Starting phenix.real_space_refine on Sat Aug 23 13:17:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kg5_37210/08_2025/8kg5_37210.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kg5_37210/08_2025/8kg5_37210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kg5_37210/08_2025/8kg5_37210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kg5_37210/08_2025/8kg5_37210.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kg5_37210/08_2025/8kg5_37210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kg5_37210/08_2025/8kg5_37210.map" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Br 6 7.06 5 S 77 5.16 5 Cl 3 4.86 5 C 7797 2.51 5 N 2020 2.21 5 O 2404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12307 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3482 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 12, 'TRANS': 436} Chain breaks: 1 Chain: "B" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3482 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 12, 'TRANS': 436} Chain breaks: 1 Chain: "C" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3482 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 12, 'TRANS': 436} Chain breaks: 1 Chain: "D" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 950 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'336': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'336': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'336': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.47, per 1000 atoms: 0.28 Number of scatterers: 12307 At special positions: 0 Unit cell: (94.17, 100.01, 146.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 6 34.99 Cl 3 17.00 S 77 16.00 O 2404 8.00 N 2020 7.00 C 7797 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 290 " distance=2.02 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.07 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.01 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.20 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.21 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.09 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.05 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.07 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.22 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.22 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.01 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.09 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.02 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.07 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.00 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.20 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.22 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 599.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 29 sheets defined 32.0% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 73 through 95 Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.784A pdb=" N VAL A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 172 Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.784A pdb=" N SER A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 removed outlier: 4.118A pdb=" N VAL A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 240 Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 354 through 358 removed outlier: 3.654A pdb=" N CYS A 358 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.580A pdb=" N ASN A 371 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 372' Processing helix chain 'A' and resid 376 through 379 Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.894A pdb=" N VAL A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 492 through 512 removed outlier: 3.665A pdb=" N LEU A 512 " --> pdb=" O LYS A 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 95 Processing helix chain 'B' and resid 148 through 158 removed outlier: 3.799A pdb=" N VAL B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 208 through 213 removed outlier: 3.562A pdb=" N CYS B 212 " --> pdb=" O ASN B 208 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 213' Processing helix chain 'B' and resid 216 through 227 removed outlier: 4.135A pdb=" N VAL B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 240 Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.579A pdb=" N ASN B 371 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 372 " --> pdb=" O THR B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 372' Processing helix chain 'B' and resid 376 through 379 Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.894A pdb=" N VAL B 384 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 477 Processing helix chain 'B' and resid 492 through 512 removed outlier: 3.667A pdb=" N LEU B 512 " --> pdb=" O LYS B 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 95 Processing helix chain 'C' and resid 148 through 157 removed outlier: 3.661A pdb=" N VAL C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 162 through 172 Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 203 through 213 removed outlier: 3.501A pdb=" N LYS C 