Starting phenix.real_space_refine on Mon Aug 25 02:08:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz8_41737/08_2025/8tz8_41737_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz8_41737/08_2025/8tz8_41737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tz8_41737/08_2025/8tz8_41737_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz8_41737/08_2025/8tz8_41737_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tz8_41737/08_2025/8tz8_41737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz8_41737/08_2025/8tz8_41737.map" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.064 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 P 2 5.49 5 S 87 5.16 5 C 8179 2.51 5 N 1927 2.21 5 O 2130 1.98 5 H 12101 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24426 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 6, 'ASP:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 7, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "C" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 7, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'LBN': 1, 'XMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'LBN': 1, 'XMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 19 Time building chain proxies: 4.72, per 1000 atoms: 0.19 Number of scatterers: 24426 At special positions: 0 Unit cell: (131.76, 129.6, 76.68, 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) S 87 16.00 P 2 15.00 O 2130 8.00 N 1927 7.00 C 8179 6.00 H 12101 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 763.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 1 sheets defined 88.0% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 103 through 130 Processing helix chain 'A' and resid 134 through 157 Processing helix chain 'A' and resid 157 through 203 Proline residue: A 167 - end of helix removed outlier: 4.813A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.968A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 251 removed outlier: 4.551A pdb=" N VAL A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 270 Processing helix chain 'A' and resid 272 through 282 removed outlier: 4.245A pdb=" N GLY A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 Processing helix chain 'A' and resid 288 through 312 removed outlier: 4.425A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 312 through 330 removed outlier: 3.690A pdb=" N VAL A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.638A pdb=" N ARG A 355 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.544A pdb=" N TYR A 385 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.222A pdb=" N ALA A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 437 through 479 removed outlier: 3.816A pdb=" N SER A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 487 through 496 Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 506 through 523 removed outlier: 4.272A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 4.108A pdb=" N ALA A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 572 through 586 removed outlier: 4.350A pdb=" N GLY A 576 " --> pdb=" O PHE A 572 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 619 removed outlier: 3.793A pdb=" N ALA A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N MET A 598 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ARG A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 618 " --> pdb=" O ILE A 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 103 Processing helix chain 'B' and resid 103 through 130 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 157 through 203 Proline residue: B 167 - end of helix removed outlier: 4.655A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.681A pdb=" N LEU B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 250 removed outlier: 4.550A pdb=" N VAL B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 271 Processing helix chain 'B' and resid 272 through 282 removed outlier: 4.198A pdb=" N GLY B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 312 removed outlier: 4.588A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Proline residue: B 296 - end of helix Processing helix chain 'B' and resid 312 through 329 removed outlier: 3.630A pdb=" N TRP B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET B 325 " --> pdb=" O VAL B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 349 through 361 Proline residue: B 356 - end of helix Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 362 through 376 removed outlier: 3.764A pdb=" N THR B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 388 removed outlier: 