Starting phenix.real_space_refine on Sun Aug 24 07:34:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sh2_40477/08_2025/8sh2_40477.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sh2_40477/08_2025/8sh2_40477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sh2_40477/08_2025/8sh2_40477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sh2_40477/08_2025/8sh2_40477.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sh2_40477/08_2025/8sh2_40477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sh2_40477/08_2025/8sh2_40477.map" } resolution = 3.74 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= 0.001 sd= 0.015 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: 4 Type Number sf(0) Gaussians S 109 5.16 5 C 11483 2.51 5 N 3122 2.21 5 O 3324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18038 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3030 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 357} Chain breaks: 1 Chain: "E" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain: "F" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 691 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain breaks: 1 Chain: "G" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain: "H" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 715 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "I" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 749 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain breaks: 1 Chain: "J" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 687 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain breaks: 1 Chain: "K" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 725 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 7, 'TRANS': 84} Chain breaks: 1 Chain: "L" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 691 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain breaks: 1 Chain: "C" Number of atoms: 3066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3066 Classifications: {'peptide': 381} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 361} Chain breaks: 1 Chain: "A" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3080 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 363} Chain: "D" Number of atoms: 3086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3086 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 364} Time building chain proxies: 5.13, per 1000 atoms: 0.28 Number of scatterers: 18038 At special positions: 0 Unit cell: (139.44, 141.93, 108.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 109 16.00 O 3324 8.00 N 3122 7.00 C 11483 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 701.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4190 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 41 sheets defined 16.1% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 344 through 348 removed outlier: 3.825A pdb=" N ALA B 348 " --> pdb=" O HIS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 372 removed outlier: 3.584A pdb=" N VAL B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 394 removed outlier: 3.566A pdb=" N VAL B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 399 removed outlier: 4.073A pdb=" N PHE B 398 " --> pdb=" O VAL B 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 36 Processing helix chain 'F' and resid 33 through 37 Processing helix chain 'F' and resid 40 through 46 Processing helix chain 'F' and resid 66 through 83 removed outlier: 3.891A pdb=" N LEU F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 111 Processing helix chain 'G' and resid 23 through 36 removed outlier: 3.696A pdb=" N LEU G 27 " --> pdb=" O THR G 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 46 Processing helix chain 'H' and resid 66 through 83 Processing helix chain 'H' and resid 99 through 109 Processing helix chain 'I' and resid 23 through 36 removed outlier: 3.557A pdb=" N LEU I 27 " --> pdb=" O THR I 23 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS I 36 " --> pdb=" O GLU I 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 37 removed outlier: 3.550A pdb=" N LEU J 37 " --> pdb=" O GLU J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 46 Processing helix chain 'J' and resid 66 through 84 removed outlier: 3.720A pdb=" N LEU J 70 " --> pdb=" O PRO J 66 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS J 72 " --> pdb=" O HIS J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 110 Processing helix chain 'K' and resid 23 through 36 removed outlier: 3.777A pdb=" N LEU K 27 " --> pdb=" O THR K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 61 Processing helix chain 'L' and resid 33 through 39 removed outlier: 4.060A pdb=" N SER L 39 " --> pdb=" O HIS L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 46 removed outlier: 4.221A pdb=" N LEU L 46 " --> pdb=" O ILE L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 82 Processing helix chain 'L' and resid 96 through 111 removed outlier: 4.230A pdb=" N MET L 105 " --> pdb=" O LEU L 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP L 111 " --> pdb=" O ALA L 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 363 through 376 removed outlier: 3.760A pdb=" N CYS C 374 " --> pdb=" O GLU C 370 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 185 removed outlier: 3.606A pdb=" N PHE A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 379 through 385 Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 363 through 375 removed outlier: 3.934A pdb=" N PHE D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 385 Processing helix chain 'D' and resid 387 through 397 removed outlier: 3.800A pdb=" N ARG D 397 " --> pdb=" O SER D 393 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 36 through 39 Processing sheet with id=AA2, first strand: chain 'B' and resid 50 through 52 Processing sheet with id=AA3, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.900A pdb=" N GLU B 84 " --> pdb=" O TRP B 132 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ARG B 134 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLN B 131 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP B 122 " --> pdb=" O GLN B 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AA5, first strand: chain 'B' and resid 145 through 146 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 153 Processing sheet with id=AA7, first strand: chain 'B' and resid 211 through 212 removed outlier: 7.175A pdb=" N THR B 211 " --> pdb=" O TRP B 255 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLU B 257 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU B 254 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 222 " --> pdb=" O PHE B 233 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 