: -0.29 (0.21), residues: 640 loop : -0.41 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 81 TYR 0.017 0.001 TYR C 96 PHE 0.020 0.002 PHE D 209 TRP 0.020 0.002 TRP F 142 HIS 0.005 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00454 (22874) covalent geometry : angle 0.67914 (30913) SS BOND : bond 0.00530 ( 1) SS BOND : angle 1.48827 ( 2) hydrogen bonds : bond 0.03344 ( 995) hydrogen bonds : angle 5.16148 ( 2766) metal coordination : bond 0.02951 ( 5) metal coordination : angle 18.73306 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5564 Ramachandran restraints generated. 2782 Oldfield, 0 Emsley, 2782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 201 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8537 (m-30) cc_final: 0.8142 (m-30) REVERT: A 160 MET cc_start: 0.8499 (mmm) cc_final: 0.8170 (tpp) REVERT: A 362 MET cc_start: 0.9086 (mpp) cc_final: 0.8423 (mpp) REVERT: A 434 MET cc_start: 0.6733 (OUTLIER) cc_final: 0.6016 (pmt) REVERT: A 440 HIS cc_start: 0.9254 (p-80) cc_final: 0.8978 (p90) REVERT: B 153 LYS cc_start: 0.9434 (tmtt) cc_final: 0.9026 (tmtt) REVERT: B 250 LYS cc_start: 0.9484 (OUTLIER) cc_final: 0.9202 (tppt) REVERT: B 375 MET cc_start: 0.7570 (tmm) cc_final: 0.7093 (tmm) REVERT: B 407 ASP cc_start: 0.9728 (t0) cc_final: 0.9443 (p0) REVERT: C 155 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8866 (mm-30) REVERT: C 160 MET cc_start: 0.8799 (mmm) cc_final: 0.8168 (mmt) REVERT: C 224 MET cc_start: 0.9108 (mpp) cc_final: 0.8829 (tpp) REVERT: C 362 MET cc_start: 0.8874 (mpp) cc_final: 0.8412 (mpp) REVERT: C 375 MET cc_start: 0.8842 (mmm) cc_final: 0.8591 (mmm) REVERT: D 310 MET cc_start: 0.9263 (pmm) cc_final: 0.8685 (pmm) REVERT: D 434 MET cc_start: 0.9154 (tmm) cc_final: 0.8802 (ppp) REVERT: D 445 MET cc_start: 0.9232 (ttm) cc_final: 0.9006 (ttp) REVERT: D 451 ASN cc_start: 0.9475 (m-40) cc_final: 0.9217 (t0) REVERT: E 260 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7748 (ptt180) REVERT: E 307 MET cc_start: 0.9163 (ptp) cc_final: 0.8728 (ptp) REVERT: F 88 GLU cc_start: 0.8278 (mp0) cc_final: 0.7750 (tm-30) REVERT: F 103 MET cc_start: 0.9370 (tmm) cc_final: 0.8777 (tmm) REVERT: F 109 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7989 (ttp-170) REVERT: F 120 TYR cc_start: 0.8535 (t80) cc_final: 0.8292 (t80) REVERT: F 310 MET cc_start: 0.8145 (tpp) cc_final: 0.7863 (tpp) REVERT: F 362 MET cc_start: 0.8829 (mpp) cc_final: 0.8544 (mpp) REVERT: G 155 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8166 (tm-30) REVERT: G 246 MET cc_start: 0.9433 (mtp) cc_final: 0.9179 (mtp) REVERT: G 397 MET cc_start: 0.9041 (ppp) cc_final: 0.8728 (ppp) REVERT: G 434 MET cc_start: 0.9560 (ppp) cc_final: 0.9296 (ppp) outliers start: 62 outliers final: 56 residues processed: 244 average time/residue: 0.1516 time to fit residues: 59.4542 Evaluate side-chains 261 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 201 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 310 MET Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 366 HIS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 454 HIS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 260 ARG Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 328 ARG Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 278 GLN Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 29 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 259 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 GLN ** F 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.059984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.041501 restraints weight = 121348.842| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 6.15 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 22880 Z= 0.249 Angle : 0.746 28.701 30921 Z= 0.356 Chirality : 0.045 0.280 3377 Planarity : 0.004 0.046 3970 Dihedral : 4.972 44.572 3054 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.32 % Favored : 94.61 % Rotamer: Outliers : 2.53 % Allowed : 21.92 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.16), residues: 2782 helix: 0.42 (0.16), residues: 1090 sheet: -0.32 (0.21), residues: 634 loop : -0.45 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 223 TYR 0.020 0.002 TYR C 96 PHE 0.024 0.002 PHE D 209 TRP 0.021 0.002 TRP F 142 HIS 0.006 0.001 HIS G 141 Details of bonding type rmsd covalent geometry : bond 0.00534 (22874) covalent geometry : angle 0.69602 (30913) SS BOND : bond 0.00591 ( 1) SS BOND : angle 1.58217 ( 2) hydrogen bonds : bond 0.03468 ( 995) hydrogen bonds : angle 5.24294 ( 2766) metal coordination : bond 0.03099 ( 5) metal coordination : angle 19.32758 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4204.84 seconds wall clock time: 73 minutes 37.96 seconds (4417.96 seconds total)