3.736A pdb=" N LEU B 382 " --> pdb=" O ALA B 378 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 414 removed outlier: 4.195A pdb=" N ALA B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 437 through 448 Processing helix chain 'B' and resid 449 through 479 Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.621A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 504 removed outlier: 3.597A pdb=" N ALA B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY B 504 " --> pdb=" O ALA B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 523 removed outlier: 4.125A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 removed outlier: 3.931A pdb=" N ALA B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 574 through 586 removed outlier: 3.613A pdb=" N VAL B 578 " --> pdb=" O SER B 574 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 584 " --> pdb=" O GLY B 580 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET B 585 " --> pdb=" O GLY B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 596 removed outlier: 3.616A pdb=" N THR B 594 " --> pdb=" O LYS B 590 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 596 " --> pdb=" O ASP B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 619 Processing helix chain 'C' and resid 91 through 103 Processing helix chain 'C' and resid 103 through 130 Processing helix chain 'C' and resid 130 through 157 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 157 through 198 Proline residue: C 167 - end of helix removed outlier: 4.430A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.871A pdb=" N LEU C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 252 removed outlier: 3.709A pdb=" N GLY C 238 " --> pdb=" O PRO C 234 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 271 through 281 removed outlier: 4.020A pdb=" N ALA C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL C 280 " --> pdb=" O GLY C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 287 Processing helix chain 'C' and resid 288 through 312 removed outlier: 4.220A pdb=" N LEU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Proline residue: C 296 - end of helix Processing helix chain 'C' and resid 312 through 330 removed outlier: 3.855A pdb=" N VAL C 324 " --> pdb=" O LYS C 320 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET C 325 " --> pdb=" O VAL C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 342 Processing helix chain 'C' and resid 349 through 361 removed outlier: 3.573A pdb=" N ARG C 355 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Proline residue: C 356 - end of helix Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 362 through 375 removed outlier: 3.828A pdb=" N GLY C 373 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 388 removed outlier: 3.965A pdb=" N GLY C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 414 Proline residue: C 404 - end of helix removed outlier: 3.850A pdb=" N LEU C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 437 through 449 removed outlier: 3.908A pdb=" N SER C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 480 removed outlier: 3.816A pdb=" N MET C 480 " --> pdb=" O TRP C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.573A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 506 through 523 removed outlier: 4.173A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 removed outlier: 3.908A pdb=" N ALA C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 573 through 586 removed outlier: 4.558A pdb=" N ILE C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 618 removed outlier: 3.600A pdb=" N THR C 594 " --> pdb=" O LYS C 590 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N MET C 598 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ARG C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 600 " --> pdb=" O GLY C 596 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 546 through 547 964 hydrogen bonds defined for protein. 