272 through 277 removed outlier: 3.905A pdb=" N SER B 272 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE B 284 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N HIS B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS B 280 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TYR B 300 " --> pdb=" O HIS B 280 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE B 282 " --> pdb=" O TRP B 298 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TRP B 298 " --> pdb=" O PHE B 282 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N PHE B 284 " --> pdb=" O ASP B 296 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASP B 296 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 286 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B 297 " --> pdb=" O PHE B 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 322 through 326 Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 8 removed outlier: 7.033A pdb=" N THR E 13 " --> pdb=" O ILE F 30 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N LYS F 32 " --> pdb=" O THR E 13 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N PHE E 15 " --> pdb=" O LYS F 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 43 through 45 removed outlier: 3.664A pdb=" N LEU G 77 " --> pdb=" O ARG G 8 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR G 13 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N LYS H 32 " --> pdb=" O THR G 13 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N PHE G 15 " --> pdb=" O LYS H 32 " (cutoff:3.500A) removed outlier: 9.854A pdb=" N VAL H 60 " --> pdb=" O TYR H 18 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS H 20 " --> pdb=" O VAL H 60 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 44 through 45 removed outlier: 3.727A pdb=" N VAL I 75 " --> pdb=" O MET I 6 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU I 77 " --> pdb=" O ARG I 8 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 13 through 19 removed outlier: 8.887A pdb=" N VAL K 75 " --> pdb=" O PHE K 4 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N MET K 6 " --> pdb=" O VAL K 75 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU K 77 " --> pdb=" O MET K 6 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG K 8 " --> pdb=" O LEU K 77 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 28 through 32 Processing sheet with id=AB6, first strand: chain 'C' and resid 36 through 39 removed outlier: 3.648A pdb=" N VAL C 46 " --> pdb=" O TRP C 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 50 through 52 Processing sheet with id=AB8, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.974A pdb=" N GLU C 84 " --> pdb=" O TRP C 132 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ARG C 134 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLN C 131 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP C 122 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE C 118 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 145 through 146 removed outlier: 3.709A pdb=" N GLY C 162 " --> pdb=" O ASN C 192 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 149 through 153 Processing sheet with id=AC2, first strand: chain 'C' and resid 211 through 212 removed outlier: 6.873A pdb=" N THR C 211 " --> pdb=" O TRP C 255 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N GLU C 257 " --> pdb=" O THR C 211 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASP C 244 " --> pdb=" O GLY C 234 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 272 through 275 removed outlier: 4.222A pdb=" N SER C 272 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE C 284 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS C 280 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR C 300 " --> pdb=" O HIS C 280 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE C 282 " --> pdb=" O TRP C 298 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TRP C 298 " --> pdb=" O PHE C 282 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N PHE C 284 " --> pdb=" O ASP C 296 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASP C 296 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY C 286 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA C 297 " --> pdb=" O PHE C 310 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 322 through 326 Processing sheet with id=AC5, first strand: chain 'A' and resid 36 through 38 removed outlier: 3.503A pdb=" N VAL A 36 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 77 " --> pdb=" O ASN A 72 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AC7, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.872A pdb=" N GLU A 84 " --> pdb=" O TRP A 132 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ARG A 134 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN A 131 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP A 122 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE A 118 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AC9, first strand: chain 'A' and resid 145 through 146 removed outlier: 4.880A pdb=" N LYS A 156 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 198 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE A 158 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N HIS A 196 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE A 160 " --> pdb=" O HIS A 194 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N HIS A 194 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 162 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 149 through 153 removed outlier: 4.880A pdb=" N LYS A 156 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 198 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE A 158 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N HIS A 196 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE A 160 " --> pdb=" O HIS A 194 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N HIS A 194 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 162 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 211 through 212 removed outlier: 7.013A pdb=" N THR A 211 " --> pdb=" O TRP A 255 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N GLU A 257 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU A 254 " --> pdb=" O ASN A 249 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 261 through 262 removed outlier: 7.731A pdb=" N GLN A 261 " --> pdb=" O TRP A 307 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N GLN A 309 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU A 294 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE A 287 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASP A 296 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE A 