209 " --> pdb=" O PRO C 205 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLN C 210 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 227 removed outlier: 4.172A pdb=" N VAL C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 240 Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 354 through 358 removed outlier: 3.654A pdb=" N CYS C 358 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.579A pdb=" N ASN C 371 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER C 372 " --> pdb=" O THR C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 372' Processing helix chain 'C' and resid 376 through 379 Processing helix chain 'C' and resid 380 through 385 removed outlier: 3.894A pdb=" N VAL C 384 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 477 Processing helix chain 'C' and resid 492 through 512 removed outlier: 3.667A pdb=" N LEU C 512 " --> pdb=" O LYS C 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'E' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 352 removed outlier: 7.025A pdb=" N ILE A 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA A 47 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR A 311 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU A 45 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N CYS A 313 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY A 43 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS A 359 " --> pdb=" O PHE A 366 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 349 through 352 removed outlier: 7.025A pdb=" N ILE A 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA A 47 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR A 311 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU A 45 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N CYS A 313 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY A 43 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 38 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU A 30 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL A 469 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE A 32 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 193 through 194 removed outlier: 4.063A pdb=" N LEU A 193 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL A 300 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N MET A 289 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN A 302 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N SER A 287 " --> pdb=" O GLN A 302 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 180 Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA6, first strand: chain 'A' and resid 404 through 406 removed outlier: 3.603A pdb=" N CYS A 416 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 434 removed outlier: 6.654A pdb=" N ALA A 424 " --> pdb=" O ILE A 432 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 349 through 352 removed outlier: 7.025A pdb=" N ILE B 309 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA B 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR B 311 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU B 45 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS B 313 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY B 43 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 359 " --> pdb=" O PHE B 366 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 349 through 352 removed outlier: 7.025A pdb=" N ILE B 309 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA B 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR B 311 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU B 45 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS B 313 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY B 43 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 38 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU B 30 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL B 469 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE B 32 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 193 through 194 removed outlier: 4.063A pdb=" N LEU B 193 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA B 298 " --> pdb=" O CYS B 290 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 180 Processing sheet with id=AB3, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AB4, first strand: chain 'B' and resid 404 through 406 removed outlier: 4.075A pdb=" N CYS B 416 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 431 through 434 removed outlier: 6.654A pdb=" N ALA B 424 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR B 434 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N CYS B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 349 through 352 removed outlier: 7.025A pdb=" N ILE C 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA C 47 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR C 311 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU C 45 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N CYS C 313 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY C 43 " --> pdb=" O CYS C 313 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS C 359 " --> pdb=" O PHE C 366 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 349 through 352 removed outlier: 7.025A pdb=" N ILE C 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA C 47 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR C 311 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU C 45 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N CYS C 313 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY C 43 " --> pdb=" O CYS C 313 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 38 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU C 30 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL C 469 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE C 32 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 193 through 194 removed outlier: 4.063A pdb=" N LEU C 193 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA C 298 " --> pdb=" O CYS C 290 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 64 through 66 removed outlier: 7.100A pdb=" N VAL D 100 " --> pdb=" O LYS C 65 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 176 through 180 Processing sheet with id=AC2, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AC3, first strand: chain 'C' and resid 404 through 406 removed outlier: 4.004A pdb=" N CYS C 416 " --> pdb=" O GLY C 438 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 438 " --> pdb=" O CYS C 416 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 431 through 434 removed outlier: 6.654A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.569A pdb=" N ALA D 93 " --> pdb=" O ASN D 35 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AC8, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AC9, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AD1, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.027A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 45 through 48 removed outlier: 5.493A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1539 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: 2.60 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 3446 1.33 - 1.49: 3406 1.49 - 1.64: 5546 1.64 - 1.79: 27 1.79 - 1.94: 84 Bond restraints: 12509 Sorted by residual: bond pdb=" C43 336 B 601 " pdb=" C49 336 B 601 " ideal model delta sigma weight residual 1.532 1.367 0.165 2.00e-02 2.50e+03 6.84e+01 bond pdb=" C43 336 A 601 " pdb=" C49 336 A 601 " ideal model delta sigma weight residual 1.532 1.367 0.165 2.00e-02 2.50e+03 6.83e+01 bond pdb=" C43 336 C 601 " pdb=" C49 336 C 601 " ideal model delta sigma weight residual 1.532 1.367 0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" C49 336 B 601 " pdb=" C51 336 B 601 " ideal model delta sigma weight residual 1.531 1.375 0.156 2.00e-02 2.50e+03 6.06e+01 bond pdb=" C49 336 C 601 " pdb=" C51 336 C 601 " ideal model delta sigma weight residual 1.531 1.376 0.155 2.00e-02 2.50e+03 6.04e+01 ... (remaining 12504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 16625 3.31 - 6.61: 297 6.61 - 9.92: 37 9.92 - 13.22: 3 13.22 - 16.53: 12 Bond angle restraints: 16974 Sorted by residual: angle pdb=" N ILE B 292 " pdb=" CA ILE B 292 " pdb=" C ILE B 292 " ideal model delta sigma weight residual 112.17 105.55 6.62 9.50e-01 1.11e+00 4.85e+01 angle pdb=" N CYS A 212 " pdb=" CA CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sigma weight residual 112.30 103.02 9.28 1.52e+00 4.33e-01 3.73e+01 angle pdb=" N ILE C 292 " pdb=" CA ILE C 292 " pdb=" C ILE C 292 " ideal model delta sigma weight residual 112.90 107.40 5.50 9.60e-01 1.09e+00 3.28e+01 angle pdb=" N VAL C 482 " pdb=" CA VAL C 482 " pdb=" C VAL C 482 " ideal model delta sigma weight residual 113.71 108.32 5.39 9.50e-01 1.11e+00 3.22e+01 angle pdb=" N VAL A 482 " pdb=" CA VAL A 482 " pdb=" C VAL A 482 " ideal model delta sigma weight residual 113.71 108.33 5.38 9.50e-01 1.11e+00 3.20e+01 ... (remaining 16969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.55: 7022 19.55 - 39.09: 534 39.09 - 58.64: 90 58.64 - 78.18: 32 78.18 - 97.73: 13 Dihedral angle restraints: 7691 sinusoidal: 3078 harmonic: 4613 Sorted by residual: dihedral pdb=" CB CYS A 416 " pdb=" SG CYS A 416 " pdb=" SG CYS A 422 " pdb=" CB CYS A 422 " ideal model delta sinusoidal sigma weight residual 93.00 -177.23 -89.77 1 1.00e+01 1.00e-02 9.56e+01 dihedral pdb=" CB CYS B 322 " pdb=" SG CYS B 322 " pdb=" SG CYS B 333 " pdb=" CB CYS B 333 " ideal model delta sinusoidal sigma weight residual 93.00 8.51 84.49 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" CB CYS A 69 " pdb=" SG CYS A 69 " pdb=" SG CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sinusoidal sigma weight residual -86.00 -163.19 77.19 1 1.00e+01 1.00e-02 7.47e+01 ... (remaining 7688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1818 0.097 - 0.193: 184 0.193 - 0.290: 16 0.290 - 0.387: 2 0.387 - 0.484: 3 Chirality restraints: 2023 Sorted by residual: chirality pdb=" C49 336 C 601 " pdb=" C43 336 C 601 " pdb=" C51 336 C 601 " pdb=" C61 336 C 601 " both_signs ideal model delta sigma weight residual False -2.61 -2.13 -0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" C49 336 A 601 " pdb=" C43 336 A 601 " pdb=" C51 336 A 601 " pdb=" C61 336 A 601 " both_signs ideal model delta sigma weight residual False -2.61 -2.13 -0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" C49 336 B 601 " pdb=" C43 336 B 601 " pdb=" C51 336 B 601 " pdb=" C61 336 B 601 " both_signs ideal model delta sigma weight residual False -2.61 -2.13 -0.48 2.00e-01 2.50e+01 5.75e+00 ... (remaining 2020 not shown) Planarity restraints: 2129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 91 " 0.080 2.00e-02 2.50e+03 5.57e-02 6.21e+01 pdb=" CG TYR E 91 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR E 91 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR E 91 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR E 91 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR E 91 " -0.054 2.00e-02 2.50e+03 pdb=" CZ TYR E 91 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR E 91 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 35 " 0.083 2.00e-02 2.50e+03 4.97e-02 6.18e+01 pdb=" CG TRP E 35 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP E 35 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP E 35 " -0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP E 35 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TRP E 35 " -0.023 2.00e-02 2.50e+03 pdb=" CE3 TRP E 35 " -0.077 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 35 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 35 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 35 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 237 " -0.047 2.00e-02 2.50e+03 2.88e-02 1.45e+01 pdb=" CG PHE A 237 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 237 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 237 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE A 237 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 237 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 237 " -0.028 2.00e-02 2.50e+03 ... (remaining 2126 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1644 2.75 - 3.29: 12139 3.29 - 3.82: 19622 3.82 - 4.36: 24635 4.36 - 4.90: 42661 Nonbonded interactions: 100701 Sorted by model distance: nonbonded pdb=" O ILE E 2 " pdb=" OG1 THR E 97 " model vdw 2.212 3.040 nonbonded pdb=" OD2 ASP B 392 " pdb=" OG SER B 493 " model vdw 2.212 3.040 nonbonded pdb=" OG SER B 46 " pdb=" OG1 THR B 311 " model vdw 2.232 3.040 nonbonded pdb=" OG SER C 46 " pdb=" OG1 THR C 311 " model vdw 2.232 3.040 nonbonded pdb=" OG SER A 46 " pdb=" OG1 THR A 311 " model vdw 2.233 3.040 ... (remaining 100696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.370 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.011 0.185 12533 Z= 0.564 Angle : 1.459 72.633 17022 Z= 0.788 Chirality : 0.061 0.484 2023 Planarity : 0.005 0.056 2129 Dihedral : 14.600 97.728 4639 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.49 % Allowed : 6.74 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.81 (0.18), residues: 1561 helix: -1.50 (0.22), residues: 438 sheet: -2.57 (0.21), residues: 435 loop : -3.12 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.105 0.003 TYR E 91 PHE 0.047 0.002 PHE A 237 TRP 0.083 0.004 TRP E 35 HIS 0.016 0.003 HIS D 100G Details of bonding type rmsd covalent geometry : bond 0.00980 (12509) covalent geometry : angle 1.15425 (16974) SS BOND : bond 0.09318 ( 24) SS BOND : angle 16.86025 ( 48) hydrogen bonds : bond 0.18972 ( 525) hydrogen bonds : angle 8.45012 ( 1539) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 255 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8045 (tp30) cc_final: 0.7468 (mm-30) REVERT: A 202 GLN cc_start: 0.7731 (tp-100) cc_final: 0.7521 (tm-30) REVERT: B 80 LYS cc_start: 0.8436 (tttt) cc_final: 0.7519 (mmtt) REVERT: B 396 MET cc_start: 0.8311 (ptm) cc_final: 0.7862 (ttp) REVERT: C 427 LYS cc_start: 0.8386 (mtmm) cc_final: 0.7986 (mtmm) REVERT: D 63 PHE cc_start: 0.8173 (m-80) cc_final: 0.7757 (m-80) outliers start: 7 outliers final: 2 residues processed: 259 average time/residue: 0.1236 time to fit residues: 45.4422 Evaluate side-chains 147 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain B residue 291 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 325 ASN A 361 GLN B 81 GLN B 165 ASN B 361 GLN C 81 GLN C 210 GLN C 361 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 GLN D 6 GLN D 35 ASN D 39 GLN D 100GHIS E 53 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.141265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.103785 restraints weight = 14677.885| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.33 r_work: 0.3145 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12533 Z= 0.143 Angle : 0.688 10.159 17022 Z= 0.330 Chirality : 0.050 0.720 2023 Planarity : 0.004 0.042 2129 Dihedral : 10.050 106.257 1750 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.97 % Allowed : 10.60 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.20), residues: 1561 helix: 0.26 (0.26), residues: 435 sheet: -2.02 (0.22), residues: 429 loop : -2.51 (0.20), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 