Starting phenix.real_space_refine on Wed May 14 21:55:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kg5_37210/05_2025/8kg5_37210.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kg5_37210/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8kg5_37210/05_2025/8kg5_37210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kg5_37210/05_2025/8kg5_37210.map" model { file = "/net/cci-nas-00/data/ceres_data/8kg5_37210/05_2025/8kg5_37210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kg5_37210/05_2025/8kg5_37210.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.69, per 1000 atoms: 0.62 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: 2.58 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.74 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: 3.96 Time building geometry restraints manager: 3.06 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: 2.620 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.110 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.440 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.083 0.004 TRP E 35 HIS 0.016 0.003 HIS D 100G PHE 0.047 0.002 PHE A 237 TYR 0.105 0.003 TYR E 91 ARG 0.002 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.18972 ( 525) hydrogen bonds : angle 8.45012 ( 1539) SS BOND : bond 0.09318 ( 24) SS BOND : angle 16.86025 ( 48) covalent geometry : bond 0.00980 (12509) covalent geometry : angle 1.15425 (16974) *********************** 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 : 1.332 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: 0.7523 (tm-30) REVERT: B 80 LYS cc_start: 0.8436 (tttt) cc_final: 0.7518 (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: 0.7984 (mtmm) REVERT: D 63 PHE cc_start: 0.8173 (m-80) cc_final: 0.7756 (m-80) outliers start: 7 outliers final: 2 residues processed: 259 average time/residue: 0.2544 time to fit residues: 92.7641 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 : 1.345 ------------------------------------------------------------------------------- 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 130 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 0.0020 chunk 89 optimal weight: 0.7980 chunk 139 optimal weight: 20.0000 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.142910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105332 restraints weight = 14602.901| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.33 r_work: 0.3167 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12533 Z= 0.124 Angle : 0.675 10.422 17022 Z= 0.324 Chirality : 0.050 0.703 2023 Planarity : 0.004 0.043 2129 Dihedral : 10.052 106.698 1750 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.83 % Allowed : 10.60 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.20), residues: 1561 helix: 0.22 (0.25), residues: 441 sheet: -2.00 (0.22), residues: 429 loop : -2.47 (0.21), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 314 HIS 0.003 0.001 HIS D 100G PHE 0.018 0.001 PHE C 488 TYR 0.016 0.001 TYR A 417 ARG 0.004 0.000 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 525) hydrogen bonds : angle 5.26481 ( 1539) SS BOND : bond 0.00344 ( 24) SS BOND : angle 1.91292 ( 48) covalent geometry : bond 0.00276 (12509) covalent geometry : angle 0.66824 (16974) *********************** 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 203 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8285 (tp30) cc_final: 0.7858 (tp30) REVERT: A 202 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7346 (tm-30) REVERT: B 79 ILE cc_start: 0.8476 (tp) cc_final: 0.8271 (tp) REVERT: B 80 LYS cc_start: 0.8561 (tttt) cc_final: 0.7499 (mmtt) REVERT: B 97 MET cc_start: 0.5063 (mtm) cc_final: 0.4354 (mmm) REVERT: B 425 SER cc_start: 0.8107 (m) cc_final: 0.7818 (t) REVERT: C 324 THR cc_start: 0.8837 (p) cc_final: 0.8601 (m) REVERT: C 427 LYS cc_start: 0.8451 (mtmm) cc_final: 0.8220 (mtmm) REVERT: E 88 CYS cc_start: 0.7502 (p) cc_final: 0.7146 (p) outliers start: 26 outliers final: 16 residues processed: 196 average time/residue: 0.2382 time to fit residues: 68.3179 Evaluate side-chains 155 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 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 472 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 144 VAL 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 8 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 12 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 150 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 462 GLN D 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.139736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.101882 restraints weight = 14638.156| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.33 r_work: 0.3116 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12533 Z= 0.159 Angle : 0.674 10.725 17022 Z= 0.318 Chirality : 0.049 0.700 2023 Planarity : 0.004 0.040 2129 Dihedral : 9.875 106.976 1748 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.39 % Allowed : 12.71 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.20), residues: 1561 helix: 0.83 (0.27), residues: 435 sheet: -1.69 (0.22), residues: 438 loop : -2.27 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 