Starting phenix.real_space_refine on Wed Jul 30 11:33:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kg5_37210/07_2025/8kg5_37210.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kg5_37210/07_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_37210/07_2025/8kg5_37210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kg5_37210/07_2025/8kg5_37210.map" model { file = "/net/cci-nas-00/data/ceres_data/8kg5_37210/07_2025/8kg5_37210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kg5_37210/07_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 8.37, per 1000 atoms: 0.68 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: 3.10 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: 2.22 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: 6.23 Time building geometry restraints manager: 3.48 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: 3.150 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: 0.080 Set scattering table: 0.120 Process input model: 38.030 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 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:4.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.420 ------------------------------------------------------------------------------- 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 : 1.601 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: 0.3134 time to fit residues: 114.6153 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 : 1.531 ------------------------------------------------------------------------------- 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 = 0.142927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105357 restraints weight = 14600.514| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.33 r_work: 0.3166 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 1.404 Fit side-chains revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8287 (tp30) cc_final: 0.7860 (tp30) REVERT: A 202 GLN cc_start: 0.7888 (tp-100) cc_final: 0.7349 (tm-30) REVERT: B 79 ILE cc_start: 0.8479 (tp) cc_final: 0.8274 (tp) REVERT: B 80 LYS cc_start: 0.8564 (tttt) cc_final: 0.7502 (mmtt) REVERT: B 97 MET cc_start: 0.5062 (mtm) cc_final: 0.4355 (mmm) REVERT: B 425 SER cc_start: 0.8110 (m) cc_final: 0.7822 (t) REVERT: C 324 THR cc_start: 0.8836 (p) cc_final: 0.8601 (m) REVERT: C 427 LYS cc_start: 0.8452 (mtmm) cc_final: 0.8221 (mtmm) REVERT: E 88 CYS cc_start: 0.7503 (p) cc_final: 0.7149 (p) outliers start: 26 outliers final: 16 residues processed: 196 average time/residue: 0.2324 time to fit residues: 66.5006 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 : 1.296 ------------------------------------------------------------------------------- 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: 0.0870 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: 1.0962 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.140846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.102990 restraints weight = 14651.798| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.33 r_work: 0.3110 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12533 Z= 0.150 Angle : 0.668 10.783 17022 Z= 0.315 Chirality : 0.049 0.691 2023 Planarity : 0.004 0.040 2129 Dihedral : 9.852 106.956 1748 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.32 % Allowed : 12.71 % Favored : 84.97 % 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: -1.85 (0.20), residues: 1561 helix: 0.84 (0.27), residues: 435 sheet: -1.68 (0.22), residues: 438 loop : -2.26 (0.21), residues: 688 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 0.013 0.001 PHE D 63 TYR 0.022 0.001 TYR A 417 ARG 0.005 0.000 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 525) hydrogen bonds : angle 4.87274 ( 1539) SS BOND : bond 0.00426 ( 24) SS BOND : angle 1.84284 ( 48) covalent geometry : bond 0.00353 (12509) covalent geometry : angle 0.66214 (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 182 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 1.594 Fit side-chains revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8239 (tp30) cc_final: 0.7826 (tp30) REVERT: A 88 ASN cc_start: 0.7542 (m-40) cc_final: 0.7299 (m-40) REVERT: A 202 GLN cc_start: 0.7883 (tp-100) cc_final: 0.7188 (tm-30) REVERT: A 282 ARG cc_start: 0.8626 (mtt-85) cc_final: 0.8303 (mtt-85) REVERT: B 80 LYS cc_start: 0.8541 (tttt) cc_final: 0.7485 (mmtt) REVERT: B 97 MET cc_start: 0.5083 (mtm) cc_final: 0.4546 (mmm) REVERT: B 201 LYS cc_start: 0.7887 (mttt) cc_final: 0.7619 (mtmt) REVERT: B 251 MET cc_start: 0.9251 (mmp) cc_final: 0.8747 (mmp) REVERT: B 425 SER cc_start: 0.8154 (m) cc_final: 0.7816 (t) REVERT: B 487 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6618 (tt0) REVERT: C 324 THR cc_start: 0.8873 (p) cc_final: 0.8633 (m) REVERT: D 10 GLU cc_start: 0.6540 (tp30) cc_final: 0.6289 (tp30) REVERT: E 45 LYS cc_start: 0.7459 (tttt) cc_final: 0.7036 (tttm) REVERT: E 88 CYS cc_start: 0.7629 (p) cc_final: 0.7184 (p) outliers start: 33 outliers final: 20 residues processed: 171 average time/residue: 0.3118 time to fit residues: 80.0092 Evaluate side-chains 162 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 1.430 ------------------------------------------------------------------------------- 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 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: 1.9990 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: 6.9990 chunk 134 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.136101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.099814 restraints weight = 15524.114| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.17 r_work: 0.3072 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 12533 Z= 0.327 Angle : 0.796 9.949 17022 Z= 0.379 Chirality : 0.054 0.839 2023 Planarity : 0.004 0.041 2129 Dihedral : 10.338 111.019 1748 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.44 % Allowed : 13.55 % Favored : 83.01 % 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: -2.06 (0.20), residues: 1561 helix: 0.46 (0.25), residues: 456 sheet: -1.67 (0.20), residues: 509 loop : -2.45 (0.22), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 314 HIS 0.006 0.002 HIS A 317 PHE 0.014 0.002 PHE E 62 TYR 0.020 0.002 TYR C 441 ARG 0.004 0.001 ARG B 429 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 525) hydrogen bonds : angle 5.16105 ( 1539) SS BOND : bond 0.00803 ( 24) SS BOND : angle 1.69460 ( 48) covalent geometry : bond 0.00796 (12509) covalent geometry : angle 0.79217 (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 181 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 132 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8291 (tp30) cc_final: 0.8008 (tp30) REVERT: A 88 ASN cc_start: 0.7702 (m-40) cc_final: 0.7461 (m-40) REVERT: A 282 ARG cc_start: 0.8845 (mtt-85) cc_final: 0.8583 (mtt-85) REVERT: B 97 MET cc_start: 0.5151 (mtm) cc_final: 0.4494 (mmm) REVERT: B 201 LYS cc_start: 0.7950 (mttt) cc_final: 0.7564 (mtmt) REVERT: B 202 GLN cc_start: 0.8009 (tp40) cc_final: 0.7307 (mp10) REVERT: B 254 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8254 (t0) REVERT: B 283 GLN cc_start: 0.9149 (mt0) cc_final: 0.8938 (mt0) REVERT: B 425 SER cc_start: 0.8506 (m) cc_final: 0.8168 (t) REVERT: B 487 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6927 (tt0) REVERT: E 45 LYS cc_start: 0.7600 (tttt) cc_final: 0.7040 (tttm) REVERT: E 88 CYS cc_start: 0.7705 (p) cc_final: 0.7360 (p) outliers start: 49 outliers final: 35 residues processed: 168 average time/residue: 0.2147 time to fit residues: 55.7966 Evaluate side-chains 154 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 334 LEU 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: 0.9980 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 59 optimal weight: 0.0570 overall best weight: 0.7298 ------------------------------------------------------------------------------- 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 = 0.139786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103566 restraints weight = 14910.736| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.27 r_work: 0.3146 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12533 Z= 0.122 Angle : 0.635 11.036 17022 Z= 0.299 Chirality : 0.048 0.661 2023 Planarity : 0.003 0.041 2129 Dihedral : 9.974 106.245 1748 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.18 % Allowed : 16.01 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.46 (0.21), residues: 1561 helix: 1.22 (0.26), residues: 438 sheet: -1.40 (0.21), residues: 518 loop : -2.17 (0.23), residues: 605 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 0.013 0.001 PHE D 63 TYR 0.013 0.001 TYR B 299 ARG 0.006 0.000 ARG B 429 Details of bonding type rmsd hydrogen bonds : bond 0.02682 ( 525) hydrogen bonds : angle 4.61232 ( 1539) SS BOND : bond 0.00370 ( 24) SS BOND : angle 1.20290 ( 48) covalent geometry : bond 0.00283 (12509) covalent geometry : angle 0.63300 (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 175 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8179 (tp30) cc_final: 0.7769 (tp30) REVERT: A 88 ASN cc_start: 0.7698 (m-40) cc_final: 0.7415 (m-40) REVERT: A 427 LYS cc_start: 0.8313 (mtmt) cc_final: 0.8064 (mtmm) REVERT: B 60 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7742 (mm-30) REVERT: B 97 MET cc_start: 0.5160 (mtm) cc_final: 0.4685 (mmm) REVERT: B 201 LYS