Starting phenix.real_space_refine on Mon Jun 16 02:42:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sh2_40477/06_2025/8sh2_40477.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sh2_40477/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sh2_40477/06_2025/8sh2_40477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sh2_40477/06_2025/8sh2_40477.map" model { file = "/net/cci-nas-00/data/ceres_data/8sh2_40477/06_2025/8sh2_40477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sh2_40477/06_2025/8sh2_40477.cif" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.00, per 1000 atoms: 0.61 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: 4.42 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.36 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: 6.60 Time building geometry restraints manager: 5.20 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.800 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 42.770 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.250 ------------------------------------------------------------------------------- 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 : 14.58 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.080 0.002 TRP D 383 HIS 0.013 0.001 HIS F 68 PHE 0.063 0.003 PHE H 29 TYR 0.025 0.002 TYR B 247 ARG 0.011 0.001 ARG C 397 Details of bonding type rmsd hydrogen bonds : bond 0.14847 ( 591) hydrogen bonds : angle 8.52711 ( 1560) covalent geometry : bond 0.00578 (18540) covalent geometry : angle 1.19662 (25144) *********************** 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 : 1.960 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 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: 0.5560 (p0) REVERT: B 147 LYS cc_start: 0.5493 (mttt) cc_final: 0.4358 (mttt) REVERT: B 292 GLN cc_start: 0.9464 (tp-100) cc_final: 0.9146 (tm-30) REVERT: B 373 ILE cc_start: 0.7510 (mm) cc_final: 0.7307 (mm) REVERT: E 86 GLU cc_start: 0.6458 (tm-30) cc_final: 0.5382 (mp0) REVERT: F 30 ILE cc_start: 0.6690 (tp) cc_final: 0.6242 (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: 0.8037 (tt0) REVERT: G 6 MET cc_start: 0.7852 (mmp) cc_final: 0.7629 (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: 0.7283 (ppp) REVERT: H 58 ASN cc_start: 0.7215 (m110) cc_final: 0.6878 (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: 0.8589 (t) REVERT: K 25 PHE cc_start: 0.9685 (m-80) cc_final: 0.9305 (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: 0.6094 (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: 0.5683 (tmm) REVERT: C 369 LEU cc_start: 0.7568 (mt) cc_final: 0.7367 (mp) REVERT: C 386 LEU cc_start: 0.1724 (OUTLIER) cc_final: 0.0985 (pp) REVERT: A 61 PHE cc_start: 0.5688 (t80) cc_final: 0.5344 (t80) REVERT: A 203 PHE cc_start: 0.7579 (m-80) cc_final: 0.7318 (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: 0.3717 (mttt) REVERT: D 331 GLU cc_start: 0.6892 (mt-10) cc_final: 0.5974 (mt-10) REVERT: D 338 CYS cc_start: 0.3184 (t) cc_final: 0.2819 (t) outliers start: 7 outliers final: 1 residues processed: 448 average time/residue: 0.3329 time to fit residues: 217.8132 Evaluate side-chains 302 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 299 time to evaluate : 3.804 ------------------------------------------------------------------------------- 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 185 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 30.0000 chunk 172 optimal weight: 3.9990 chunk 66 optimal weight: 40.0000 chunk 104 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 199 optimal weight: 0.4980 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 HIS ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS J 68 HIS K 10 HIS K 49 GLN L 58 ASN ** L 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 HIS ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 GLN C 392 HIS A 43 HIS ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** 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 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 HIS D 360 GLN D 396 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5183 r_free = 0.5183 target = 0.263325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.234468 restraints weight = 25920.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.234564 restraints weight = 34414.