429 TYR 0.017 0.001 TYR A 417 PHE 0.020 0.001 PHE C 488 TRP 0.008 0.001 TRP B 314 HIS 0.003 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00328 (12509) covalent geometry : angle 0.68154 (16974) SS BOND : bond 0.00435 ( 24) SS BOND : angle 1.90555 ( 48) hydrogen bonds : bond 0.03633 ( 525) hydrogen bonds : angle 5.27529 ( 1539) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8286 (tp30) cc_final: 0.7862 (tp30) REVERT: A 202 GLN cc_start: 0.7918 (tp-100) cc_final: 0.7338 (tm-30) REVERT: B 80 LYS cc_start: 0.8551 (tttt) cc_final: 0.7492 (mmtt) REVERT: B 97 MET cc_start: 0.5091 (mtm) cc_final: 0.4363 (mmm) REVERT: B 425 SER cc_start: 0.8218 (m) cc_final: 0.7909 (t) REVERT: C 324 THR cc_start: 0.8831 (p) cc_final: 0.8595 (m) REVERT: C 427 LYS cc_start: 0.8430 (mtmm) cc_final: 0.8058 (mtmm) REVERT: C 448 ASP cc_start: 0.8504 (m-30) cc_final: 0.8131 (m-30) REVERT: E 88 CYS cc_start: 0.7560 (p) cc_final: 0.7184 (p) outliers start: 28 outliers final: 19 residues processed: 197 average time/residue: 0.1124 time to fit residues: 32.4605 Evaluate side-chains 157 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 66 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 143 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 325 ASN B 276 ASN C 210 GLN C 462 GLN D 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.140761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.102960 restraints weight = 14762.616| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.33 r_work: 0.3111 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12533 Z= 0.149 Angle : 0.666 10.828 17022 Z= 0.314 Chirality : 0.048 0.685 2023 Planarity : 0.004 0.041 2129 Dihedral : 9.856 106.910 1748 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.32 % Allowed : 12.85 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.20), residues: 1561 helix: 0.86 (0.27), residues: 435 sheet: -1.68 (0.22), residues: 438 loop : -2.27 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 282 TYR 0.021 0.001 TYR A 417 PHE 0.014 0.001 PHE D 63 TRP 0.009 0.001 TRP B 314 HIS 0.003 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00348 (12509) covalent geometry : angle 0.66091 (16974) SS BOND : bond 0.00421 ( 24) SS BOND : angle 1.65687 ( 48) hydrogen bonds : bond 0.03171 ( 525) hydrogen bonds : angle 4.85211 ( 1539) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8241 (tp30) cc_final: 0.7835 (tp30) REVERT: A 88 ASN cc_start: 0.7574 (m-40) cc_final: 0.7333 (m-40) REVERT: A 202 GLN cc_start: 0.7925 (tp-100) cc_final: 0.7180 (tm-30) REVERT: A 487 GLU cc_start: 0.7549 (tp30) cc_final: 0.6919 (mm-30) REVERT: B 80 LYS cc_start: 0.8564 (tttt) cc_final: 0.7500 (mmtt) REVERT: B 97 MET cc_start: 0.5142 (mtm) cc_final: 0.4552 (mmm) REVERT: B 425 SER cc_start: 0.8141 (m) cc_final: 0.7820 (t) REVERT: B 487 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6652 (tt0) REVERT: C 324 THR cc_start: 0.8869 (p) cc_final: 0.8634 (m) REVERT: C 427 LYS cc_start: 0.8413 (mtmm) cc_final: 0.8199 (mtmm) REVERT: D 10 GLU cc_start: 0.6578 (tp30) cc_final: 0.6312 (tp30) REVERT: E 45 LYS cc_start: 0.7488 (tttt) cc_final: 0.7067 (tttm) REVERT: E 88 CYS cc_start: 0.7617 (p) cc_final: 0.7185 (p) outliers start: 33 outliers final: 22 residues processed: 178 average time/residue: 0.1081 time to fit residues: 28.9431 Evaluate side-chains 162 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 103 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 130 optimal weight: 0.0070 chunk 124 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN A 388 ASN B 94 GLN C 462 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.143161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105545 restraints weight = 14611.458| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.33 r_work: 0.3146 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12533 Z= 0.110 Angle : 0.621 11.239 17022 Z= 0.290 Chirality : 0.047 0.642 2023 Planarity : 0.003 0.039 2129 Dihedral : 9.712 103.724 1748 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.32 % Allowed : 13.69 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.21), residues: 1561 helix: 1.21 (0.27), residues: 438 sheet: -1.35 (0.21), residues: 507 loop : -2.19 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 282 TYR 0.015 0.001 TYR A 417 PHE 0.012 0.001 PHE E 62 TRP 0.009 0.001 TRP B 314 HIS 0.003 0.001 HIS D 100G Details of bonding type rmsd covalent geometry : bond 0.00252 (12509) covalent geometry : angle 0.61722 (16974) SS BOND : bond 0.00341 ( 24) SS BOND : angle 1.35832 ( 48) hydrogen bonds : bond 0.02653 ( 525) hydrogen bonds : angle 4.56707 ( 1539) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8193 (tp30) cc_final: 0.7666 (tp30) REVERT: A 202 GLN cc_start: 0.7924 (tp-100) cc_final: 0.7196 (tm-30) REVERT: A 487 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6931 (mm-30) REVERT: B 60 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7636 (mm-30) REVERT: B 97 MET cc_start: 0.5170 (mtm) cc_final: 0.4645 (mmm) REVERT: B 201 LYS cc_start: 0.7930 (mttt) cc_final: 0.7660 (mtpt) REVERT: B 425 SER cc_start: 0.8059 (m) cc_final: 0.7756 (t) REVERT: B 427 LYS cc_start: 0.8699 (tptt) cc_final: 0.8152 (pttt) REVERT: B 487 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6607 (tt0) REVERT: C 186 SER cc_start: 0.9058 (p) cc_final: 0.8828 (m) REVERT: C 324 THR cc_start: 0.8821 (p) cc_final: 0.8561 (m) REVERT: E 45 LYS cc_start: 0.7541 (tttt) cc_final: 0.7151 (tttm) REVERT: E 88 CYS cc_start: 0.7180 (p) cc_final: 0.6933 (p) outliers start: 33 outliers final: 22 residues processed: 180 average time/residue: 0.0961 time to fit residues: 26.8422 Evaluate side-chains 164 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 134 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 137 optimal weight: 0.0270 chunk 146 optimal weight: 2.