314 HIS 0.004 0.002 HIS A 317 PHE 0.014 0.001 PHE D 63 TYR 0.022 0.002 TYR A 417 ARG 0.005 0.000 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.03215 ( 525) hydrogen bonds : angle 4.89668 ( 1539) SS BOND : bond 0.00436 ( 24) SS BOND : angle 1.72291 ( 48) covalent geometry : bond 0.00377 (12509) covalent geometry : angle 0.66823 (16974) *********************** 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 181 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 1.441 Fit side-chains revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8239 (tp30) cc_final: 0.7843 (tp30) REVERT: A 88 ASN cc_start: 0.7589 (m-40) cc_final: 0.7347 (m-40) REVERT: A 202 GLN cc_start: 0.7911 (tp-100) cc_final: 0.7233 (tm-30) REVERT: A 282 ARG cc_start: 0.8669 (mtt-85) cc_final: 0.8321 (mtt-85) REVERT: B 80 LYS cc_start: 0.8604 (tttt) cc_final: 0.7542 (mmtt) REVERT: B 97 MET cc_start: 0.5127 (mtm) cc_final: 0.4570 (mmm) REVERT: B 201 LYS cc_start: 0.7914 (mttt) cc_final: 0.7647 (mtmt) REVERT: B 251 MET cc_start: 0.9246 (mmp) cc_final: 0.8777 (mmp) REVERT: B 425 SER cc_start: 0.8193 (m) cc_final: 0.7869 (t) REVERT: B 429 ARG cc_start: 0.8612 (mtm-85) cc_final: 0.8409 (ttm110) REVERT: B 487 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6683 (tt0) REVERT: C 324 THR cc_start: 0.8878 (p) cc_final: 0.8642 (m) REVERT: D 10 GLU cc_start: 0.6574 (tp30) cc_final: 0.6331 (tp30) REVERT: E 45 LYS cc_start: 0.7523 (tttt) cc_final: 0.7092 (tttm) REVERT: E 88 CYS cc_start: 0.7651 (p) cc_final: 0.7210 (p) outliers start: 34 outliers final: 21 residues processed: 170 average time/residue: 0.2296 time to fit residues: 58.0771 Evaluate side-chains 163 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL 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 95 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 384 VAL 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 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 133 optimal weight: 20.0000 chunk 131 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 81 GLN B 94 GLN B 325 ASN C 276 ASN C 317 HIS C 325 ASN C 462 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.130689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.093770 restraints weight = 15172.967| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.27 r_work: 0.3028 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.109 12533 Z= 0.381 Angle : 0.841 10.742 17022 Z= 0.403 Chirality : 0.056 0.865 2023 Planarity : 0.004 0.042 2129 Dihedral : 10.533 112.559 1748 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.37 % Allowed : 13.90 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.20), residues: 1561 helix: 0.34 (0.25), residues: 456 sheet: -1.74 (0.20), residues: 503 loop : -2.48 (0.22), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 314 HIS 0.006 0.002 HIS A 317 PHE 0.014 0.002 PHE E 62 TYR 0.022 0.002 TYR C 441 ARG 0.003 0.001 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 525) hydrogen bonds : angle 5.28355 ( 1539) SS BOND : bond 0.00871 ( 24) SS BOND : angle 1.78718 ( 48) covalent geometry : bond 0.00928 (12509) covalent geometry : angle 0.83638 (16974) *********************** 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 178 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8272 (tp30) cc_final: 0.7994 (tp30) REVERT: A 88 ASN cc_start: 0.7720 (m-40) cc_final: 0.7490 (m-40) REVERT: A 282 ARG cc_start: 0.8887 (mtt-85) cc_final: 0.8664 (mtt-85) REVERT: B 202 GLN cc_start: 0.8057 (tp40) cc_final: 0.7350 (mp10) REVERT: B 254 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8267 (t0) REVERT: B 425 SER cc_start: 0.8569 (m) cc_final: 0.8206 (t) REVERT: B 429 ARG cc_start: 0.8678 (mtm-85) cc_final: 0.8190 (mtp85) REVERT: B 487 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6987 (tt0) REVERT: E 45 LYS cc_start: 0.7595 (tttt) cc_final: 0.7058 (tttm) REVERT: E 88 CYS cc_start: 0.7759 (p) cc_final: 0.7449 (p) outliers start: 48 outliers final: 34 residues processed: 167 average time/residue: 0.2096 time to fit residues: 54.4752 Evaluate side-chains 154 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 350 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 161 GLU Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 266 ILE 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 402 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 29 THR 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 214 ILE Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 384 VAL 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 100 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 134 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 137 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.139797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.103118 restraints weight = 15042.527| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.32 r_work: 0.3128 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12533 Z= 0.121 Angle : 0.636 10.942 17022 Z= 0.298 Chirality : 0.048 0.677 2023 Planarity : 0.003 0.042 2129 Dihedral : 10.062 107.030 1748 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.53 % Allowed : 16.08 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.21), residues: 