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.237488 restraints weight = 29915.446| |-----------------------------------------------------------------------------| r_work (final): 0.4910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4793 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 18540 Z= 0.288 Angle : 0.818 11.404 25144 Z= 0.429 Chirality : 0.050 0.237 2669 Planarity : 0.006 0.067 3243 Dihedral : 6.335 50.582 2444 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.43 % Allowed : 10.65 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.15), residues: 2214 helix: -2.05 (0.23), residues: 360 sheet: -1.14 (0.19), residues: 632 loop : -1.84 (0.15), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 321 HIS 0.011 0.002 HIS D 109 PHE 0.033 0.003 PHE F 77 TYR 0.028 0.003 TYR D 163 ARG 0.028 0.001 ARG F 63 Details of bonding type rmsd hydrogen bonds : bond 0.04926 ( 591) hydrogen bonds : angle 6.94066 ( 1560) covalent geometry : bond 0.00637 (18540) covalent geometry : angle 0.81790 (25144) *********************** 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 372 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 324 time to evaluate : 2.178 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: G 48 ASP cc_start: 0.4344 (m-30) cc_final: 0.4069 (m-30) REVERT: H 75 MET cc_start: 0.3334 (tmm) cc_final: 0.2902 (ppp) REVERT: J 45 MET cc_start: 0.1251 (mtt) cc_final: 0.0677 (ttt) REVERT: C 44 MET cc_start: 0.0351 (mtt) cc_final: 0.0110 (mtt) REVERT: C 386 LEU cc_start: 0.0059 (OUTLIER) cc_final: -0.1029 (pp) REVERT: A 119 TYR cc_start: 0.7273 (m-80) cc_final: 0.6971 (m-80) REVERT: A 120 MET cc_start: 0.6805 (tmm) cc_final: 0.6454 (tmm) REVERT: D 271 HIS cc_start: 0.8076 (p-80) cc_final: 0.7856 (p90) outliers start: 48 outliers final: 28 residues processed: 349 average time/residue: 0.3596 time to fit residues: 185.5594 Evaluate side-chains 298 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 269 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 77 LEU 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 31 GLU Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 193 ASP 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 308 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 396 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 205 optimal weight: 0.0970 chunk 159 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN L 58 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** 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 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN D 350 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5137 r_free = 0.5137 target = 0.257232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.234457 restraints weight = 24776.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.228944 restraints weight = 28545.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.228547 restraints weight = 24011.540| |-----------------------------------------------------------------------------| r_work (final): 0.4950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4899 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18540 Z= 0.226 Angle : 0.741 10.053 25144 Z= 0.384 Chirality : 0.047 0.233 2669 Planarity : 0.005 0.070 3243 Dihedral : 6.045 48.954 2442 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.04 % Allowed : 14.05 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.16), residues: 2214 helix: -1.65 (0.24), residues: 377 sheet: -1.38 (0.19), residues: 620 loop : -1.63 (0.16), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 270 HIS 0.010 0.001 HIS L 27 PHE 0.036 0.002 PHE B 233 TYR 0.033 0.003 TYR H 83 ARG 0.007 0.001 ARG K 8 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 591) hydrogen bonds : angle 6.66869 ( 1560) covalent geometry : bond 0.00496 (18540) covalent geometry : angle 0.74149 (25144) *********************** 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 355 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 295 time to evaluate : 2.104 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 120 MET cc_start: 0.6220 (tpt) cc_final: 0.5761 (tpp) REVERT: F 83 TYR cc_start: 0.5937 (OUTLIER) cc_final: 0.5683 (m-80) REVERT: J 45 MET cc_start: 0.1002 (mtt) cc_final: 0.0543 (ttt) REVERT: C 35 HIS cc_start: 0.6441 (OUTLIER) cc_final: 0.5794 (p-80) REVERT: C 44 MET cc_start: 0.0788 (mtt) cc_final: 0.0555 (mtt) REVERT: C 386 LEU cc_start: 0.0490 (OUTLIER) cc_final: -0.0855 (pp) REVERT: A 119 TYR cc_start: 0.7577 (m-80) cc_final: 0.7188 (m-80) REVERT: A 120 MET cc_start: 0.6849 (tmm) cc_final: 0.6568 (tmm) REVERT: D 120 MET cc_start: 0.5916 (OUTLIER) cc_final: 0.5231 (tpp) outliers start: 60 outliers final: 33 residues processed: 327 average time/residue: 0.3369 time to fit residues: 161.5381 Evaluate side-chains 293 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 256 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 252 THR 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 B residue 378 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 342 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 145 LYS 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 120 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 7.9990 chunk 213 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 42 optimal weight: 40.0000 chunk 183 optimal weight: 0.6980 chunk 206 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 68 HIS ** 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 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 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.259016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.224835 restraints weight = 24677.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.226802 restraints weight = 33433.