282 " --> pdb=" O PRO A 275 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N PHE A 284 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU A 273 " --> pdb=" O PHE A 284 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 323 through 326 Processing sheet with id=AD5, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AD6, first strand: chain 'D' and resid 50 through 52 Processing sheet with id=AD7, first strand: chain 'D' and resid 84 through 85 removed outlier: 6.927A pdb=" N GLU D 84 " --> pdb=" O TRP D 132 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ARG D 134 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN D 131 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP D 122 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE D 118 " --> pdb=" O ILE D 135 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AD9, first strand: chain 'D' and resid 149 through 153 Processing sheet with id=AE1, first strand: chain 'D' and resid 175 through 177 Processing sheet with id=AE2, first strand: chain 'D' and resid 211 through 212 removed outlier: 7.282A pdb=" N THR D 211 " --> pdb=" O TRP D 255 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N GLU D 257 " --> pdb=" O THR D 211 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU D 254 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU D 245 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N MET D 242 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ARG D 236 " --> pdb=" O MET D 242 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP D 244 " --> pdb=" O GLY D 234 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 273 through 277 removed outlier: 6.173A pdb=" N LEU D 273 " --> pdb=" O PHE D 284 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N PHE D 284 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N PHE D 282 " --> pdb=" O PRO D 275 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY D 285 " --> pdb=" O ASP D 296 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ASP D 296 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE D 287 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU D 294 " --> pdb=" O PHE D 287 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 323 through 326 Processing sheet with id=AE5, first strand: chain 'D' and resid 337 through 338 594 hydrogen bonds defined for protein. 1560 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5645 1.34 - 1.46: 4495 1.46 - 1.58: 8241 1.58 - 1.70: 0 1.70 - 1.83: 159 Bond restraints: 18540 Sorted by residual: bond pdb=" C SER A 216 " pdb=" N PRO A 217 " ideal model delta sigma weight residual 1.333 1.372 -0.039 1.01e-02 9.80e+03 1.47e+01 bond pdb=" C HIS C 312 " pdb=" N PRO C 313 " ideal model delta sigma weight residual 1.331 1.360 -0.029 7.90e-03 1.60e+04 1.31e+01 bond pdb=" N LEU I 35 " pdb=" CA LEU I 35 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.32e-02 5.74e+03 9.66e+00 bond pdb=" N PRO K 38 " pdb=" CA PRO K 38 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.31e-02 5.83e+03 8.45e+00 bond pdb=" C SER A 181 " pdb=" N PHE A 182 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.30e-02 5.92e+03 5.27e+00 ... (remaining 18535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 24342 2.97 - 5.94: 664 5.94 - 8.91: 95 8.91 - 11.88: 35 11.88 - 14.85: 8 Bond angle restraints: 25144 Sorted by residual: angle pdb=" N PHE B 233 " pdb=" CA PHE B 233 " pdb=" C PHE B 233 " ideal model delta sigma weight residual 107.49 118.88 -11.39 1.74e+00 3.30e-01 4.29e+01 angle pdb=" N VAL B 276 " pdb=" CA VAL B 276 " pdb=" C VAL B 276 " ideal model delta sigma weight residual 111.45 105.54 5.91 9.30e-01 1.16e+00 4.04e+01 angle pdb=" C LYS E 46 " pdb=" N ASP E 47 " pdb=" CA ASP E 47 " ideal model delta sigma weight residual 122.82 131.45 -8.63 1.42e+00 4.96e-01 3.69e+01 angle pdb=" N GLY B 161 " pdb=" CA GLY B 161 " pdb=" C GLY B 161 " ideal model delta sigma weight residual 111.80 121.89 -10.09 1.82e+00 3.02e-01 3.07e+01 angle pdb=" C LYS B 154 " pdb=" CA LYS B 154 " pdb=" CB LYS B 154 " ideal model delta sigma weight residual 116.63 110.25 6.38 1.16e+00 7.43e-01 3.02e+01 ... (remaining 25139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 9906 17.75 - 35.50: 830 35.50 - 53.25: 120 53.25 - 71.00: 23 71.00 - 88.75: 8 Dihedral angle restraints: 10887 sinusoidal: 4391 harmonic: 6496 Sorted by residual: dihedral pdb=" CA LEU B 320 " pdb=" C LEU B 320 " pdb=" N TRP B 321 " pdb=" CA TRP B 321 " ideal model delta harmonic sigma weight residual -180.00 -151.22 -28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA HIS C 43 " pdb=" C HIS C 43 " pdb=" N MET C 44 " pdb=" CA MET C 44 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA PRO B 64 " pdb=" C PRO B 64 " pdb=" N ARG B 65 " pdb=" CA ARG B 65 " ideal model delta harmonic sigma weight residual -180.00 -153.67 -26.33 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 10884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2412 0.101 - 0.201: 228 0.201 - 0.302: 21 0.302 - 0.402: 4 0.402 - 0.503: 4 Chirality restraints: 2669 Sorted by residual: chirality pdb=" CB ILE C 158 " pdb=" CA ILE C 158 " pdb=" CG1 ILE C 158 " pdb=" CG2 ILE C 158 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.31e+00 chirality pdb=" CB ILE J 65 " pdb=" CA ILE J 65 " pdb=" CG1 ILE J 65 " pdb=" CG2 ILE J 65 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.07e+00 chirality pdb=" CB ILE H 30 " pdb=" CA ILE H 30 " pdb=" CG1 ILE H 30 " pdb=" CG2 ILE H 30 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.38e+00 ... (remaining 2666 not shown) Planarity restraints: 3243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 383 " 0.028 2.00e-02 2.50e+03 3.21e-02 2.58e+01 pdb=" CG TRP D 383 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP D 383 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP D 383 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP D 383 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP D 383 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 383 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 383 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 383 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 383 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 29 " -0.036 2.00e-02 2.50e+03 2.85e-02 1.42e+01 pdb=" CG PHE H 29 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE H 29 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE H 29 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE H 29 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 29 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE H 29 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE F 65 " -0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO F 66 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO F 66 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 66 " -0.046 5.00e-02 4.00e+02 ... (remaining 3240 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 5827 2.84 - 3.35: 15674 3.35 - 3.87: 33158 3.87 - 4.38: 37076 4.38 - 4.90: 60601 Nonbonded interactions: 152336 Sorted by model distance: nonbonded pdb=" O LYS H 80 " pdb=" OG1 THR H 84 " model vdw 2.321 3.040 nonbonded pdb=" O LYS J 80 " pdb=" OG1 THR J 84 " model vdw 2.329 3.040 nonbonded pdb=" O ARG G 9 " pdb=" OG1 THR G 12 " model vdw 2.353 3.040 nonbonded pdb=" OG1 THR C 288 " pdb=" OD1 ASP C 290 " model vdw 2.355 3.040 nonbonded pdb=" OG SER C 358 " pdb=" O GLN C 360 " model vdw 2.355 3.040 ... (remaining 152331 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 381 or resid 387 through 406)) selection = chain 'B' selection = (chain 'C' and (resid 25 through 381 or resid 387 through 406)) selection = (chain 'D' and (resid 25 through 381 or resid 387 through 406)) } ncs_group { reference = (chain 'E' and (resid 1 through 79 or resid 86 through 96)) selection = (chain 'G' and (resid 1 through 79 or resid 86 through 96)) selection = (chain 'I' and (resid 1 through 79 or resid 86 through 96)) selection = (chain 'K' and resid 1 through 96) } ncs_group { reference = (chain 'F' and (resid 17 through 47 or resid 58 through 112)) selection = (chain 'H' and (resid 17 through 47 or resid 55 through 56 or resid 60 through 1 \ 12)) selection = chain 'J' selection = (chain 'L' and (resid 17 through 47 or resid 58 through 112)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.730 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.630 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4096 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 : 0.006 0.059 18540 Z= 0.312 Angle : 1.197 14.848 25144 Z= 0.668 Chirality : 0.063 0.503 2669 Planarity : 0.008 0.084 3243 Dihedral : 13.349 88.748 6697 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.35 % Allowed : 1.72 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.82 (0.15), residues: 2214 helix: -3.16 (0.20), residues: 356 sheet: -0.91 (0.20), residues: 589 loop : -1.98 (0.15), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 397 TYR 0.025 0.002 TYR B 247 PHE 0.063 0.003 PHE H 29 TRP 0.080 0.002 TRP D 383 HIS 0.013 0.001 HIS F 68 Details of bonding type rmsd covalent geometry : bond 0.00578 (18540) covalent geometry : angle 1.19662 (25144) hydrogen bonds : bond 0.14847 ( 591) hydrogen bonds : angle 8.52711 ( 1560) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 444 time to evaluate : 0.762 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: 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: B 73 MET cc_start: 0.5883 (pmm) cc_final: 0.5513 (mtm) REVERT: B 121 LEU cc_start: 0.8424 (tp) cc_final: 0.7461 (tp) REVERT: B 146 ASP cc_start: 0.5883 (p0) cc_final: 0.5559 (p0) REVERT: B 147 LYS cc_start: 0.5493 (mttt) cc_final: 0.4357 (mttt) REVERT: B 292 GLN cc_start: 0.9464 (tp-100) cc_final: 0.9102 (tm-30) REVERT: B 373 ILE cc_start: 0.7510 (mm) cc_final: 0.7306 (mm) REVERT: E 86 GLU cc_start: 0.6458 (tm-30) cc_final: 0.5383 (mp0) REVERT: F 30 ILE cc_start: 0.6690 (tp) cc_final: 0.6241 (tp) REVERT: F 83 TYR cc_start: 0.7439 (m-80) cc_final: 0.7052 (m-80) REVERT: F 98 GLU cc_start: 0.8295 (pm20) cc_final: 0.8038 (tt0) REVERT: G 6 MET cc_start: 0.7852 (mmp) cc_final: 0.7628 (mmm) REVERT: G 82 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7052 (p0) REVERT: H 45 MET cc_start: 0.7604 (ttt) cc_final: 0.7316 (ppp) REVERT: H 58 ASN cc_start: 0.7215 (m110) cc_final: 0.6880 (m-40) REVERT: H 105 MET cc_start: 0.6465 (tpt) cc_final: 0.5669 (mmp) REVERT: J 45 MET cc_start: 0.1515 (mtt) cc_final: 0.0529 (ttt) REVERT: K 23 THR cc_start: 0.8956 (p) cc_final: 0.8590 (t) REVERT: K 25 PHE cc_start: 0.9685 (m-80) cc_final: 0.9314 (m-80) REVERT: K 91 GLU cc_start: 0.8674 (tp30) cc_final: 0.8070 (pp20) REVERT: L 29 PHE cc_start: 0.6810 (m-80) cc_final: 0.6078 (m-80) REVERT: L 105 MET cc_start: 0.4834 (ppp) cc_final: 0.4245 (ppp) REVERT: C 88 PRO cc_start: 0.7125 (Cg_endo) cc_final: 0.6629 (Cg_exo) REVERT: C 120 MET cc_start: 0.6089 (tmm) cc_final: 0.5684 (tmm) REVERT: C 369 LEU cc_start: 0.7568 (mt) cc_final: 0.7366 (mp) REVERT: C 386 LEU cc_start: 0.1724 (OUTLIER) cc_final: 0.0986 (pp) REVERT: A 61 PHE cc_start: 0.5688 (t80) cc_final: 0.5342 (t80) REVERT: A 203 PHE cc_start: 0.7579 (m-80) cc_final: 0.7317 (m-10) REVERT: A 284 PHE cc_start: 0.2844 (t80) cc_final: 0.2454 (t80) REVERT: D 65 ARG cc_start: 0.6930 (ptm160) cc_final: 0.6549 (ptm-80) REVERT: D 254 GLU cc_start: 0.8112 (tt0) cc_final: 0.7437 (tp30) REVERT: D 307 TRP cc_start: 0.5825 (m100) cc_final: 0.5253 (m100) REVERT: D 317 LYS cc_start: 0.4421 (pttm) cc_final: 0.3716 (mttt) REVERT: D 331 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6581 (mt-10) REVERT: D 338 CYS cc_start: 0.3184 (t) cc_final: 0.2820 (t) outliers start: 7 outliers final: 1 residues processed: 448 average time/residue: 0.1605 time to fit residues: 105.7799 Evaluate side-chains 304 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 301 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain A residue 91 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.0770 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 GLN ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS J 35 HIS J 68 HIS K 10 HIS C 43 HIS ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 GLN A 43 HIS ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN D 350 HIS D 360 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5239 r_free = 0.5239 target = 0.270068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5062 r_free = 0.5062 target = 0.247564 restraints weight = 26198.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5078 r_free = 0.5078 target = 0.250567 restraints weight = 37514.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.5089 r_free = 0.5089 target = 0.251996 restraints weight = 26214.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5093 r_free = 0.5093 target = 0.252699 restraints weight = 19084.