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN B 325 ASN C 325 ASN C 462 GLN D 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.138195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.100282 restraints weight = 14963.906| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.34 r_work: 0.3073 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12533 Z= 0.192 Angle : 0.682 10.948 17022 Z= 0.319 Chirality : 0.049 0.719 2023 Planarity : 0.004 0.038 2129 Dihedral : 9.795 106.677 1748 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.09 % Allowed : 14.75 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.21), residues: 1561 helix: 1.23 (0.27), residues: 438 sheet: -1.29 (0.21), residues: 512 loop : -2.16 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 429 TYR 0.015 0.002 TYR C 441 PHE 0.010 0.001 PHE E 62 TRP 0.008 0.001 TRP B 314 HIS 0.004 0.002 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00465 (12509) covalent geometry : angle 0.67888 (16974) SS BOND : bond 0.00618 ( 24) SS BOND : angle 1.41274 ( 48) hydrogen bonds : bond 0.03119 ( 525) hydrogen bonds : angle 4.73880 ( 1539) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 133 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8216 (tp30) cc_final: 0.7871 (tp30) REVERT: A 202 GLN cc_start: 0.7907 (tp-100) cc_final: 0.7012 (tm-30) REVERT: A 370 MET cc_start: 0.8391 (ttp) cc_final: 0.8148 (ttm) REVERT: B 97 MET cc_start: 0.5148 (mtm) cc_final: 0.4538 (mmm) REVERT: B 201 LYS cc_start: 0.7928 (mttt) cc_final: 0.7631 (mtpt) REVERT: B 425 SER cc_start: 0.8206 (m) cc_final: 0.7859 (t) REVERT: B 487 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6701 (tt0) REVERT: E 45 LYS cc_start: 0.7530 (tttt) cc_final: 0.6975 (tttm) REVERT: E 88 CYS cc_start: 0.7484 (p) cc_final: 0.7147 (p) outliers start: 44 outliers final: 32 residues processed: 165 average time/residue: 0.0996 time to fit residues: 25.0948 Evaluate side-chains 160 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 39 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 141 optimal weight: 9.9990 chunk 106 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 95 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 GLN ** D 81 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 = 0.3736 r_free = 0.3736 target = 0.142676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105093 restraints weight = 14651.083| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.33 r_work: 0.3150 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12533 Z= 0.105 Angle : 0.610 11.464 17022 Z= 0.282 Chirality : 0.047 0.627 2023 Planarity : 0.003 0.038 2129 Dihedral : 9.677 104.005 1748 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.46 % Allowed : 15.94 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.21), residues: 1561 helix: 1.56 (0.27), residues: 435 sheet: -1.05 (0.22), residues: 512 loop : -2.05 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 282 TYR 0.014 0.001 TYR B 299 PHE 0.013 0.001 PHE D 63 TRP 0.010 0.001 TRP B 314 HIS 0.002 0.001 HIS D 100G Details of bonding type rmsd covalent geometry : bond 0.00238 (12509) covalent geometry : angle 0.60787 (16974) SS BOND : bond 0.00277 ( 24) SS BOND : angle 1.15354 ( 48) hydrogen bonds : bond 0.02506 ( 525) hydrogen bonds : angle 4.43640 ( 1539) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8177 (tp30) cc_final: 0.7761 (tp30) REVERT: A 202 GLN cc_start: 0.7926 (tp-100) cc_final: 0.7027 (tm-30) REVERT: A 487 GLU cc_start: 0.7522 (tp30) cc_final: 0.6909 (mm-30) REVERT: B 97 MET cc_start: 0.5178 (mtm) cc_final: 0.4669 (mmm) REVERT: B 201 LYS cc_start: 0.7987 (mttt) cc_final: 0.7708 (mtpt) REVERT: B 425 SER cc_start: 0.8125 (m) cc_final: 0.7821 (t) REVERT: B 427 LYS cc_start: 0.8716 (tptt) cc_final: 0.8187 (pttt) REVERT: C 386 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8740 (tp) REVERT: C 485 SER cc_start: 0.8147 (m) cc_final: 0.7857 (p) REVERT: E 45 LYS cc_start: 0.7576 (tttt) cc_final: 0.7006 (tttm) REVERT: E 88 CYS cc_start: 0.7233 (p) cc_final: 0.6985 (p) outliers start: 35 outliers final: 28 residues processed: 175 average time/residue: 0.1019 time to fit residues: 27.0531 Evaluate side-chains 160 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 54 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 108 optimal weight: 0.0000 