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.226484 restraints weight = 24421.846| |-----------------------------------------------------------------------------| r_work (final): 0.4871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4951 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18540 Z= 0.164 Angle : 0.695 9.108 25144 Z= 0.350 Chirality : 0.045 0.270 2669 Planarity : 0.005 0.059 3243 Dihedral : 5.672 47.311 2442 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.09 % Allowed : 15.11 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.16), residues: 2214 helix: -1.50 (0.24), residues: 376 sheet: -1.40 (0.19), residues: 603 loop : -1.50 (0.16), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 383 HIS 0.013 0.001 HIS D 271 PHE 0.042 0.002 PHE I 4 TYR 0.027 0.002 TYR L 76 ARG 0.006 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 591) hydrogen bonds : angle 6.42006 ( 1560) covalent geometry : bond 0.00363 (18540) covalent geometry : angle 0.69452 (25144) *********************** 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 338 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 277 time to evaluate : 2.073 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: B 120 MET cc_start: 0.6242 (tpt) cc_final: 0.5672 (tpp) REVERT: B 121 LEU cc_start: 0.5288 (tp) cc_final: 0.5007 (mt) REVERT: H 76 TYR cc_start: 0.6177 (OUTLIER) cc_final: 0.5773 (t80) REVERT: J 45 MET cc_start: 0.1347 (mtt) cc_final: 0.0701 (ttt) REVERT: C 35 HIS cc_start: 0.6375 (OUTLIER) cc_final: 0.5790 (p-80) REVERT: C 386 LEU cc_start: 0.0344 (OUTLIER) cc_final: -0.0501 (pp) REVERT: A 119 TYR cc_start: 0.7424 (m-80) cc_final: 0.7146 (m-80) REVERT: A 120 MET cc_start: 0.6841 (tmm) cc_final: 0.6516 (tmm) REVERT: A 308 ILE cc_start: 0.6440 (OUTLIER) cc_final: 0.5909 (mt) REVERT: D 31 GLU cc_start: 0.5695 (OUTLIER) cc_final: 0.5206 (pm20) REVERT: D 120 MET cc_start: 0.5907 (OUTLIER) cc_final: 0.5289 (tpp) outliers start: 61 outliers final: 32 residues processed: 306 average time/residue: 0.4125 time to fit residues: 190.9685 Evaluate side-chains 292 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 254 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 307 TRP Chi-restraints excluded: chain B residue 379 LEU 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 41 THR Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain I residue 7 ILE 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 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 91 MET Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 320 LEU 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 120 MET Chi-restraints excluded: chain D residue 184 ASN 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 65 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 168 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 43 optimal weight: 0.0010 chunk 172 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 139 optimal weight: 0.4980 chunk 198 optimal weight: 2.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN ** H 58 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 187 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 221 HIS ** 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 = 0.5173 r_free = 0.5173 target = 0.261420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.234416 restraints weight = 24854.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.233892 restraints weight = 32290.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.233368 restraints weight = 19784.644| |-----------------------------------------------------------------------------| r_work (final): 0.4997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4754 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18540 Z= 0.126 Angle : 0.670 10.123 25144 Z= 0.334 Chirality : 0.044 0.247 2669 Planarity : 0.004 0.057 3243 Dihedral : 5.430 45.117 2442 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.84 % Allowed : 15.72 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.16), residues: 2214 helix: -1.38 (0.25), residues: 377 sheet: -1.19 (0.19), residues: 619 loop : -1.41 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 270 HIS 0.008 0.001 HIS A 196 PHE 0.040 0.002 PHE I 4 TYR 0.033 0.002 TYR L 76 ARG 0.012 0.000 ARG I 29 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 591) hydrogen bonds : angle 6.20452 ( 1560) covalent geometry : bond 0.00282 (18540) covalent geometry : angle 0.66986 (25144) *********************** 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 328 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 272 time to evaluate : 2.846 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: 0.6249 (tpt) cc_final: 0.5753 (tpp) REVERT: B 271 HIS cc_start: 0.5700 (OUTLIER) cc_final: 0.4399 (p-80) REVERT: J 45 MET cc_start: 0.1181 (mtt) cc_final: 0.0547 (ttt) REVERT: C 386 LEU cc_start: 0.0227 (OUTLIER) cc_final: -0.0491 (pp) REVERT: A 104 TYR cc_start: 0.7156 (m-80) cc_final: 0.6857 (m-80) REVERT: A 119 TYR cc_start: 0.7398 (m-80) cc_final: 0.7141 (m-80) REVERT: A 120 MET cc_start: 0.6718 (tmm) cc_final: 0.6490 (tmm) REVERT: D 120 MET cc_start: 0.5857 (OUTLIER) cc_final: 0.5222 (tpp) outliers start: 56 outliers final: 38 residues processed: 303 average time/residue: 0.3878 time to fit residues: 172.8317 Evaluate side-chains 296 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 255 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 379 LEU 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 41 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 65 ILE 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 145 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 274 THR 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 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 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 37 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 217 optimal weight: 8.9990 chunk 179 optimal weight: 50.0000 chunk 219 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 184 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 89 optimal weight: 50.0000 chunk 81 optimal weight: 50.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 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 194 HIS ** 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 246 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.247078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.222754 restraints weight = 24296.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.214455 restraints weight = 28660.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.213817 restraints weight = 28764.667| |-----------------------------------------------------------------------------| r_work (final): 0.4750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5345 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.157 18540 Z= 0.481 Angle : 1.020 16.523 25144 Z= 0.541 Chirality : 0.056 0.354 2669 Planarity : 0.007 0.094 3243 Dihedral : 6.973 52.816 2442 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 34.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.54 % Favored : 92.28 % Rotamer: Outliers : 4.11 % Allowed : 16.89 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.16), residues: 2214 helix: -1.36 (0.24), residues: 380 sheet: -1.86 (0.20), residues: 583 loop : -1.70 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.005 TRP C 307 HIS 0.024 0.003 HIS A 109 PHE 0.049 0.004 PHE A 282 TYR 0.048 0.004 TYR A 163 ARG 0.018 0.001 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.06988 ( 591) hydrogen bonds : angle 7.44371 ( 1560) covalent geometry : bond 0.01056 (18540) covalent geometry : angle 1.01963 (25144) *********************** 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 345 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 264 time to evaluate : 2.089 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: B 320 LEU cc_start: 0.7239 (pt) cc_final: 0.6832 (mt) REVERT: H 76 TYR cc_start: 0.6429 (OUTLIER) cc_final: 0.5978 (t80) REVERT: J 45 MET cc_start: 0.1228 (mtt) cc_final: 0.0633 (ttt) REVERT: L 45 MET cc_start: 0.2807 (ppp) cc_final: 0.0700 (pmm) REVERT: C 35 HIS cc_start: 0.7106 (OUTLIER) cc_final: 0.6694 (p-80) REVERT: C 342 LEU cc_start: 0.6289 (OUTLIER) cc_final: 0.6040 (tp) REVERT: C 386 LEU cc_start: 0.1182 (OUTLIER) cc_final: 0.0802 (mt) REVERT: A 72 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7777 (m110) REVERT: A 282 PHE cc_start: 0.7421 (t80) cc_final: 0.6760 (t80) REVERT: A 304 LYS cc_start: 0.6439 (mttp) cc_final: 0.5941 (mttp) REVERT: A 321 TRP cc_start: 0.8001 (OUTLIER) cc_final: 0.7497 (m-10) REVERT: D 120 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.5471 (tpp) REVERT: D 189 ARG cc_start: 0.6337 (mtm180) cc_final: 0.5142 (mtm180) REVERT: D 322 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.7230 (p-80) REVERT: D 360 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6542 (tm-30) outliers start: 81 outliers final: 54 residues processed: 315 average time/residue: 0.3460 time to fit residues: 158.6387 Evaluate side-chains 304 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 241 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 112 CYS 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 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 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 145 LYS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 172 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 A residue 354 ILE 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 97 VAL 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 283 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 360 GLN 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 65 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 197 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 395 ASN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS ** A 114 ASN ** 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 184 ASN ** 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 = 0.5133 r_free = 0.5133 target = 0.256841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4933 r_free = 0.4933 target = 0.230982 restraints weight = 24658.