2850 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: 5.11 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 12083 1.01 - 1.21: 28 1.21 - 1.41: 5215 1.41 - 1.61: 7272 1.61 - 1.81: 163 Bond restraints: 24761 Sorted by residual: bond pdb=" C11 XMO A 801 " pdb=" O12 XMO A 801 " ideal model delta sigma weight residual 1.398 1.681 -0.283 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C11 XMO C 801 " pdb=" O12 XMO C 801 " ideal model delta sigma weight residual 1.398 1.677 -0.279 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C11 XMO B 801 " pdb=" O12 XMO B 801 " ideal model delta sigma weight residual 1.398 1.676 -0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" C10 XMO C 801 " pdb=" C11 XMO C 801 " ideal model delta sigma weight residual 1.534 1.289 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C10 XMO B 801 " pdb=" C11 XMO B 801 " ideal model delta sigma weight residual 1.534 1.289 0.245 2.00e-02 2.50e+03 1.49e+02 ... (remaining 24756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 44504 3.22 - 6.44: 97 6.44 - 9.66: 10 9.66 - 12.88: 2 12.88 - 16.11: 2 Bond angle restraints: 44615 Sorted by residual: angle pdb=" O1 LBN C 802 " pdb=" P1 LBN C 802 " pdb=" O2 LBN C 802 " ideal model delta sigma weight residual 93.45 109.56 -16.11 3.00e+00 1.11e-01 2.88e+01 angle pdb=" O1 LBN A 802 " pdb=" P1 LBN A 802 " pdb=" O2 LBN A 802 " ideal model delta sigma weight residual 93.45 109.49 -16.04 3.00e+00 1.11e-01 2.86e+01 angle pdb=" O3 LBN C 802 " pdb=" P1 LBN C 802 " pdb=" O4 LBN C 802 " ideal model delta sigma weight residual 119.36 109.56 9.80 3.00e+00 1.11e-01 1.07e+01 angle pdb=" O3 LBN A 802 " pdb=" P1 LBN A 802 " pdb=" O4 LBN A 802 " ideal model delta sigma weight residual 119.36 109.64 9.72 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C02 XMO B 801 " pdb=" C04 XMO B 801 " pdb=" O06 XMO B 801 " ideal model delta sigma weight residual 111.45 120.15 -8.70 3.00e+00 1.11e-01 8.40e+00 ... (remaining 44610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.98: 11444 32.98 - 65.96: 362 65.96 - 98.94: 15 98.94 - 131.92: 4 131.92 - 164.89: 4 Dihedral angle restraints: 11829 sinusoidal: 6099 harmonic: 5730 Sorted by residual: dihedral pdb=" C01 XMO C 801 " pdb=" C02 XMO C 801 " pdb=" C04 XMO C 801 " pdb=" O06 XMO C 801 " ideal model delta sinusoidal sigma weight residual 296.92 132.03 164.89 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C01 XMO C 801 " pdb=" C02 XMO C 801 " pdb=" C04 XMO C 801 " pdb=" O05 XMO C 801 " ideal model delta sinusoidal sigma weight residual 116.78 -47.37 164.15 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C01 XMO B 801 " pdb=" C02 XMO B 801 " pdb=" C04 XMO B 801 " pdb=" O06 XMO B 801 " ideal model delta sinusoidal sigma weight residual 296.92 148.56 148.36 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 11826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1873 0.074 - 0.148: 114 0.148 - 0.222: 1 0.222 - 0.296: 0 0.296 - 0.369: 3 Chirality restraints: 1991 Sorted by residual: chirality pdb=" C10 XMO B 801 " pdb=" C09 XMO B 801 " pdb=" C11 XMO B 801 " pdb=" O22 XMO B 801 " both_signs ideal model delta sigma weight residual False 2.74 2.37 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C10 XMO C 801 " pdb=" C09 XMO C 801 " pdb=" C11 XMO C 801 " pdb=" O22 XMO C 801 " both_signs ideal model delta sigma weight residual False 2.74 2.38 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" C10 XMO A 801 " pdb=" C09 XMO A 801 " pdb=" C11 XMO A 801 " pdb=" O22 XMO A 801 " both_signs ideal model delta sigma weight residual False 2.74 2.42 0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 1988 not shown) Planarity restraints: 3631 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 290 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C PHE C 290 " 0.033 2.00e-02 2.50e+03 pdb=" O PHE C 290 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA C 291 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 599 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C ARG A 599 " 0.032 2.00e-02 2.50e+03 pdb=" O ARG A 599 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA A 600 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 608 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C CYS A 608 " -0.031 2.00e-02 2.50e+03 pdb=" O CYS A 608 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE A 609 " 0.010 2.00e-02 2.50e+03 ... (remaining 3628 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 901 2.18 - 2.79: 46951 2.79 - 3.39: 67449 3.39 - 4.00: 83999 4.00 - 4.60: 133737 Nonbonded interactions: 333037 Sorted by model distance: nonbonded pdb=" OE1 GLN A 206 " pdb=" H GLN A 206 " model vdw 1.580 2.450 nonbonded pdb=" O SER A 451 " pdb="HD22 ASN A 455 " model vdw 1.588 2.450 nonbonded pdb=" H ARG A 436 " pdb=" OE1 GLU A 440 " model vdw 1.593 2.450 nonbonded pdb=" OE1 GLU A 525 " pdb=" H GLU A 525 " model vdw 1.597 2.450 nonbonded pdb=" O LEU C 248 " pdb=" HG1 THR C 252 " model vdw 1.608 2.450 ... (remaining 333032 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 90 through 104 or (resid 105 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 106 or (resid 107 thro \ ugh 110 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 