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.5099 r_free = 0.5099 target = 0.253569 restraints weight = 16295.412| |-----------------------------------------------------------------------------| r_work (final): 0.5065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4306 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18540 Z= 0.159 Angle : 0.720 12.235 25144 Z= 0.366 Chirality : 0.046 0.187 2669 Planarity : 0.006 0.062 3243 Dihedral : 5.873 47.485 2444 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.93 % Allowed : 9.89 % Favored : 88.18 % 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: -2.31 (0.16), residues: 2214 helix: -2.03 (0.23), residues: 362 sheet: -0.81 (0.19), residues: 624 loop : -1.76 (0.15), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 43 TYR 0.022 0.002 TYR F 79 PHE 0.030 0.002 PHE F 77 TRP 0.034 0.002 TRP D 270 HIS 0.009 0.001 HIS L 68 Details of bonding type rmsd covalent geometry : bond 0.00347 (18540) covalent geometry : angle 0.71997 (25144) hydrogen bonds : bond 0.03946 ( 591) hydrogen bonds : angle 6.66087 ( 1560) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 321 time to evaluate : 0.708 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 2 ASP cc_start: 0.5337 (t0) cc_final: 0.4834 (p0) REVERT: I 1 MET cc_start: 0.3558 (tmm) cc_final: 0.3201 (tmm) REVERT: J 45 MET cc_start: 0.1197 (mtt) cc_final: 0.0641 (ttt) REVERT: C 386 LEU cc_start: 0.0011 (OUTLIER) cc_final: -0.0872 (pp) REVERT: A 112 ARG cc_start: 0.4653 (mtp180) cc_final: 0.4036 (ttp80) REVERT: A 119 TYR cc_start: 0.6684 (m-80) cc_final: 0.6200 (m-80) REVERT: A 120 MET cc_start: 0.6697 (tmm) cc_final: 0.6384 (tmm) REVERT: A 284 PHE cc_start: 0.5378 (t80) cc_final: 0.4663 (t80) outliers start: 38 outliers final: 20 residues processed: 338 average time/residue: 0.1621 time to fit residues: 80.6497 Evaluate side-chains 284 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 263 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain D residue 47 TRP Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 322 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 chunk 139 optimal weight: 0.3980 chunk 79 optimal weight: 50.0000 chunk 158 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 GLN ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 HIS ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5146 r_free = 0.5146 target = 0.258614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.232621 restraints weight = 24933.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.225995 restraints weight = 29323.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.224942 restraints weight = 25231.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.225341 restraints weight = 22551.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.224915 restraints weight = 17782.372| |-----------------------------------------------------------------------------| r_work (final): 0.4848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5004 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 18540 Z= 0.246 Angle : 0.754 12.357 25144 Z= 0.392 Chirality : 0.047 0.286 2669 Planarity : 0.005 0.058 3243 Dihedral : 5.976 47.189 2442 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.64 % Allowed : 13.24 % Favored : 84.13 % 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: -2.22 (0.16), residues: 2214 helix: -1.53 (0.24), residues: 371 sheet: -1.11 (0.19), residues: 619 loop : -1.63 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 9 TYR 0.036 0.003 TYR H 83 PHE 0.036 0.002 PHE E 79 TRP 0.033 0.003 TRP A 321 HIS 0.011 0.002 HIS L 27 Details of bonding type rmsd covalent geometry : bond 0.00539 (18540) covalent geometry : angle 0.75373 (25144) hydrogen bonds : bond 0.04397 ( 591) hydrogen bonds : angle 6.53027 ( 1560) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 297 time to evaluate : 0.771 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6798 (mm) REVERT: B 120 MET cc_start: 0.6127 (tpt) cc_final: 0.5816 (tpt) REVERT: J 45 MET cc_start: 0.1020 (mtt) cc_final: 0.0469 (ttt) REVERT: C 386 LEU cc_start: 0.0316 (OUTLIER) cc_final: -0.0841 (pp) REVERT: A 119 TYR cc_start: 0.7350 (m-80) cc_final: 0.7088 (m-80) REVERT: A 120 MET cc_start: 0.6913 (tmm) cc_final: 0.6577 (tmm) REVERT: D 120 MET cc_start: 0.5898 (OUTLIER) cc_final: 0.5281 (tpp) outliers start: 52 outliers final: 25 residues processed: 320 average time/residue: 0.1652 time to fit residues: 77.3742 Evaluate side-chains 285 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 257 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 307 TRP Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 169 optimal weight: 0.2980 chunk 141 optimal weight: 9.9990 chunk 200 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 165 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 79 optimal weight: 50.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** 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 = 0.5158 r_free = 0.5158 target = 0.259976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.228738 restraints weight = 24688.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.226108 restraints weight = 32778.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.226496 restraints weight = 25200.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.226723 restraints weight = 23170.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.227155 restraints weight = 19293.700| |-----------------------------------------------------------------------------| r_work (final): 0.4869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4968 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18540 Z= 0.176 Angle : 0.700 9.069 25144 Z= 0.355 Chirality : 0.045 0.269 2669 Planarity : 0.005 0.057 3243 Dihedral : 5.698 44.747 2442 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.69 % Allowed : 15.06 % Favored : 82.25 % 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: -2.10 (0.16), residues: 2214 helix: -1.40 (0.25), residues: 372 sheet: -1.21 (0.19), residues: 608 loop : -1.46 (0.16), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 238 TYR 0.026 0.002 TYR L 76 PHE 0.041 0.002 PHE I 4 TRP 0.025 0.002 TRP A 47 HIS 0.014 0.001 HIS D 271 Details of bonding type rmsd covalent geometry : bond 0.00386 (18540) covalent geometry : angle 0.69981 (25144) hydrogen bonds : bond 0.03868 ( 591) hydrogen bonds : angle 6.44499 ( 1560) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 279 time to evaluate : 0.752 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.4945 (mpp) cc_final: 0.2453 (mtm) REVERT: B 120 MET cc_start: 0.6272 (tpt) cc_final: 0.5906 (tpt) REVERT: I 6 MET cc_start: 0.3291 (pmm) cc_final: 0.0581 (pmm) REVERT: J 45 MET cc_start: 0.1172 (mtt) cc_final: 0.0516 (ttt) REVERT: C 386 LEU cc_start: 0.0364 (OUTLIER) cc_final: -0.0830 (pp) REVERT: A 119 TYR cc_start: 0.7446 (m-80) cc_final: 0.7081 (m-80) REVERT: A 120 MET cc_start: 0.6819 (tmm) cc_final: 0.6524 (tmm) REVERT: A 271 HIS cc_start: 0.6900 (p-80) cc_final: 0.6612 (p90) outliers start: 53 outliers final: 31 residues processed: 311 average time/residue: 0.1619 time to fit residues: 74.1176 Evaluate side-chains 285 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 TRP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 364 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 80 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 153 optimal weight: 0.8980 chunk 46 optimal weight: 0.0970 chunk 63 optimal weight: 50.0000 chunk 210 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 HIS ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5146 r_free = 0.5146 target = 0.258544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.229052 restraints weight = 24708.