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.222296 restraints weight = 28870.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.221300 restraints weight = 30834.274| |-----------------------------------------------------------------------------| r_work (final): 0.4816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5132 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18540 Z= 0.157 Angle : 0.739 11.042 25144 Z= 0.372 Chirality : 0.045 0.216 2669 Planarity : 0.005 0.060 3243 Dihedral : 5.825 45.760 2442 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.84 % Allowed : 19.42 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.17), residues: 2214 helix: -1.20 (0.25), residues: 373 sheet: -1.63 (0.20), residues: 600 loop : -1.52 (0.16), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 383 HIS 0.008 0.001 HIS A 196 PHE 0.032 0.002 PHE A 61 TYR 0.034 0.002 TYR L 76 ARG 0.010 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 591) hydrogen bonds : angle 6.55400 ( 1560) covalent geometry : bond 0.00344 (18540) covalent geometry : angle 0.73934 (25144) *********************** 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 315 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 259 time to evaluate : 2.170 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 320 LEU cc_start: 0.7260 (pt) cc_final: 0.6817 (mt) REVERT: G 68 ARG cc_start: 0.5027 (tpt-90) cc_final: 0.4808 (tpt-90) REVERT: H 76 TYR cc_start: 0.6506 (OUTLIER) cc_final: 0.6124 (t80) REVERT: H 105 MET cc_start: 0.5806 (tpt) cc_final: 0.5448 (tpt) REVERT: J 17 MET cc_start: 0.3545 (tpp) cc_final: 0.2830 (tmm) REVERT: J 45 MET cc_start: 0.1204 (mtt) cc_final: 0.0519 (ttt) REVERT: J 79 TYR cc_start: 0.5094 (t80) cc_final: 0.4847 (t80) REVERT: K 1 MET cc_start: 0.2890 (tpt) cc_final: 0.2425 (tpt) REVERT: C 35 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.6507 (p-80) REVERT: A 73 MET cc_start: 0.4586 (ptp) cc_final: 0.4371 (mtm) REVERT: A 78 TRP cc_start: 0.3967 (m100) cc_final: 0.3409 (m100) REVERT: A 304 LYS cc_start: 0.6164 (mttp) cc_final: 0.5835 (mttp) REVERT: A 308 ILE cc_start: 0.6596 (OUTLIER) cc_final: 0.6106 (mt) REVERT: A 320 LEU cc_start: 0.8459 (pt) cc_final: 0.8257 (pp) REVERT: D 31 GLU cc_start: 0.5713 (OUTLIER) cc_final: 0.5187 (pm20) REVERT: D 189 ARG cc_start: 0.5937 (mtm180) cc_final: 0.4995 (mtm180) outliers start: 56 outliers final: 39 residues processed: 291 average time/residue: 0.3262 time to fit residues: 140.6985 Evaluate side-chains 286 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 243 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 112 CYS 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 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 145 LYS Chi-restraints excluded: chain A residue 172 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 308 ILE 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 184 ASN Chi-restraints excluded: chain D residue 252 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 88 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 98 optimal weight: 50.0000 chunk 97 optimal weight: 0.2980 chunk 183 optimal weight: 0.3980 chunk 1 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** 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 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5150 r_free = 0.5150 target = 0.258704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.233614 restraints weight = 24595.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.223942 restraints weight = 27601.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.222343 restraints weight = 30233.504| |-----------------------------------------------------------------------------| r_work (final): 0.4832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5082 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18540 Z= 0.142 Angle : 0.731 11.580 25144 Z= 0.364 Chirality : 0.045 0.221 2669 Planarity : 0.005 0.110 3243 Dihedral : 5.449 43.761 2440 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.64 % Allowed : 19.78 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.17), residues: 2214 helix: -1.10 (0.26), residues: 368 sheet: -1.54 (0.20), residues: 604 loop : -1.40 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 321 HIS 0.007 0.001 HIS A 271 PHE 0.031 0.002 PHE I 4 TYR 0.037 0.002 TYR L 76 ARG 0.020 0.001 ARG C 77 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 591) hydrogen bonds : angle 6.29310 ( 1560) covalent geometry : bond 0.00316 (18540) covalent geometry : angle 0.73063 (25144) *********************** 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 309 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 257 time to evaluate : 1.936 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: 0.6865 (OUTLIER) cc_final: 0.6582 (mm) REVERT: H 76 TYR cc_start: 0.6433 (OUTLIER) cc_final: 0.6033 (t80) REVERT: H 105 MET cc_start: 0.5586 (tpt) cc_final: 0.5290 (tpt) REVERT: J 17 MET cc_start: 0.3634 (tpp) cc_final: 0.3196 (ptt) REVERT: C 44 MET cc_start: -0.0072 (mtt) cc_final: -0.0520 (ptp) REVERT: A 73 MET cc_start: 0.4425 (ptp) cc_final: 0.4147 (mtm) REVERT: A 78 TRP cc_start: 0.3818 (m100) cc_final: 0.3364 (m100) REVERT: A 304 LYS cc_start: 0.5989 (mttp) cc_final: 0.5724 (mttp) REVERT: A 308 ILE cc_start: 0.6557 (OUTLIER) cc_final: 0.6073 (mt) REVERT: D 31 GLU cc_start: 0.5439 (OUTLIER) cc_final: 0.5001 (pm20) outliers start: 52 outliers final: 42 residues processed: 284 average time/residue: 0.3198 time to fit residues: 135.1266 Evaluate side-chains 286 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 112 CYS Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 369 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 145 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 ILE 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 184 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 299 THR 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 50 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 101 optimal weight: 20.0000 chunk 157 optimal weight: 0.0050 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 131 optimal weight: 0.0970 overall best weight: 1.7796 ------------------------------------------------------------------------------- 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** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 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 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5133 r_free = 0.5133 target = 0.256530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.231985 restraints weight = 24600.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.224619 restraints weight = 28384.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.223845 restraints weight = 26239.269| |-----------------------------------------------------------------------------| r_work (final): 0.4839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5071 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 18540 Z= 0.178 Angle : 0.751 12.831 25144 Z= 0.376 Chirality : 0.046 0.223 2669 Planarity : 0.005 0.065 3243 Dihedral : 5.543 44.275 2440 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.48 % Allowed : 20.49 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.17), residues: 2214 helix: -1.15 (0.26), residues: 372 sheet: -1.58 (0.20), residues: 616 loop : -1.30 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 321 HIS 0.010 0.001 HIS D 271 PHE 0.041 0.002 PHE F 77 TYR 0.036 0.002 TYR L 76 ARG 0.011 0.001 ARG C 77 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 591) hydrogen bonds : angle 6.32341 ( 1560) covalent geometry : bond 0.00398 (18540) covalent geometry : angle 0.75139 (25144) *********************** 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 292 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 1.988 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: 0.6857 (OUTLIER) cc_final: 0.6548 (mm) REVERT: B 120 MET cc_start: 0.6306 (tpp) cc_final: 0.5739 (tpp) REVERT: B 320 LEU cc_start: 0.6992 (pt) cc_final: 0.6684 (mt) REVERT: G 68 ARG cc_start: 0.4892 (tpt-90) cc_final: 0.4662 (tpt-90) REVERT: H 76 TYR cc_start: 0.6266 (OUTLIER) cc_final: 0.5933 (t80) REVERT: H 105 MET cc_start: 0.5650 (tpt) cc_final: 0.5312 (tpt) REVERT: I 1 MET cc_start: 0.3642 (tmm) cc_final: 0.2603 (tpt) REVERT: A 73 MET cc_start: 0.4307 (ptp) cc_final: 0.3650 (mtm) REVERT: A 321 TRP cc_start: 0.7606 (OUTLIER) cc_final: 0.7017 (m-10) REVERT: D 31 GLU cc_start: 0.5254 (OUTLIER) cc_final: 0.4854 (pm20) outliers start: 49 outliers final: 39 residues processed: 271 average time/residue: 0.3353 time to fit residues: 135.6142 Evaluate side-chains 280 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 237 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain H residue 76 TYR Chi-restraints excluded: chain I residue 7 ILE 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 276 VAL Chi-restraints excluded: chain C residue 369 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 145 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 274 THR 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 184 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 299 THR 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 78 optimal weight: 20.0000 chunk 93 optimal weight: 50.0000 chunk 117 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 207 optimal weight: 0.3980 chunk 160 optimal weight: 5.9990 chunk 184 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 30.0000 chunk 100 optimal weight: 30.0000 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 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS ** C 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 ASN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 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 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS ** 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 = 0.5108 r_free = 0.5108 target = 0.253405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.228617 restraints weight = 24475.