111 through 113 or (resid 114 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 115 through 176 or (resid 17 \ 7 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 178 through 420 or (resid 421 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 422 through 435 or (resid 436 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 437 through 801)) selection = (chain 'B' and (resid 90 through 162 or (resid 163 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 164 through 433 or (re \ sid 434 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 435 through 609 or (resid 610 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 611 through 801)) selection = (chain 'C' and (resid 90 through 162 or (resid 163 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 164 through 433 or (re \ sid 434 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 435 through 609 or (resid 610 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 611 through 801)) } 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: 1.180 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: 0.150 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.540 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 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 : 0.010 0.283 12660 Z= 0.480 Angle : 0.622 16.106 17229 Z= 0.301 Chirality : 0.039 0.369 1991 Planarity : 0.004 0.039 2089 Dihedral : 13.771 164.894 4351 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.71 (0.21), residues: 1593 helix: 2.31 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.55 (0.31), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 319 TYR 0.009 0.001 TYR A 357 PHE 0.018 0.001 PHE C 413 TRP 0.006 0.001 TRP B 316 HIS 0.002 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00977 (12660) covalent geometry : angle 0.62191 (17229) hydrogen bonds : bond 0.13906 ( 964) hydrogen bonds : angle 5.42330 ( 2850) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 302 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TRP cc_start: 0.6533 (m100) cc_final: 0.6120 (m100) REVERT: A 264 LYS cc_start: 0.7884 (mttt) cc_final: 0.7602 (mtpt) REVERT: A 345 ILE cc_start: 0.8286 (mm) cc_final: 0.8063 (mp) REVERT: A 497 MET cc_start: 0.7602 (tmm) cc_final: 0.7321 (tmm) REVERT: B 370 MET cc_start: 0.7987 (mtm) cc_final: 0.7731 (mtp) REVERT: B 458 VAL cc_start: 0.8301 (t) cc_final: 0.8020 (t) REVERT: B 530 GLN cc_start: 0.7731 (tt0) cc_final: 0.7531 (tt0) REVERT: B 585 MET cc_start: 0.8711 (mtt) cc_final: 0.8457 (mtt) REVERT: C 242 GLN cc_start: 0.8341 (mt0) cc_final: 0.8118 (mt0) REVERT: C 357 TYR cc_start: 0.8340 (m-80) cc_final: 0.8100 (m-80) REVERT: C 370 MET cc_start: 0.8805 (mtm) cc_final: 0.8569 (mtm) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.2015 time to fit residues: 89.3786 Evaluate side-chains 220 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.112580 restraints weight = 41695.993| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.95 r_work: 0.3192 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12660 Z= 0.123 Angle : 0.478 5.305 17229 Z= 0.252 Chirality : 0.035 0.130 1991 Planarity : 0.003 0.045 2089 Dihedral : 10.091 163.133 1827 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.36 % Allowed : 7.98 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.25 (0.21), residues: 1593 helix: 2.64 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.37 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 589 TYR 0.011 0.001 TYR B 231 PHE 0.016 0.001 PHE C 413 TRP 0.007 0.001 TRP B 184 HIS 0.002 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00265 (12660) covalent geometry : angle 0.47778 (17229) hydrogen bonds : bond 0.04512 ( 964) hydrogen bonds : angle 3.93030 ( 2850) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 236 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 219 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TRP cc_start: 0.6599 (m100) cc_final: 0.6066 (m100) REVERT: A 264 LYS cc_start: 0.7787 (mttt) cc_final: 0.7515 (mtpt) REVERT: A 345 ILE cc_start: 0.8445 (mm) cc_final: 0.8231 (mp) REVERT: A 428 MET cc_start: 0.7562 (mmt) cc_final: 0.7333 (mmt) REVERT: B 158 GLU cc_start: 0.6931 (pm20) cc_final: 0.6691 (pm20) REVERT: B 202 LEU cc_start: 0.8751 (mp) cc_final: 0.8529 (mt) REVERT: B 242 GLN cc_start: 0.8455 (mt0) cc_final: 0.8126 (mt0) REVERT: B 349 GLU cc_start: 0.6491 (mp0) cc_final: 0.6168 (mm-30) REVERT: B 370 MET cc_start: 0.7904 (mtm) cc_final: 0.7555 (mtp) REVERT: B 458 VAL cc_start: 0.8359 (t) cc_final: 0.8045 (t) REVERT: B 485 GLN cc_start: 0.8407 (mp10) cc_final: 0.8030 (mp10) REVERT: B 503 MET cc_start: 0.9122 (mtp) cc_final: 0.8780 (mtp) REVERT: B 598 MET cc_start: 0.7804 (tpt) cc_final: 0.7503 (tpt) REVERT: C 219 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7385 (mp) REVERT: C 357 TYR cc_start: 0.8641 (m-80) cc_final: 0.8388 (m-80) outliers start: 17 outliers final: 10 residues processed: 227 average time/residue: 0.1955 time to fit residues: 67.8738 Evaluate side-chains 217 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 206 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 458 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.141655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107114 restraints weight = 42345.266| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.94 r_work: 0.3121 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12660 Z= 0.185 Angle : 0.503 5.259 17229 Z= 0.271 Chirality : 0.037 0.165 1991 Planarity : 0.004 0.048 2089 Dihedral : 9.158 134.485 1827 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.36 % Allowed : 8.62 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.21), residues: 1593 helix: 2.42 (0.14), residues: 1318 sheet: None (None), residues: 0 loop : -0.51 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 436 TYR 0.012 0.001 TYR A 357 PHE 0.024 0.001 PHE B 413 TRP 0.007 0.001 TRP B 150 HIS 0.004 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00433 (12660) covalent geometry : angle 0.50331 (17229) hydrogen bonds : bond 0.05307 ( 964) hydrogen bonds : angle 4.00877 ( 2850) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7865 (mttt) cc_final: 0.7553 (mtpt) REVERT: A 345 ILE cc_start: 0.8479 (mm) cc_final: 0.8178 (mt) REVERT: A 430 MET cc_start: 0.8370 (mtt) cc_final: 0.8054 (mtt) REVERT: B 157 TYR cc_start: 0.7393 (m-10) cc_final: 0.7133 (m-80) REVERT: B 158 GLU cc_start: 0.7044 (pm20) cc_final: 0.6695 (pm20) REVERT: B 370 MET cc_start: 0.8083 (mtm) cc_final: 0.7636 (mtp) REVERT: B 444 GLN cc_start: 0.7206 (mm-40) cc_final: 0.6520 (tt0) REVERT: B 503 MET cc_start: 0.9157 (mtp) cc_final: 0.8716 (mtp) REVERT: B 598 MET cc_start: 0.7998 (tpt) cc_final: 0.7620 (tpt) REVERT: C 219 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7609 (mp) REVERT: C 257 MET cc_start: 0.7270 (ptt) cc_final: 0.6855 (ptp) outliers start: 17 outliers final: 11 residues processed: 219 average time/residue: 0.1839 time to fit residues: 62.6112 Evaluate side-chains 206 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 194 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 104 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.144607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.109008 restraints weight = 42326.941| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.06 r_work: 0.3094 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12660 Z= 0.140 Angle : 0.459 5.083 17229 Z= 0.245 Chirality : 0.035 0.158 1991 Planarity : 0.003 0.048 2089 Dihedral : 8.136 98.092 1827 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.96 % Allowed : 10.53 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.06 (0.21), residues: 1593 helix: 2.55 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.61 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.011 0.001 TYR A 357 PHE 0.015 0.001 PHE B 413 TRP 0.006 0.001 TRP B 316 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00320 (12660) covalent geometry : angle 0.45890 (17229) hydrogen bonds : bond 0.04500 ( 964) hydrogen bonds : angle 3.83757 ( 2850) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7765 (mttt) cc_final: 0.7458 (mtpt) REVERT: A 345 ILE cc_start: 0.8391 (mm) cc_final: 0.8077 (mt) REVERT: A 428 MET cc_start: 0.7435 (mmt) cc_final: 0.7192 (mmt) REVERT: B 157 TYR cc_start: 0.7237 (m-10) cc_final: 0.6989 (m-80) REVERT: B 158 GLU cc_start: 0.6956 (pm20) cc_final: 0.6370 (pm20) REVERT: B 370 MET cc_start: 0.7919 (mtm) cc_final: 0.7618 (mtp) REVERT: B 444 GLN cc_start: 0.7032 (mm-40) cc_final: 0.6279 (tt0) REVERT: B 503 MET cc_start: 0.9095 (mtp) cc_final: 0.8638 (mtp) REVERT: B 598 MET cc_start: 0.7821 (tpt) cc_final: 0.7431 (tpt) REVERT: C 219 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7484 (mp) REVERT: C 257 MET cc_start: 0.7287 (ptt) cc_final: 0.6891 (ptp) outliers start: 12 outliers final: 10 residues processed: 203 average time/residue: 0.1986 time to fit residues: 62.3108 Evaluate side-chains 196 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 106 optimal weight: 20.0000 chunk 140 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.140972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105599 