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.231332 restraints weight = 34650.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.230948 restraints weight = 21595.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.231105 restraints weight = 18709.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.231533 restraints weight = 16962.513| |-----------------------------------------------------------------------------| r_work (final): 0.4908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4823 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18540 Z= 0.177 Angle : 0.699 9.791 25144 Z= 0.353 Chirality : 0.045 0.257 2669 Planarity : 0.005 0.059 3243 Dihedral : 5.598 44.915 2442 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.14 % Allowed : 15.26 % Favored : 81.59 % 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: -2.04 (0.16), residues: 2214 helix: -1.30 (0.25), residues: 378 sheet: -1.28 (0.19), residues: 608 loop : -1.36 (0.16), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG I 29 TYR 0.033 0.002 TYR L 76 PHE 0.042 0.002 PHE E 79 TRP 0.027 0.002 TRP B 270 HIS 0.008 0.001 HIS D 271 Details of bonding type rmsd covalent geometry : bond 0.00397 (18540) covalent geometry : angle 0.69871 (25144) hydrogen bonds : bond 0.03829 ( 591) hydrogen bonds : angle 6.35960 ( 1560) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 267 time to evaluate : 0.737 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: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.6302 (tpt) cc_final: 0.5897 (tpp) REVERT: I 6 MET cc_start: 0.2659 (pmm) cc_final: 0.2374 (pmm) REVERT: J 45 MET cc_start: 0.1169 (mtt) cc_final: 0.0508 (ttt) REVERT: C 73 MET cc_start: 0.3698 (mpp) cc_final: 0.3452 (mpp) REVERT: C 342 LEU cc_start: 0.5678 (OUTLIER) cc_final: 0.4586 (tt) REVERT: C 386 LEU cc_start: 0.0267 (OUTLIER) cc_final: -0.0918 (pp) REVERT: A 119 TYR cc_start: 0.7515 (m-80) cc_final: 0.7097 (m-80) REVERT: A 120 MET cc_start: 0.6810 (tmm) cc_final: 0.6562 (tmm) REVERT: D 120 MET cc_start: 0.5813 (OUTLIER) cc_final: 0.5207 (tpp) outliers start: 62 outliers final: 40 residues processed: 306 average time/residue: 0.1593 time to fit residues: 72.1615 Evaluate side-chains 297 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 307 TRP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 364 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 65 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 150 optimal weight: 0.0270 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5132 r_free = 0.5132 target = 0.256903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.231592 restraints weight = 24159.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.222006 restraints weight = 26451.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.221925 restraints weight = 24961.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.222793 restraints weight = 22915.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.222931 restraints weight = 17093.745| |-----------------------------------------------------------------------------| r_work (final): 0.4840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5060 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18540 Z= 0.198 Angle : 0.714 10.710 25144 Z= 0.364 Chirality : 0.045 0.233 2669 Planarity : 0.005 0.055 3243 Dihedral : 5.606 43.782 2442 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 21.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.99 % Allowed : 17.14 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.17), residues: 2214 helix: -1.26 (0.25), residues: 383 sheet: -1.35 (0.19), residues: 621 loop : -1.29 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 29 TYR 0.033 0.002 TYR L 76 PHE 0.034 0.002 PHE I 4 TRP 0.030 0.002 TRP B 270 HIS 0.013 0.001 HIS A 271 Details of bonding type rmsd covalent geometry : bond 0.00437 (18540) covalent geometry : angle 0.71392 (25144) hydrogen bonds : bond 0.04014 ( 591) hydrogen bonds : angle 6.36732 ( 1560) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 271 time to evaluate : 0.751 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.6355 (tpt) cc_final: 0.5873 (tpp) REVERT: B 121 LEU cc_start: 0.5263 (mt) cc_final: 0.4836 (mt) REVERT: G 68 ARG cc_start: 0.5119 (tpt-90) cc_final: 0.4807 (tpt-90) REVERT: J 45 MET cc_start: 0.1369 (mtt) cc_final: 0.0584 (ttt) REVERT: C 35 HIS cc_start: 0.6761 (OUTLIER) cc_final: 0.6253 (p-80) REVERT: C 342 LEU cc_start: 0.5824 (OUTLIER) cc_final: 0.5617 (tp) REVERT: C 386 LEU cc_start: 0.0280 (OUTLIER) cc_final: -0.0900 (pp) REVERT: A 119 TYR cc_start: 0.7524 (m-80) cc_final: 0.7192 (m-80) REVERT: A 120 MET cc_start: 0.6807 (tmm) cc_final: 0.6579 (tmm) REVERT: A 271 HIS cc_start: 0.6843 (p90) cc_final: 0.6548 (p90) REVERT: D 78 TRP cc_start: 0.3922 (m100) cc_final: 0.2971 (m100) REVERT: D 120 MET cc_start: 0.5925 (OUTLIER) cc_final: 0.5297 (tpp) outliers start: 59 outliers final: 41 residues processed: 304 average time/residue: 0.1652 time to fit residues: 73.5941 Evaluate side-chains 293 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 248 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 307 TRP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain K residue 8 ARG Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 364 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 49 optimal weight: 7.9990 chunk 210 optimal weight: 0.5980 chunk 169 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 180 optimal weight: 30.0000 chunk 212 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 81 optimal weight: 40.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5132 r_free = 0.5132 target = 0.257153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.230752 restraints weight = 24631.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.225871 restraints weight = 30352.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.224651 restraints weight = 26373.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.225764 restraints weight = 24288.