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.221759 restraints weight = 27361.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.218959 restraints weight = 25622.172| |-----------------------------------------------------------------------------| r_work (final): 0.4799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5183 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 18540 Z= 0.238 Angle : 0.798 12.329 25144 Z= 0.405 Chirality : 0.048 0.251 2669 Planarity : 0.005 0.055 3243 Dihedral : 5.824 46.029 2440 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 24.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.33 % Allowed : 20.44 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.17), residues: 2214 helix: -1.12 (0.26), residues: 372 sheet: -1.49 (0.20), residues: 592 loop : -1.38 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP C 307 HIS 0.010 0.001 HIS A 271 PHE 0.041 0.002 PHE F 77 TYR 0.036 0.003 TYR L 76 ARG 0.015 0.001 ARG D 238 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 591) hydrogen bonds : angle 6.58528 ( 1560) covalent geometry : bond 0.00529 (18540) covalent geometry : angle 0.79807 (25144) ********************** 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 291 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 245 time to evaluate : 1.917 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 120 MET cc_start: 0.6337 (tpp) cc_final: 0.5752 (tpp) REVERT: B 320 LEU cc_start: 0.7096 (pt) cc_final: 0.6810 (mt) REVERT: H 76 TYR cc_start: 0.6329 (OUTLIER) cc_final: 0.5995 (t80) REVERT: H 105 MET cc_start: 0.5691 (tpt) cc_final: 0.5332 (tpt) REVERT: I 1 MET cc_start: 0.3688 (tmm) cc_final: 0.2733 (tpt) REVERT: C 44 MET cc_start: 0.0142 (mtt) cc_final: -0.0535 (ptp) REVERT: A 73 MET cc_start: 0.4490 (ptp) cc_final: 0.3444 (ptp) REVERT: A 282 PHE cc_start: 0.7141 (t80) cc_final: 0.6650 (t80) REVERT: A 320 LEU cc_start: 0.8627 (pt) cc_final: 0.8415 (pp) REVERT: A 321 TRP cc_start: 0.7877 (OUTLIER) cc_final: 0.7348 (m-10) REVERT: D 120 MET cc_start: 0.6696 (tmm) cc_final: 0.6405 (tmm) outliers start: 46 outliers final: 41 residues processed: 274 average time/residue: 0.3341 time to fit residues: 134.6900 Evaluate side-chains 280 residues out of total 1972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 237 time to evaluate : 2.056 ------------------------------------------------------------------------------- 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 252 THR Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 PHE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 75 VAL 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 L residue 103 LEU Chi-restraints excluded: chain L residue 112 CYS Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 369 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 145 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 274 THR 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 97 VAL Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 299 THR 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 90 optimal weight: 40.0000 chunk 217 optimal weight: 0.4980 chunk 203 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 chunk 168 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 205 optimal weight: 0.1980 chunk 3 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 139 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 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 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5162 r_free = 0.5162 target = 0.260304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4997 r_free = 0.4997 target = 0.238648 restraints weight = 24826.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.230891 restraints weight = 29101.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.230230 restraints weight = 31445.398| |-----------------------------------------------------------------------------| r_work (final): 0.4882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4925 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18540 Z= 0.138 Angle : 0.761 16.710 25144 Z= 0.374 Chirality : 0.045 0.252 2669 Planarity : 0.005 0.067 3243 Dihedral : 5.417 42.262 2440 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.13 % Allowed : 21.20 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.17), residues: 2214 helix: -1.15 (0.26), residues: 368 sheet: -1.41 (0.20), residues: 595 loop : -1.24 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP C 307 HIS 0.012 0.001 HIS F 35 PHE 0.043 0.002 PHE F 77 TYR 0.037 0.002 TYR L 76 ARG 0.019 0.001 ARG I 29 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 591) hydrogen bonds : angle 6.28866 ( 1560) covalent geometry : bond 0.00308 (18540) covalent geometry : angle 0.76064 (25144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7133.15 seconds wall clock time: 126 minutes 15.13 seconds (7575.13 seconds total)