cc_start: 0.7990 (mttt) cc_final: 0.7523 (mtmt) REVERT: B 202 GLN cc_start: 0.7985 (tp40) cc_final: 0.7305 (mp10) REVERT: B 425 SER cc_start: 0.8245 (m) cc_final: 0.7976 (t) REVERT: B 427 LYS cc_start: 0.8767 (tptt) cc_final: 0.8219 (pttt) REVERT: B 487 GLU cc_start: 0.7132 (tp30) cc_final: 0.6868 (tt0) REVERT: C 338 ASP cc_start: 0.8376 (m-30) cc_final: 0.8170 (m-30) REVERT: E 45 LYS cc_start: 0.7587 (tttt) cc_final: 0.7018 (tttm) outliers start: 31 outliers final: 24 residues processed: 167 average time/residue: 0.2196 time to fit residues: 55.4961 Evaluate side-chains 163 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 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 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 386 ILE Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 100 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: 2.9990 chunk 114 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 74 optimal weight: 0.0470 chunk 33 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN 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 = 0.3705 r_free = 0.3705 target = 0.139384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.102646 restraints weight = 15170.119| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.31 r_work: 0.3140 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12533 Z= 0.126 Angle : 0.633 11.178 17022 Z= 0.294 Chirality : 0.048 0.668 2023 Planarity : 0.003 0.038 2129 Dihedral : 9.751 105.113 1748 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.25 % Allowed : 16.57 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.19 (0.21), residues: 1561 helix: 1.49 (0.27), residues: 435 sheet: -1.15 (0.21), residues: 512 loop : -2.12 (0.23), residues: 614 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 0.012 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 0.02647 ( 525) hydrogen bonds : angle 4.53015 ( 1539) SS BOND : bond 0.00335 ( 24) SS BOND : angle 1.19128 ( 48) covalent geometry : bond 0.00296 (12509) covalent geometry : angle 0.63108 (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 172 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8216 (tp30) cc_final: 0.7810 (tp30) REVERT: A 88 ASN cc_start: 0.7733 (m-40) cc_final: 0.7462 (m-40) REVERT: A 427 LYS cc_start: 0.8353 (mtmt) cc_final: 0.8105 (mtmm) REVERT: B 97 MET cc_start: 0.5118 (mtm) cc_final: 0.4646 (mmm) REVERT: B 201 LYS cc_start: 0.8049 (mttt) cc_final: 0.7496 (mmtm) REVERT: B 202 GLN cc_start: 0.8003 (tp40) cc_final: 0.7314 (mp10) REVERT: B 251 MET cc_start: 0.9191 (mmp) cc_final: 0.8925 (mmp) REVERT: B 425 SER cc_start: 0.8223 (m) cc_final: 0.7955 (t) REVERT: B 427 LYS cc_start: 0.8777 (tptt) cc_final: 0.8269 (pttt) REVERT: E 45 LYS cc_start: 0.7616 (tttt) cc_final: 0.7021 (tttm) outliers start: 32 outliers final: 25 residues processed: 165 average time/residue: 0.2139 time to fit residues: 53.5902 Evaluate side-chains 153 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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 334 LEU Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 382 CYS 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 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: 0.5980 chunk 89 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 C 426 ASN C 462 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.138788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102213 restraints weight = 14913.136| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.29 r_work: 0.3110 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12533 Z= 0.142 Angle : 0.642 11.231 17022 Z= 0.298 Chirality : 0.048 0.660 2023 Planarity : 0.003 0.037 2129 Dihedral : 9.775 105.974 1748 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.46 % Allowed : 16.64 % 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: -1.08 (0.21), residues: 1561 helix: 1.58 (0.27), residues: 435 sheet: -1.07 (0.21), residues: 512 loop : -2.08 (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 0.017 0.001 PHE B 505 TYR 0.014 0.001 TYR B 299 ARG 0.005 0.000 ARG B 429 Details of bonding type rmsd hydrogen bonds : bond 0.02706 ( 525) hydrogen bonds : angle 4.52181 ( 1539) SS BOND : bond 0.00455 ( 24) SS BOND : angle 1.19528 ( 48) covalent geometry : bond 0.00339 (12509) covalent geometry : angle 0.63961 (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 175 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8197 (tp30) cc_final: 0.7778 (tp30) REVERT: A 88 ASN cc_start: 0.7671 (m-40) cc_final: 0.7388 (m-40) REVERT: A 427 LYS cc_start: 0.8315 (mtmt) cc_final: 0.8035 (mtmm) REVERT: B 97 MET cc_start: 0.5178 (mtm) cc_final: 0.4684 (mmm) REVERT: B 201 LYS cc_start: 0.8047 (mttt) cc_final: 