chunk 74 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 19 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 ASN C 462 GLN D 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.143431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106754 restraints weight = 14759.181| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.30 r_work: 0.3173 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12533 Z= 0.109 Angle : 0.613 11.625 17022 Z= 0.284 Chirality : 0.047 0.613 2023 Planarity : 0.003 0.037 2129 Dihedral : 9.615 103.418 1748 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.39 % Allowed : 16.01 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.21), residues: 1561 helix: 1.65 (0.27), residues: 435 sheet: -0.92 (0.22), residues: 512 loop : -1.97 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 429 TYR 0.017 0.001 TYR A 417 PHE 0.017 0.001 PHE B 505 TRP 0.009 0.001 TRP B 314 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00251 (12509) covalent geometry : angle 0.61094 (16974) SS BOND : bond 0.00317 ( 24) SS BOND : angle 1.12247 ( 48) hydrogen bonds : bond 0.02535 ( 525) hydrogen bonds : angle 4.38765 ( 1539) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8228 (tp30) cc_final: 0.7854 (tp30) REVERT: A 202 GLN cc_start: 0.7998 (tp-100) cc_final: 0.7144 (tm-30) REVERT: A 487 GLU cc_start: 0.7522 (tp30) cc_final: 0.6981 (mm-30) REVERT: B 97 MET cc_start: 0.5145 (mtm) cc_final: 0.4716 (mmm) REVERT: B 201 LYS cc_start: 0.8024 (mttt) cc_final: 0.7546 (mtpt) REVERT: B 202 GLN cc_start: 0.7913 (tp40) cc_final: 0.7154 (mp10) REVERT: B 425 SER cc_start: 0.8147 (m) cc_final: 0.7878 (t) REVERT: B 427 LYS cc_start: 0.8699 (tptt) cc_final: 0.8232 (pttt) REVERT: C 186 SER cc_start: 0.9094 (p) cc_final: 0.8857 (m) REVERT: C 386 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8771 (tp) REVERT: C 485 SER cc_start: 0.8223 (m) cc_final: 0.7918 (p) REVERT: E 45 LYS cc_start: 0.7718 (tttt) cc_final: 0.7131 (tttm) REVERT: E 88 CYS cc_start: 0.7359 (p) cc_final: 0.7041 (p) outliers start: 34 outliers final: 27 residues processed: 176 average time/residue: 0.1018 time to fit residues: 27.5638 Evaluate side-chains 167 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 13 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN C 426 ASN C 462 GLN D 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.141465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.104807 restraints weight = 14904.799| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.30 r_work: 0.3149 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12533 Z= 0.137 Angle : 0.633 11.604 17022 Z= 0.294 Chirality : 0.047 0.640 2023 Planarity : 0.003 0.037 2129 Dihedral : 9.661 104.707 1748 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.60 % Allowed : 15.94 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.21), residues: 1561 helix: 1.67 (0.27), residues: 435 sheet: -0.90 (0.22), residues: 512 loop : -1.91 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 429 TYR 0.014 0.001 TYR B 299 PHE 0.014 0.001 PHE B 505 TRP 0.007 0.001 TRP B 314 HIS 0.003 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00326 (12509) covalent geometry : angle 0.63082 (16974) SS BOND : bond 0.00412 ( 24) SS BOND : angle 1.18660 ( 48) hydrogen bonds : bond 0.02680 ( 525) hydrogen bonds : angle 4.43342 ( 1539) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 79 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7951 (tp) REVERT: A 82 GLU cc_start: 0.8201 (tp30) cc_final: 0.7839 (tp30) REVERT: A 202 GLN cc_start: 0.8066 (tp-100) cc_final: 0.7170 (tm-30) REVERT: B 97 MET cc_start: 0.5004 (mtm) cc_final: 0.4633 (mmm) REVERT: B 201 LYS cc_start: 0.8015 (mttt) cc_final: 0.7540 (mtpt) REVERT: B 202 GLN cc_start: 0.7946 (tp40) cc_final: 0.7190 (mp10) REVERT: B 425 SER cc_start: 0.8248 (m) cc_final: 0.7968 (t) REVERT: B 427 LYS cc_start: 0.8753 (tptt) cc_final: 0.8267 (pttt) REVERT: C 222 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7930 (mt-10) REVERT: C 485 SER cc_start: 0.8248 (m) cc_final: 0.7945 (p) REVERT: E 88 CYS cc_start: 0.7382 (p) cc_final: 0.7073 (p) outliers start: 37 outliers final: 31 residues processed: 165 average time/residue: 0.1023 time to fit residues: 26.0124 Evaluate side-chains 162 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN C 426 ASN C 462 GLN D 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.141781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.104799 restraints weight = 14793.864| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.31 r_work: 0.3136 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12533 Z= 0.122 Angle : 0.619 11.697 17022 Z= 0.287 Chirality : 0.047 0.618 2023 Planarity : 0.003 0.038 2129 Dihedral : 9.682 105.429 1748 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.39 % Allowed : 16.36 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.22), residues: 1561 helix: 1.76 (0.27), residues: 435 sheet: -0.78 (0.22), residues: 506 loop : -1.87 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 429 TYR 0.014 0.001 TYR B 299 PHE 0.008 0.001 PHE