restraints weight = 42750.541| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.04 r_work: 0.3050 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12660 Z= 0.211 Angle : 0.515 5.578 17229 Z= 0.279 Chirality : 0.037 0.160 1991 Planarity : 0.004 0.049 2089 Dihedral : 8.385 104.734 1827 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.52 % Allowed : 11.17 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.67 (0.21), residues: 1593 helix: 2.24 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.57 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 436 TYR 0.013 0.001 TYR A 357 PHE 0.021 0.001 PHE C 413 TRP 0.007 0.001 TRP B 150 HIS 0.004 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00502 (12660) covalent geometry : angle 0.51532 (17229) hydrogen bonds : bond 0.05416 ( 964) hydrogen bonds : angle 4.04416 ( 2850) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 HIS cc_start: 0.6775 (t70) cc_final: 0.6076 (m90) REVERT: A 157 TYR cc_start: 0.7544 (m-10) cc_final: 0.7326 (m-80) REVERT: A 264 LYS cc_start: 0.7906 (mttt) cc_final: 0.7586 (mtpt) REVERT: A 345 ILE cc_start: 0.8437 (mm) cc_final: 0.8113 (mt) REVERT: A 428 MET cc_start: 0.7516 (mmt) cc_final: 0.7278 (mmp) REVERT: B 112 TRP cc_start: 0.5870 (t60) cc_final: 0.5332 (t-100) REVERT: B 158 GLU cc_start: 0.7046 (pm20) cc_final: 0.6370 (pm20) REVERT: B 370 MET cc_start: 0.8065 (mtm) cc_final: 0.7668 (mtp) REVERT: B 444 GLN cc_start: 0.7069 (mm-40) cc_final: 0.6578 (tt0) REVERT: B 598 MET cc_start: 0.7972 (tpt) cc_final: 0.7607 (tpt) REVERT: C 219 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7520 (mp) REVERT: C 257 MET cc_start: 0.7363 (ptt) cc_final: 0.6981 (ptp) outliers start: 19 outliers final: 14 residues processed: 214 average time/residue: 0.2167 time to fit residues: 72.5386 Evaluate side-chains 202 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 62 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 145 optimal weight: 0.0770 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.140315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106966 restraints weight = 42072.063| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.94 r_work: 0.3077 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12660 Z= 0.127 Angle : 0.450 5.052 17229 Z= 0.239 Chirality : 0.035 0.133 1991 Planarity : 0.003 0.050 2089 Dihedral : 7.602 84.278 1827 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.96 % Allowed : 12.37 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.03 (0.21), residues: 1593 helix: 2.51 (0.15), residues: 1311 sheet: None (None), residues: 0 loop : -0.52 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 589 TYR 0.011 0.001 TYR A 357 PHE 0.012 0.001 PHE B 413 TRP 0.007 0.001 TRP B 178 HIS 0.002 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00286 (12660) covalent geometry : angle 0.44968 (17229) hydrogen bonds : bond 0.04326 ( 964) hydrogen bonds : angle 3.80516 ( 2850) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 157 TYR cc_start: 0.7617 (m-10) cc_final: 0.7360 (m-80) REVERT: A 264 LYS cc_start: 0.7815 (mttt) cc_final: 0.7498 (mtpt) REVERT: A 345 ILE cc_start: 0.8454 (mm) cc_final: 0.8129 (mt) REVERT: A 428 MET cc_start: 0.7558 (mmt) cc_final: 0.7249 (mmt) REVERT: A 430 MET cc_start: 0.8409 (mtt) cc_final: 0.8033 (mtt) REVERT: B 158 GLU cc_start: 0.7194 (pm20) cc_final: 0.6563 (pm20) REVERT: B 370 MET cc_start: 0.7992 (mtm) cc_final: 0.7709 (mtp) REVERT: B 444 GLN cc_start: 0.7154 (mm-40) cc_final: 0.6563 (tt0) REVERT: B 598 MET cc_start: 0.7819 (tpt) cc_final: 0.7452 (tpt) REVERT: C 219 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7536 (mp) REVERT: C 257 MET cc_start: 0.7274 (ptt) cc_final: 0.6882 (ptp) REVERT: C 413 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8171 (t80) REVERT: C 485 GLN cc_start: 0.8606 (mp10) cc_final: 0.8208 (mp10) outliers start: 12 outliers final: 9 residues processed: 205 average time/residue: 0.1656 time to fit residues: 52.7561 Evaluate side-chains 199 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 188 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 82 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.139214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106007 restraints weight = 42039.516| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.93 r_work: 0.3080 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12660 Z= 0.147 Angle : 0.465 5.247 17229 Z= 0.248 Chirality : 0.035 0.141 1991 Planarity : 0.004 0.050 2089 Dihedral : 7.527 85.096 1827 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.20 % Allowed : 12.37 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.04 (0.21), residues: 1593 helix: 2.51 (0.15), residues: 1311 sheet: None (None), residues: 0 loop : -0.50 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 355 TYR 0.011 0.001 TYR A 357 PHE 0.015 0.001 PHE C 413 TRP 0.014 0.001 TRP B 184 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00340 (12660) covalent geometry : angle 0.46490 (17229) hydrogen bonds : bond 0.04545 ( 964) hydrogen bonds : angle 3.82431 ( 2850) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7856 (mttt) cc_final: 0.7531 (mtpt) REVERT: A 345 ILE cc_start: 0.8470 (mm) cc_final: 0.8145 (mt) REVERT: A 428 MET cc_start: 0.7602 (mmt) cc_final: 0.7305 (mmt) REVERT: B 112 TRP cc_start: 0.5891 (t60) cc_final: 0.5367 (t-100) REVERT: B 158 GLU cc_start: 0.7329 (pm20) cc_final: 0.6684 (pm20) REVERT: B 184 TRP cc_start: 0.7661 (m-10) cc_final: 0.7457 (m-10) REVERT: B 370 MET cc_start: 0.8027 (mtm) cc_final: 0.7747 (mtp) REVERT: B 444 GLN cc_start: 0.7321 (mm-40) cc_final: 0.6778 (tt0) REVERT: B 598 MET cc_start: 0.7887 (tpt) cc_final: 0.7473 (tpt) REVERT: C 219 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7639 (mp) REVERT: C 257 MET cc_start: 0.7298 (ptt) cc_final: 0.6906 (ptp) REVERT: C 413 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8244 (t80) REVERT: C 485 GLN cc_start: 0.8638 (mp10) cc_final: 0.8228 (mp10) outliers start: 15 outliers final: 12 residues processed: 207 average time/residue: 0.2011 time to fit residues: 64.9428 Evaluate side-chains 208 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 147 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.138208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.103535 restraints weight = 42274.469| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.97 r_work: 0.3068 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12660 Z= 0.168 Angle : 0.480 5.799 17229 Z= 0.257 Chirality : 0.036 0.143 1991 Planarity : 0.004 0.050 2089 Dihedral : 7.623 87.372 1827 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.28 % Allowed : 12.93 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.88 (0.21), residues: 1593 helix: 2.40 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -0.54 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 436 TYR 0.012 0.001 TYR A 357 PHE 0.016 0.001 PHE C 413 TRP 0.010 0.001 TRP B 178 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00394 (12660) covalent geometry : angle 0.47986 (17229) hydrogen bonds : bond 0.04769 ( 964) hydrogen bonds : angle 3.88241 ( 2850) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7942 (mttt) cc_final: 0.7625 (mtpt) REVERT: A 345 ILE cc_start: 0.8502 (mm) cc_final: 0.8166 (mt) REVERT: A 428 MET cc_start: 0.7590 (mmt) cc_final: 0.7264 (mmt) REVERT: A 430 MET cc_start: 0.8433 (mtt) cc_final: 0.8078 (mtt) REVERT: B 112 TRP cc_start: 0.5887 (t60) cc_final: 0.5409 (t-100) REVERT: B 158 GLU cc_start: 0.7356 (pm20) cc_final: 0.6694 (pm20) REVERT: B 370 MET cc_start: 0.8047 (mtm) cc_final: 0.7779 (mtp) REVERT: B 444 GLN cc_start: 0.7318 (mm-40) cc_final: 0.6780 (tt0) REVERT: B 503 MET cc_start: 0.9056 (mtp) cc_final: 0.8678 (mtp) REVERT: B 598 MET cc_start: 0.7923 (tpt) cc_final: 0.7527 (tpt) REVERT: C 257 MET cc_start: 0.7510 (ptt) cc_final: 0.7127 (ptp) REVERT: C 363 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7782 (mtpt) REVERT: C 413 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8263 (t80) REVERT: C 485 GLN cc_start: 0.8734 (mp10) cc_final: 0.8331 (mp10) outliers start: 16 outliers final: 12 residues processed: 208 average time/residue: 0.2159 time to fit residues: 68.7903 Evaluate side-chains 204 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 27 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 132 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.105972 restraints weight = 42347.616| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.93 r_work: 0.3078 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12660 Z= 0.142 Angle : 0.463 5.926 17229 Z= 0.246 Chirality : 0.035 0.137 1991 Planarity : 0.004 0.050 2089 Dihedral : 7.474 83.054 1827 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.96 % Allowed : 13.09 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.01 (0.21), residues: 1593 helix: 2.50 (0.15), residues: 1311 sheet: None (None), residues: 0 loop : -0.53 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 355 TYR 0.011 0.001 TYR A 357 PHE 0.014 0.001 PHE C 413 TRP 0.015 0.001 TRP B 184 HIS 0.003 0.001 HIS C 152 Details of bonding type