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.225578 restraints weight = 18609.708| |-----------------------------------------------------------------------------| r_work (final): 0.4854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5011 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 18540 Z= 0.189 Angle : 0.722 10.626 25144 Z= 0.366 Chirality : 0.045 0.229 2669 Planarity : 0.005 0.055 3243 Dihedral : 5.587 42.302 2442 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.09 % Allowed : 17.60 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.17), residues: 2214 helix: -1.16 (0.25), residues: 383 sheet: -1.40 (0.20), residues: 593 loop : -1.28 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 29 TYR 0.035 0.002 TYR L 76 PHE 0.035 0.002 PHE F 77 TRP 0.028 0.002 TRP D 270 HIS 0.011 0.001 HIS A 271 Details of bonding type rmsd covalent geometry : bond 0.00420 (18540) covalent geometry : angle 0.72230 (25144) hydrogen bonds : bond 0.03839 ( 591) hydrogen bonds : angle 6.30132 ( 1560) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 255 time to evaluate : 0.657 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.6341 (tpt) cc_final: 0.5873 (tpp) REVERT: B 121 LEU cc_start: 0.5271 (OUTLIER) cc_final: 0.4856 (mt) REVERT: B 320 LEU cc_start: 0.7014 (pt) cc_final: 0.6633 (mt) REVERT: H 18 TYR cc_start: 0.3047 (m-80) cc_final: 0.2845 (m-80) REVERT: J 17 MET cc_start: 0.3065 (tpp) cc_final: 0.2374 (ptt) REVERT: J 45 MET cc_start: 0.1288 (mtt) cc_final: 0.0540 (ttt) REVERT: C 35 HIS cc_start: 0.6789 (OUTLIER) cc_final: 0.6333 (p-80) REVERT: C 73 MET cc_start: 0.3764 (mpp) cc_final: 0.3380 (mpp) REVERT: C 386 LEU cc_start: 0.0442 (OUTLIER) cc_final: -0.0784 (pp) REVERT: A 119 TYR cc_start: 0.7502 (m-80) cc_final: 0.7275 (m-80) REVERT: A 120 MET cc_start: 0.6840 (tmm) cc_final: 0.6626 (tmm) REVERT: A 271 HIS cc_start: 0.6961 (p90) cc_final: 0.6588 (p90) REVERT: A 320 LEU cc_start: 0.8457 (pt) cc_final: 0.8243 (pp) REVERT: D 31 GLU cc_start: 0.5364 (OUTLIER) cc_final: 0.4933 (pm20) REVERT: D 120 MET cc_start: 0.5945 (OUTLIER) cc_final: 0.5332 (tpp) outliers start: 61 outliers final: 44 residues processed: 296 average time/residue: 0.1580 time to fit residues: 69.2733 Evaluate side-chains 295 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 246 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 307 TRP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain K residue 8 ARG Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 120 MET Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 364 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 33 optimal weight: 0.0470 chunk 81 optimal weight: 30.0000 chunk 23 optimal weight: 8.9990 chunk 100 optimal weight: 30.0000 chunk 74 optimal weight: 50.0000 chunk 82 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 93 optimal weight: 50.0000 chunk 118 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 overall best weight: 2.4682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 HIS ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5122 r_free = 0.5122 target = 0.255456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.229767 restraints weight = 24443.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.221833 restraints weight = 28117.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.220877 restraints weight = 25452.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.221365 restraints weight = 23123.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.221339 restraints weight = 19984.852| |-----------------------------------------------------------------------------| r_work (final): 0.4814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5121 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 18540 Z= 0.215 Angle : 0.752 10.797 25144 Z= 0.383 Chirality : 0.046 0.275 2669 Planarity : 0.005 0.056 3243 Dihedral : 5.720 42.063 2442 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.94 % Allowed : 18.46 % Favored : 78.60 % 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: -2.03 (0.17), residues: 2214 helix: -1.07 (0.25), residues: 384 sheet: -1.36 (0.21), residues: 564 loop : -1.40 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 238 TYR 0.038 0.002 TYR L 76 PHE 0.026 0.002 PHE E 79 TRP 0.035 0.002 TRP D 270 HIS 0.012 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00475 (18540) covalent geometry : angle 0.75233 (25144) hydrogen bonds : bond 0.04044 ( 591) hydrogen bonds : angle 6.40598 ( 1560) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 259 time to evaluate : 0.686 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: 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: B 121 LEU cc_start: 0.5173 (OUTLIER) cc_final: 0.4884 (mt) REVERT: B 320 LEU cc_start: 0.7033 (pt) cc_final: 0.6659 (mt) REVERT: H 76 TYR cc_start: 0.6250 (OUTLIER) cc_final: 0.5972 (t80) REVERT: K 1 MET cc_start: 0.3028 (tpt) cc_final: 0.2745 (tpt) REVERT: C 35 HIS cc_start: 0.6807 (OUTLIER) cc_final: 0.6455 (p-80) REVERT: C 386 LEU cc_start: 0.0589 (OUTLIER) cc_final: -0.0670 (pp) REVERT: A 242 MET cc_start: 0.1285 (ptt) cc_final: 0.1082 (ptt) REVERT: A 271 HIS cc_start: 0.7163 (p90) cc_final: 0.6783 (p90) REVERT: A 304 LYS cc_start: 0.5895 (mttp) cc_final: 0.5510 (mttp) REVERT: A 320 LEU cc_start: 0.8588 (pt) cc_final: 0.8381 (pp) REVERT: D 189 ARG cc_start: 0.6122 (mtm180) cc_final: 0.5226 (mtm180) outliers start: 58 outliers final: 44 residues processed: 295 average time/residue: 0.1620 time to fit residues: 70.5320 Evaluate side-chains 296 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 248 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 307 TRP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain K residue 8 ARG Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 364 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 113 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 168 optimal weight: 0.6980 chunk 172 optimal weight: 0.5980 chunk 218 optimal weight: 7.9990 chunk 79 optimal weight: 50.0000 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** 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 = 0.5132 r_free = 0.5132 target = 0.257028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.231515 restraints weight = 24482.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.222391 restraints weight = 27399.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.220104 restraints weight = 27745.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.220787 restraints weight = 25665.