C 483 TRP 0.008 0.001 TRP B 314 HIS 0.003 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00288 (12509) covalent geometry : angle 0.61737 (16974) SS BOND : bond 0.00382 ( 24) SS BOND : angle 1.13516 ( 48) hydrogen bonds : bond 0.02559 ( 525) hydrogen bonds : angle 4.35618 ( 1539) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8180 (tp30) cc_final: 0.7764 (tp30) REVERT: A 97 MET cc_start: 0.6919 (mmm) cc_final: 0.6665 (mmm) REVERT: A 417 TYR cc_start: 0.8619 (m-10) cc_final: 0.8375 (m-80) REVERT: B 97 MET cc_start: 0.5118 (mtm) cc_final: 0.4641 (mmm) REVERT: B 201 LYS cc_start: 0.8019 (mttt) cc_final: 0.7326 (mtmt) REVERT: B 202 GLN cc_start: 0.7892 (tp40) cc_final: 0.7135 (mp10) REVERT: B 425 SER cc_start: 0.8151 (m) cc_final: 0.7845 (t) REVERT: B 427 LYS cc_start: 0.8741 (tptt) cc_final: 0.8206 (pttt) REVERT: C 222 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7865 (mt-10) REVERT: C 485 SER cc_start: 0.8154 (m) cc_final: 0.7853 (p) REVERT: E 88 CYS cc_start: 0.7384 (p) cc_final: 0.7036 (p) outliers start: 34 outliers final: 31 residues processed: 173 average time/residue: 0.0986 time to fit residues: 26.4345 Evaluate side-chains 171 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 67 optimal weight: 3.9990 chunk 107 optimal weight: 0.0570 chunk 106 optimal weight: 0.0170 chunk 41 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 96 optimal weight: 0.0270 chunk 140 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN C 426 ASN C 462 GLN D 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.143944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108941 restraints weight = 14520.357| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.20 r_work: 0.3208 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12533 Z= 0.094 Angle : 0.589 11.449 17022 Z= 0.273 Chirality : 0.045 0.554 2023 Planarity : 0.003 0.039 2129 Dihedral : 9.831 111.527 1748 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.11 % Allowed : 16.78 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.22), residues: 1561 helix: 1.93 (0.27), residues: 435 sheet: -0.61 (0.23), residues: 503 loop : -1.79 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 429 TYR 0.014 0.001 TYR B 299 PHE 0.022 0.001 PHE B 505 TRP 0.011 0.001 TRP B 314 HIS 0.003 0.001 HIS D 100G Details of bonding type rmsd covalent geometry : bond 0.00209 (12509) covalent geometry : angle 0.58718 (16974) SS BOND : bond 0.00292 ( 24) SS BOND : angle 1.04362 ( 48) hydrogen bonds : bond 0.02313 ( 525) hydrogen bonds : angle 4.18693 ( 1539) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8195 (tp30) cc_final: 0.7786 (tp30) REVERT: A 97 MET cc_start: 0.6899 (mmm) cc_final: 0.6596 (mmm) REVERT: A 422 CYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7841 (p) REVERT: A 487 GLU cc_start: 0.7322 (tp30) cc_final: 0.6786 (mm-30) REVERT: B 80 LYS cc_start: 0.8663 (tttt) cc_final: 0.7597 (mmtt) REVERT: B 97 MET cc_start: 0.5081 (mtm) cc_final: 0.4712 (mmm) REVERT: B 201 LYS cc_start: 0.8028 (mttt) cc_final: 0.7347 (mtmt) REVERT: B 202 GLN cc_start: 0.7910 (tp40) cc_final: 0.7227 (mp10) REVERT: B 425 SER cc_start: 0.7976 (m) cc_final: 0.7708 (t) REVERT: B 427 LYS cc_start: 0.8727 (tptt) cc_final: 0.8228 (pttt) REVERT: C 485 SER cc_start: 0.8264 (m) cc_final: 0.7917 (p) REVERT: D 48 MET cc_start: 0.8724 (mmm) cc_final: 0.8456 (mmm) REVERT: E 88 CYS cc_start: 0.7291 (p) cc_final: 0.6980 (p) outliers start: 30 outliers final: 25 residues processed: 175 average time/residue: 0.0924 time to fit residues: 24.8473 Evaluate side-chains 171 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 127 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 3 optimal weight: 0.0070 chunk 97 optimal weight: 0.0970 chunk 19 optimal weight: 0.7980 chunk 96 optimal weight: 0.1980 chunk 107 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN A 462 GLN B 94 GLN C 426 ASN C 462 GLN D 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.145235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108754 restraints weight = 14667.044| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.30 r_work: 0.3203 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12533 Z= 0.096 Angle : 0.586 11.589 17022 Z= 0.274 Chirality : 0.045 0.537 2023 Planarity : 0.003 0.038 2129 Dihedral : 10.156 137.842 1748 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.04 % Allowed : 17.21 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.22), residues: 1561 helix: 2.02 (0.26), residues: 435 sheet: -0.60 (0.23), residues: 500 loop : -1.68 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 429 TYR 0.016 0.001 TYR A 417 PHE 0.012 0.001 PHE C 483 TRP 0.008 0.001 TRP B 314 HIS 0.002 0.001 HIS D 100G Details of bonding type rmsd covalent geometry : bond 0.00216 (12509) covalent geometry : angle 0.58438 (16974) SS BOND : bond 0.00299 ( 24) SS BOND : angle 1.05332 ( 48) hydrogen bonds : bond 0.02317 ( 525) hydrogen bonds : angle 4.12196 ( 1539) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3217.86 seconds wall clock time: 56 minutes 3.86 seconds (3363.86 seconds total)