0.7466 (mmtm) REVERT: B 202 GLN cc_start: 0.7977 (tp40) cc_final: 0.7291 (mp10) REVERT: B 425 SER cc_start: 0.8234 (m) cc_final: 0.7922 (t) REVERT: B 427 LYS cc_start: 0.8810 (tptt) cc_final: 0.8269 (pttt) REVERT: B 496 ASN cc_start: 0.8773 (m-40) cc_final: 0.8569 (m-40) REVERT: E 45 LYS cc_start: 0.7578 (tttt) cc_final: 0.7019 (tttm) outliers start: 35 outliers final: 33 residues processed: 167 average time/residue: 0.2222 time to fit residues: 56.1346 Evaluate side-chains 164 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 172 LEU 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 382 CYS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 84 optimal weight: 0.1980 chunk 5 optimal weight: 5.9990 chunk 53 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 113 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.140360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103427 restraints weight = 14959.659| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.33 r_work: 0.3141 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12533 Z= 0.109 Angle : 0.617 11.476 17022 Z= 0.285 Chirality : 0.047 0.620 2023 Planarity : 0.003 0.037 2129 Dihedral : 9.711 104.635 1748 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.53 % Allowed : 17.06 % Favored : 80.41 % 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: -0.90 (0.21), residues: 1561 helix: 1.74 (0.27), residues: 435 sheet: -0.96 (0.22), residues: 512 loop : -1.97 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 314 HIS 0.002 0.001 HIS A 317 PHE 0.008 0.001 PHE D 63 TYR 0.014 0.001 TYR B 299 ARG 0.006 0.000 ARG B 429 Details of bonding type rmsd hydrogen bonds : bond 0.02459 ( 525) hydrogen bonds : angle 4.37054 ( 1539) SS BOND : bond 0.00368 ( 24) SS BOND : angle 1.13920 ( 48) covalent geometry : bond 0.00252 (12509) covalent geometry : angle 0.61488 (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 178 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8214 (tp30) cc_final: 0.7753 (tp30) REVERT: A 88 ASN cc_start: 0.7703 (m-40) cc_final: 0.7407 (m-40) REVERT: A 427 LYS cc_start: 0.8331 (mtmt) cc_final: 0.8067 (mtmm) REVERT: B 97 MET cc_start: 0.5091 (mtm) cc_final: 0.4727 (mmm) REVERT: B 201 LYS cc_start: 0.8076 (mttt) cc_final: 0.7520 (mmtm) REVERT: B 202 GLN cc_start: 0.7952 (tp40) cc_final: 0.7264 (mp10) REVERT: B 425 SER cc_start: 0.8148 (m) cc_final: 0.7864 (t) REVERT: B 427 LYS cc_start: 0.8804 (tptt) cc_final: 0.8277 (pttt) REVERT: B 496 ASN cc_start: 0.8779 (m-40) cc_final: 0.8564 (m-40) outliers start: 36 outliers final: 30 residues processed: 170 average time/residue: 0.2160 time to fit residues: 55.6909 Evaluate side-chains 165 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 172 LEU 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 382 CYS 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 30 VAL 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: 0.7980 chunk 150 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.138440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101454 restraints weight = 14979.308| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.34 r_work: 0.3087 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12533 Z= 0.169 Angle : 0.662 11.389 17022 Z= 0.307 Chirality : 0.048 0.675 2023 Planarity : 0.004 0.037 2129 Dihedral : 9.797 106.025 1748 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.39 % Allowed : 17.63 % 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: -0.93 (0.21), residues: 1561 helix: 1.67 (0.27), residues: 435 sheet: -0.98 (0.22), residues: 512 loop : -1.95 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 314 HIS 0.004 0.001 HIS A 317 PHE 0.020 0.001 PHE B 505 TYR 0.014 0.002 TYR B 299 ARG 0.007 0.000 ARG B 429 Details of bonding type rmsd hydrogen bonds : bond 0.02840 ( 525) hydrogen bonds : angle 4.52543 ( 1539) SS BOND : bond 0.00527 ( 24) SS BOND : angle 1.27345 ( 48) covalent geometry : bond 0.00407 (12509) covalent geometry : angle 0.65907 (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 168 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 1.435 Fit side-chains revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8222 (tp30) cc_final: 0.7906 (tp30) REVERT: A 88 ASN cc_start: 0.7698 (m-40) cc_final: 0.7412 (m-40) REVERT: A 427 LYS cc_start: 0.8311 (mtmt) cc_final: 0.8033 (mtmm) REVERT: B 97 MET cc_start: 0.5215 (mtm) cc_final: 0.4671 (mmm) REVERT: B 197 ASN cc_start: 0.8566 (t0) cc_final: 0.8351 (t0) REVERT: B 201 LYS cc_start: 0.8052 (mttt) cc_final: 0.7494 (mmtm) REVERT: B 202 GLN cc_start: 0.7991 (tp40) cc_final: 0.7284 (mp10) REVERT: B 425 SER cc_start: 0.8289 (m) cc_final: 0.7984 (t) REVERT: B 496 ASN