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.220821 restraints weight = 19772.241| |-----------------------------------------------------------------------------| r_work (final): 0.4813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5122 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18540 Z= 0.173 Angle : 0.743 11.990 25144 Z= 0.372 Chirality : 0.045 0.294 2669 Planarity : 0.005 0.056 3243 Dihedral : 5.567 40.480 2442 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.54 % Allowed : 19.42 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.17), residues: 2214 helix: -1.02 (0.26), residues: 384 sheet: -1.24 (0.21), residues: 567 loop : -1.35 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 29 TYR 0.036 0.002 TYR L 76 PHE 0.034 0.002 PHE F 77 TRP 0.031 0.002 TRP D 270 HIS 0.009 0.001 HIS A 271 Details of bonding type rmsd covalent geometry : bond 0.00388 (18540) covalent geometry : angle 0.74288 (25144) hydrogen bonds : bond 0.03739 ( 591) hydrogen bonds : angle 6.28146 ( 1560) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 251 time to evaluate : 0.727 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: 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: B 320 LEU cc_start: 0.7103 (pt) cc_final: 0.6691 (mt) REVERT: F 43 LYS cc_start: 0.7137 (mtmm) cc_final: 0.6828 (mppt) REVERT: H 76 TYR cc_start: 0.6227 (OUTLIER) cc_final: 0.5959 (t80) REVERT: H 105 MET cc_start: 0.3685 (mmp) cc_final: 0.3454 (tpt) REVERT: C 121 LEU cc_start: 0.6527 (mt) cc_final: 0.6211 (tt) REVERT: C 386 LEU cc_start: 0.0423 (OUTLIER) cc_final: -0.0750 (pp) REVERT: A 271 HIS cc_start: 0.7031 (p90) cc_final: 0.6654 (p90) REVERT: D 31 GLU cc_start: 0.5490 (OUTLIER) cc_final: 0.5108 (pm20) REVERT: D 189 ARG cc_start: 0.6057 (mtm180) cc_final: 0.5115 (mtm180) outliers start: 50 outliers final: 44 residues processed: 284 average time/residue: 0.1645 time to fit residues: 68.7303 Evaluate side-chains 289 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 242 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 307 TRP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain K residue 8 ARG Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 68 optimal weight: 7.9990 chunk 218 optimal weight: 30.0000 chunk 213 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 90 optimal weight: 40.0000 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 125 optimal weight: 0.0570 overall best weight: 3.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS ** L 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 ASN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5090 r_free = 0.5090 target = 0.251762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.227082 restraints weight = 24039.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.219185 restraints weight = 29119.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.218809 restraints weight = 25157.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.218840 restraints weight = 23853.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.219025 restraints weight = 19697.617| |-----------------------------------------------------------------------------| r_work (final): 0.4792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5212 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 18540 Z= 0.305 Angle : 0.876 13.056 25144 Z= 0.448 Chirality : 0.050 0.261 2669 Planarity : 0.006 0.070 3243 Dihedral : 6.186 44.727 2442 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 28.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 2.74 % Allowed : 19.47 % Favored : 77.79 % 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: -2.11 (0.17), residues: 2214 helix: -1.11 (0.25), residues: 386 sheet: -1.40 (0.21), residues: 557 loop : -1.47 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 29 TYR 0.037 0.003 TYR L 76 PHE 0.041 0.003 PHE F 77 TRP 0.056 0.003 TRP D 270 HIS 0.014 0.002 HIS A 271 Details of bonding type rmsd covalent geometry : bond 0.00675 (18540) covalent geometry : angle 0.87564 (25144) hydrogen bonds : bond 0.05038 ( 591) hydrogen bonds : angle 6.83220 ( 1560) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 256 time to evaluate : 0.862 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 320 LEU cc_start: 0.7148 (pt) cc_final: 0.6806 (mt) REVERT: J 17 MET cc_start: 0.2987 (tpp) cc_final: 0.2311 (ptt) REVERT: J 45 MET cc_start: 0.1267 (mtt) cc_final: 0.0571 (ttt) REVERT: L 45 MET cc_start: 0.2633 (ppp) cc_final: 0.0471 (pmm) REVERT: A 72 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7673 (m110) REVERT: A 282 PHE cc_start: 0.7484 (t80) cc_final: 0.6946 (t80) REVERT: A 304 LYS cc_start: 0.5928 (mttp) cc_final: 0.5671 (mttp) REVERT: D 189 ARG cc_start: 0.6204 (mtm180) cc_final: 0.5073 (mtm180) outliers start: 54 outliers final: 41 residues processed: 294 average time/residue: 0.1652 time to fit residues: 71.5760 Evaluate side-chains 281 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 239 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 307 TRP Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain K residue 8 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 116 optimal weight: 30.0000 chunk 95 optimal weight: 8.9990 chunk 157 optimal weight: 0.1980 chunk 82 optimal weight: 50.0000 chunk 78 optimal weight: 30.0000 chunk 14 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 210 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS ** L 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5088 r_free = 0.5088 target = 0.251868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.227784 restraints weight = 24690.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.219592 restraints weight = 29598.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.218640 restraints weight = 28675.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.219825 restraints weight = 23857.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.219213 restraints weight = 19807.910| |-----------------------------------------------------------------------------| r_work (final): 0.4791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5208 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.228 18540 Z= 0.368 Angle : 1.020 59.143 25144 Z= 0.559 Chirality : 0.054 1.003 2669 Planarity : 0.006 0.065 3243 Dihedral : 6.228 44.872 2442 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 32.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.64 % Allowed : 20.13 % Favored : 77.23 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.13 (0.17), residues: 2214 helix: -1.12 (0.25), residues: 386 sheet: -1.42 (0.21), residues: 557 loop : -1.48 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 8 TYR 0.068 0.003 TYR H 76 PHE 0.035 0.003 PHE F 77 TRP 0.047 0.003 TRP D 270 HIS 0.021 0.002 HIS I 10 Details of bonding type rmsd covalent geometry : bond 0.00789 (18540) covalent geometry : angle 1.01951 (25144) hydrogen bonds : bond 0.05206 ( 591) hydrogen bonds : angle 6.84991 ( 1560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3681.04 seconds wall clock time: 65 minutes 5.78 seconds (3905.78 seconds total)