1561 helix: 1.19 (0.27), residues: 438 sheet: -1.45 (0.21), residues: 510 loop : -2.21 (0.23), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 314 HIS 0.003 0.001 HIS D 100G PHE 0.015 0.001 PHE D 63 TYR 0.013 0.001 TYR B 299 ARG 0.004 0.000 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.02757 ( 525) hydrogen bonds : angle 4.68414 ( 1539) SS BOND : bond 0.00376 ( 24) SS BOND : angle 1.18349 ( 48) covalent geometry : bond 0.00279 (12509) covalent geometry : angle 0.63401 (16974) *********************** 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 180 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8229 (tp30) cc_final: 0.7830 (tp30) REVERT: A 88 ASN cc_start: 0.7729 (m-40) cc_final: 0.7457 (m-40) REVERT: A 417 TYR cc_start: 0.9021 (m-80) cc_final: 0.8787 (m-80) REVERT: B 97 MET cc_start: 0.5081 (mtm) cc_final: 0.4497 (mmm) REVERT: B 201 LYS cc_start: 0.8061 (mttt) cc_final: 0.7630 (mtmt) REVERT: B 202 GLN cc_start: 0.8031 (tp40) cc_final: 0.7350 (mp10) REVERT: B 251 MET cc_start: 0.9181 (mmp) cc_final: 0.8736 (mmp) REVERT: B 425 SER cc_start: 0.8335 (m) cc_final: 0.8087 (t) REVERT: B 487 GLU cc_start: 0.7180 (tp30) cc_final: 0.6939 (tt0) REVERT: C 94 GLN cc_start: 0.7616 (mt0) cc_final: 0.7348 (mt0) REVERT: C 393 CYS cc_start: 0.7227 (m) cc_final: 0.6973 (m) REVERT: E 45 LYS cc_start: 0.7571 (tttt) cc_final: 0.7015 (tttm) outliers start: 36 outliers final: 26 residues processed: 172 average time/residue: 0.2028 time to fit residues: 53.0695 Evaluate side-chains 159 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 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 402 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 377 SER 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 100 THR 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 43 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.0170 chunk 74 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN C 462 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.138615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101471 restraints weight = 15130.929| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.36 r_work: 0.3092 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12533 Z= 0.146 Angle : 0.648 11.019 17022 Z= 0.302 Chirality : 0.048 0.694 2023 Planarity : 0.004 0.038 2129 Dihedral : 9.839 106.021 1748 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.60 % Allowed : 16.50 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.21), residues: 1561 helix: 1.41 (0.27), residues: 438 sheet: -1.27 (0.21), residues: 506 loop : -2.15 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 314 HIS 0.003 0.001 HIS A 317 PHE 0.019 0.001 PHE D 63 TYR 0.014 0.001 TYR B 299 ARG 0.006 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.02819 ( 525) hydrogen bonds : angle 4.64015 ( 1539) SS BOND : bond 0.00401 ( 24) SS BOND : angle 1.15122 ( 48) covalent geometry : bond 0.00347 (12509) covalent geometry : angle 0.64577 (16974) *********************** 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 170 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8222 (tp30) cc_final: 0.7806 (tp30) REVERT: A 88 ASN cc_start: 0.7674 (m-40) cc_final: 0.7396 (m-40) REVERT: B 97 MET cc_start: 0.5157 (mtm) cc_final: 0.4460 (mmm) REVERT: B 201 LYS cc_start: 0.8031 (mttt) cc_final: 0.7610 (mtmt) REVERT: B 202 GLN cc_start: 0.7992 (tp40) cc_final: 0.7302 (mp10) REVERT: B 425 SER cc_start: 0.8309 (m) cc_final: 0.8006 (t) REVERT: C 393 CYS cc_start: 0.7209 (m) cc_final: 0.6971 (m) REVERT: E 45 LYS cc_start: 0.7575 (tttt) cc_final: 0.6986 (tttm) outliers start: 37 outliers final: 29 residues processed: 160 average time/residue: 0.2100 time to fit residues: 50.8064 Evaluate side-chains 151 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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 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 402 VAL 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 212 CYS Chi-restraints excluded: chain C residue 377 SER 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 100 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 47 optimal weight: 0.2980 chunk 89 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.140180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103472 restraints weight = 14849.737| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.30 r_work: 0.3132 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12533 Z= 0.117 Angle : 0.623 11.342 17022 Z= 0.289 Chirality : 0.047 0.635 2023 Planarity : 0.003 0.039 2129 Dihedral : 9.760 105.049 1748 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.18 % Allowed : 17.35 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.21), residues: 1561 helix: 1.67 (0.27), residues: 435 sheet: -1.10 (0.21), residues: 512 loop : -2.08 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 314 HIS 0.003 0.001 HIS A 317 PHE 0.020 0.001 PHE D 63 TYR 0.014 0.001 TYR B 299 ARG 0.005 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.02571 ( 525) hydrogen bonds : angle 4.47326 ( 1539) SS BOND : bond 0.00271 ( 24) SS BOND : angle 1.03174 ( 48) covalent geometry : bond 0.00273 (12509) covalent geometry : angle 0.62109 (16974) *********************** 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 169 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8205 (tp30) cc_final: 0.7742 (tp30) REVERT: A 88 ASN cc_start: 0.7657 (m-40) cc_final: 0.7376 (m-40) REVERT: B 60 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7746 (mm-30) REVERT: B 97 MET cc_start: 0.5083 (mtm) cc_final: 0.4471 (mmm) REVERT: B 201 LYS cc_start: 0.8064 (mttt) cc_final: 0.7651 (mtmt) REVERT: B 202 GLN cc_start: 0.7975 (tp40) cc_final: 0.7235 (mp10) REVERT: B 251 MET cc_start: 0.9137 (mmp) cc_final: 0.8867 (mmp) REVERT: B 425 SER cc_start: 0.8188 (m) cc_final: 0.7893 (t) REVERT: B 427 LYS cc_start: 0.8739 (tptt) cc_final: 0.8142 (pttt) REVERT: B 496 ASN cc_start: 0.8744 (m-40) cc_final: 0.8542 (m-40) REVERT: C 393 CYS cc_start: 0.7152 (m) cc_final: 0.6925 (m) outliers start: 31 outliers final: 27 residues processed: 162 average time/residue: 0.2205 time to fit residues: 54.2143 Evaluate side-chains 151 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.476 ------------------------------------------------------------------------------- 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 316 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 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 402 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 377 SER 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 100 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 85 THR 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 84 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 C 426 ASN C 462 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.138194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101479 restraints weight = 14932.647| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.29 r_work: 0.3101 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12533 Z= 0.151 Angle : 0.649 11.343 17022 Z= 0.301 Chirality : 0.048 0.670 2023 Planarity : 0.003 0.037 2129 Dihedral : 9.757 105.855 1748 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.53 % Allowed : 17.35 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.21), residues: 1561 helix: 1.68 (0.27), residues: 435 sheet: -1.07 (0.22), residues: 512 loop : -2.04 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 314 HIS 0.003 0.001 HIS A 317 PHE 0.019 0.001 PHE D 63 TYR 0.014 0.001 TYR B 299 ARG 0.004 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.02749 ( 525) hydrogen bonds : angle 4.52304 ( 1539) SS BOND : bond 0.00453 ( 24) SS BOND : angle 1.07071 ( 48) covalent geometry : bond 0.00361 (12509) covalent geometry : angle 0.64739 (16974) *********************** 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 169 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8233 (tp30) cc_final: 0.7807 (tp30) REVERT: A 88 ASN cc_start: 0.7688 (m-40) cc_final: 0.7408 (m-40) REVERT: B 60 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7764 (mm-30) REVERT: B 97 MET cc_start: 0.5189 (mtm) cc_final: 0.4498 (mmm) REVERT: B 202 GLN cc_start: 0.8022 (tp40) cc_final: 0.7308 (mp10) REVERT: B 425 SER cc_start: 0.8260 (m) cc_final: 0.7952 (t) REVERT: C 393 CYS cc_start: 0.7163 (m) cc_final: 0.6931 (m) outliers start: 36 outliers final: 33 residues processed: 161 average time/residue: 0.2002 time to fit residues: 49.3610 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 : 1.299 ------------------------------------------------------------------------------- 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 316 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 A residue 502 SER 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 B residue 402 VAL 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 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 77 THR 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 85 THR 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 28 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 132 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 81 optimal weight: 0.0570 overall best weight: 1.1100 ------------------------------------------------------------------------------- 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 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.138375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101949 restraints weight = 15067.423| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.28 r_work: 0.3125 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12533 Z= 0.149 Angle : 0.652 11.357 17022 Z= 0.302 Chirality : 0.048 0.662 2023 Planarity : 0.003 0.037 2129 Dihedral : 9.765 105.733 1748 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.60 % Allowed : 17.42 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.21), residues: 1561 helix: 1.72 (0.27), residues: 435 sheet: -1.00 (0.22), residues: 512 loop : -2.02 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 314 HIS 0.003 0.001 HIS A 317 PHE 0.021 0.001 PHE D 63 TYR 0.014 0.001 TYR B 299 ARG 0.004 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.02701 ( 525) hydrogen bonds : angle 4.50726 ( 1539) SS BOND : bond 0.00458 ( 24) SS BOND : angle 1.23053 ( 48) covalent geometry : bond 0.00356 (12509) covalent geometry : angle 0.64947 (16974) *********************** 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 167 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8236 (tp30) cc_final: 0.7832 (tp30) REVERT: A 88 ASN cc_start: 0.7740 (m-40) cc_final: 0.7463 (m-40) REVERT: B 60 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7742 (mm-30) REVERT: B 97 MET cc_start: 0.5144 (mtm) cc_final: 0.4492 (mmm) REVERT: B 202 GLN cc_start: 0.8048 (tp40) cc_final: 0.7341 (mp10) REVERT: B 425 SER cc_start: 0.8300 (m) cc_final: 0.8017 (t) REVERT: B 427 LYS cc_start: 0.8792 (tptt) cc_final: 0.8167 (pttt) REVERT: C 393 CYS cc_start: 0.7201 (m) cc_final: 0.6970 (m) REVERT: D 89 MET cc_start: 0.6215 (tpp) cc_final: 0.5949 (tpt) outliers start: 37 outliers final: 33 residues processed: 159 average time/residue: 0.2083 time to fit residues: 50.6791 Evaluate side-chains 158 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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 316 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 A residue 502 SER 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 B residue 402 VAL 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 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 77 THR 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 85 THR 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 71 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 139 optimal weight: 0.4980 chunk 150 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 138 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 80 optimal weight: 0.2980 chunk 143 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.140708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104137 restraints weight = 14917.019| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.29 r_work: 0.3167 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12533 Z= 0.108 Angle : 0.618 11.623 17022 Z= 0.286 Chirality : 0.047 0.614 2023 Planarity : 0.003 0.036 2129 Dihedral : 9.666 103.960 1748 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.25 % Allowed : 17.63 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.22), residues: 1561 helix: 1.86 (0.27), residues: 435 sheet: -0.89 (0.22), residues: 512 loop : -1.94 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 314 HIS 0.002 0.001 HIS A 317 PHE 0.022 0.001 PHE B 505 TYR 0.014 0.001 TYR B 299 ARG 0.004 0.000 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.02441 ( 525) hydrogen bonds : angle 4.33777 ( 1539) SS BOND : bond 0.00337 ( 24) SS BOND : angle 1.05243 ( 48) covalent geometry : bond 0.00250 (12509) covalent geometry : angle 0.61618 (16974) ********************** 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 173 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8242 (tp30) cc_final: 0.7804 (tp30) REVERT: A 88 ASN cc_start: 0.7748 (m-40) cc_final: 0.7463 (m-40) REVERT: B 97 MET cc_start: 0.4987 (mtm) cc_final: 0.4461 (mmm) REVERT: B 202 GLN cc_start: 0.8056 (tp40) cc_final: 0.7375 (mp10) REVERT: B 425 SER cc_start: 0.8123 (m) cc_final: 0.7857 (t) REVERT: B 427 LYS cc_start: 0.8778 (tptt) cc_final: 0.8166 (pttt) REVERT: C 393 CYS cc_start: 0.7243 (m) cc_final: 0.7033 (m) outliers start: 32 outliers final: 30 residues processed: 164 average time/residue: 0.2159 time to fit residues: 53.8306 Evaluate side-chains 161 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.504 ------------------------------------------------------------------------------- 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 316 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 502 SER 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 377 SER Chi-restraints excluded: chain B residue 402 VAL 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 212 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 377 SER 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 E residue 5 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 78 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.140081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.103599 restraints weight = 14823.565| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.27 r_work: 0.3161 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3611 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= 0.114 Angle : 0.619 11.273 17022 Z= 0.286 Chirality : 0.046 0.605 2023 Planarity : 0.003 0.037 2129 Dihedral : 9.770 105.674 1747 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.39 % Allowed : 17.91 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.22), residues: 1561 helix: 1.90 (0.27), residues: 435 sheet: -0.84 (0.22), residues: 506 loop : -1.85 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 314 HIS 0.002 0.001 HIS A 317 PHE 0.018 0.001 PHE D 63 TYR 0.014 0.001 TYR B 299 ARG 0.004 0.000 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.02444 ( 525) hydrogen bonds : angle 4.30507 ( 1539) SS BOND : bond 0.00381 ( 24) SS BOND : angle 1.01146 ( 48) covalent geometry : bond 0.00266 (12509) covalent geometry : angle 0.61716 (16974) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6290.54 seconds wall clock time: 110 minutes 28.12 seconds (6628.12 seconds total)