rmsd covalent geometry : bond 0.00329 (12660) covalent geometry : angle 0.46279 (17229) hydrogen bonds : bond 0.04435 ( 964) hydrogen bonds : angle 3.80320 ( 2850) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7952 (mttt) cc_final: 0.7635 (mtpt) REVERT: A 345 ILE cc_start: 0.8527 (mm) cc_final: 0.8189 (mt) REVERT: A 428 MET cc_start: 0.7644 (mmt) cc_final: 0.7312 (mmt) REVERT: A 430 MET cc_start: 0.8436 (mtt) cc_final: 0.8092 (mtt) REVERT: B 112 TRP cc_start: 0.5911 (t60) cc_final: 0.5466 (t-100) REVERT: B 158 GLU cc_start: 0.7421 (pm20) cc_final: 0.6807 (pm20) REVERT: B 370 MET cc_start: 0.8030 (mtm) cc_final: 0.7747 (mtp) REVERT: B 444 GLN cc_start: 0.7287 (mm-40) cc_final: 0.6793 (tt0) REVERT: B 598 MET cc_start: 0.7895 (tpt) cc_final: 0.7495 (tpt) REVERT: C 257 MET cc_start: 0.7524 (ptt) cc_final: 0.7148 (ptp) REVERT: C 413 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8241 (t80) REVERT: C 485 GLN cc_start: 0.8706 (mp10) cc_final: 0.8333 (mp10) outliers start: 12 outliers final: 10 residues processed: 204 average time/residue: 0.2168 time to fit residues: 68.6963 Evaluate side-chains 200 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 122 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 0.1980 chunk 59 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.139784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.105813 restraints weight = 42333.745| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.92 r_work: 0.3101 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12660 Z= 0.168 Angle : 0.483 6.413 17229 Z= 0.258 Chirality : 0.036 0.144 1991 Planarity : 0.004 0.049 2089 Dihedral : 7.593 87.081 1827 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.88 % Allowed : 13.41 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.88 (0.21), residues: 1593 helix: 2.40 (0.15), residues: 1310 sheet: None (None), residues: 0 loop : -0.54 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 436 TYR 0.012 0.001 TYR A 357 PHE 0.017 0.001 PHE C 413 TRP 0.018 0.001 TRP B 184 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00395 (12660) covalent geometry : angle 0.48295 (17229) hydrogen bonds : bond 0.04769 ( 964) hydrogen bonds : angle 3.87863 ( 2850) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 188 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7972 (mttt) cc_final: 0.7657 (mtpt) REVERT: A 345 ILE cc_start: 0.8572 (mm) cc_final: 0.8235 (mt) REVERT: A 428 MET cc_start: 0.7732 (mmt) cc_final: 0.7391 (mmp) REVERT: A 430 MET cc_start: 0.8405 (mtt) cc_final: 0.8106 (mtt) REVERT: B 112 TRP cc_start: 0.5955 (t60) cc_final: 0.5550 (t-100) REVERT: B 158 GLU cc_start: 0.7500 (pm20) cc_final: 0.6851 (pm20) REVERT: B 370 MET cc_start: 0.8082 (mtm) cc_final: 0.7821 (mtp) REVERT: B 444 GLN cc_start: 0.7351 (mm-40) cc_final: 0.6832 (tt0) REVERT: B 598 MET cc_start: 0.7948 (tpt) cc_final: 0.7545 (tpt) REVERT: C 257 MET cc_start: 0.7548 (ptt) cc_final: 0.7179 (ptp) REVERT: C 413 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8327 (t80) REVERT: C 485 GLN cc_start: 0.8764 (mp10) cc_final: 0.8371 (mp10) outliers start: 11 outliers final: 10 residues processed: 198 average time/residue: 0.2164 time to fit residues: 66.3569 Evaluate side-chains 198 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 187 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 67 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 75 optimal weight: 0.0270 chunk 89 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.142771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109132 restraints weight = 42007.256| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.92 r_work: 0.3147 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12660 Z= 0.108 Angle : 0.440 5.748 17229 Z= 0.231 Chirality : 0.034 0.128 1991 Planarity : 0.003 0.049 2089 Dihedral : 7.239 78.961 1827 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.88 % Allowed : 13.41 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.25 (0.22), residues: 1593 helix: 2.67 (0.15), residues: 1309 sheet: None (None), residues: 0 loop : -0.45 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 355 TYR 0.009 0.001 TYR A 357 PHE 0.010 0.001 PHE C 413 TRP 0.020 0.001 TRP B 184 HIS 0.003 0.001 HIS C 152 Details of bonding type rmsd covalent geometry : bond 0.00236 (12660) covalent geometry : angle 0.43972 (17229) hydrogen bonds : bond 0.03895 ( 964) hydrogen bonds : angle 3.66631 ( 2850) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5509.01 seconds wall clock time: 94 minutes 16.98 seconds (5656.98 seconds total)