cc_start: 0.8798 (m-40) cc_final: 0.8578 (m-40) outliers start: 34 outliers final: 31 residues processed: 160 average time/residue: 0.2175 time to fit residues: 53.6780 Evaluate side-chains 161 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 1.388 ------------------------------------------------------------------------------- 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 161 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 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 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: 1.9990 chunk 47 optimal weight: 0.0670 chunk 122 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 150 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 80 optimal weight: 0.0980 chunk 143 optimal weight: 2.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- 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 D 39 GLN D 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.102579 restraints weight = 14777.795| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.28 r_work: 0.3108 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12533 Z= 0.139 Angle : 0.645 11.435 17022 Z= 0.298 Chirality : 0.048 0.652 2023 Planarity : 0.003 0.037 2129 Dihedral : 9.778 105.662 1748 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.39 % Allowed : 17.77 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.83 (0.22), residues: 1561 helix: 1.75 (0.26), residues: 435 sheet: -0.92 (0.22), residues: 512 loop : -1.91 (0.24), 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 0.014 0.001 PHE C 483 TYR 0.014 0.001 TYR B 299 ARG 0.007 0.000 ARG B 429 Details of bonding type rmsd hydrogen bonds : bond 0.02648 ( 525) hydrogen bonds : angle 4.43845 ( 1539) SS BOND : bond 0.00443 ( 24) SS BOND : angle 1.34607 ( 48) covalent geometry : bond 0.00334 (12509) covalent geometry : angle 0.64182 (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 170 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8191 (tp30) cc_final: 0.7754 (tp30) REVERT: A 88 ASN cc_start: 0.7662 (m-40) cc_final: 0.7368 (m-40) REVERT: A 427 LYS cc_start: 0.8285 (mtmt) cc_final: 0.8003 (mtmm) REVERT: B 97 MET cc_start: 0.5133 (mtm) cc_final: 0.4675 (mmm) REVERT: B 197 ASN cc_start: 0.8532 (t0) cc_final: 0.8292 (t0) REVERT: B 201 LYS cc_start: 0.8048 (mttt) cc_final: 0.7468 (mmtm) REVERT: B 202 GLN cc_start: 0.7944 (tp40) cc_final: 0.7222 (mp10) REVERT: B 425 SER cc_start: 0.8264 (m) cc_final: 0.7963 (t) REVERT: B 427 LYS cc_start: 0.8793 (tptt) cc_final: 0.8139 (pttt) REVERT: B 496 ASN cc_start: 0.8751 (m-40) cc_final: 0.8529 (m-40) outliers start: 34 outliers final: 31 residues processed: 163 average time/residue: 0.2333 time to fit residues: 57.4961 Evaluate side-chains 162 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 1.483 ------------------------------------------------------------------------------- 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 161 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 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 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: 0.3980 chunk 45 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 115 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 82 optimal weight: 0.0980 chunk 106 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 overall best weight: 0.1980 ------------------------------------------------------------------------------- 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** E 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.145372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.108620 restraints weight = 14805.512| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.35 r_work: 0.3192 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12533 Z= 0.095 Angle : 0.603 11.634 17022 Z= 0.279 Chirality : 0.046 0.587 2023 Planarity : 0.003 0.037 2129 Dihedral : 9.747 102.514 1748 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.18 % Allowed : 18.05 % Favored : 79.78 % 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: -0.60 (0.22), residues: 1561 helix: 1.94 (0.27), residues: 435 sheet: -0.70 (0.22), residues: 509 loop : -1.85 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 314 HIS 0.003 0.001 HIS D 100G PHE 0.022 0.001 PHE B 505 TYR 0.018 0.001 TYR A 417 ARG 0.007 0.000 ARG B 429 Details of bonding type rmsd hydrogen bonds : bond 0.02299 ( 525) hydrogen bonds : angle 4.20847 ( 1539) SS BOND : bond 0.00286 ( 24) SS BOND : angle 1.18600 ( 48) covalent geometry : bond 0.00212 (12509) covalent geometry : angle 0.60047 (16974) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6840.75 seconds wall clock time: 120 minutes 16.72 seconds (7216.72 seconds total)