Starting phenix.real_space_refine on Fri May 23 18:55:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz8_41737/05_2025/8tz8_41737_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz8_41737/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tz8_41737/05_2025/8tz8_41737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz8_41737/05_2025/8tz8_41737.map" model { file = "/net/cci-nas-00/data/ceres_data/8tz8_41737/05_2025/8tz8_41737_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz8_41737/05_2025/8tz8_41737_trim.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} 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: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} 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: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} 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: 11.99, per 1000 atoms: 0.49 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: 6.17 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.80 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: 8.31 Time building geometry restraints manager: 7.39 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 622 or resid 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 622 or resid 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 622 or resid 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: 0.920 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: 0.460 Extract box with map and model: 1.050 Check model and map are aligned: 0.190 Set scattering table: 0.270 Process input model: 49.690 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.220 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (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 TRP 0.006 0.001 TRP B 316 HIS 0.002 0.001 HIS A 288 PHE 0.018 0.001 PHE C 413 TYR 0.009 0.001 TYR A 357 ARG 0.002 0.000 ARG B 319 Details of bonding type rmsd hydrogen bonds : bond 0.13906 ( 964) hydrogen bonds : angle 5.42330 ( 2850) covalent geometry : bond 0.00977 (12660) covalent geometry : angle 0.62191 (17229) *********************** 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 : 1.890 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: A 181 TRP cc_start: 0.6533 (m100) cc_final: 0.6121 (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: 0.8057 (mp) REVERT: A 350 SER cc_start: 0.8346 (t) cc_final: 0.8088 (t) REVERT: A 497 MET cc_start: 0.7602 (tmm) cc_final: 0.7320 (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 585 MET cc_start: 0.8711 (mtt) cc_final: 0.8457 (mtt) REVERT: C 242 GLN cc_start: 0.8341 (mt0) cc_final: 0.8117 (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: 0.4932 time to fit residues: 218.8700 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 : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.146737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112421 restraints weight = 41509.015| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.95 r_work: 0.3190 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2232 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= 0.124 Angle : 0.477 5.317 17229 Z= 0.252 Chirality : 0.035 0.138 1991 Planarity : 0.003 0.046 2089 Dihedral : 10.217 165.530 1827 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.89 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.21), residues: 1593 helix: 2.64 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.35 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 184 HIS 0.002 0.001 HIS A 132 PHE 0.016 0.001 PHE C 413 TYR 0.011 0.001 TYR A 357 ARG 0.004 0.000 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.04541 ( 964) hydrogen bonds : angle 3.93705 ( 2850) covalent geometry : bond 0.00264 (12660) covalent geometry : angle 0.47739 (17229) *********************** 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 238 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TRP cc_start: 0.6606 (m100) cc_final: 0.6072 (m100) REVERT: A 264 LYS cc_start: 0.7796 (mttt) cc_final: 0.7524 (mtpt) REVERT: A 342 ASN cc_start: 0.8874 (t0) cc_final: 0.8579 (m-40) REVERT: A 428 MET cc_start: 0.7589 (mmt) cc_final: 0.7362 (mmt) REVERT: A 497 MET cc_start: 0.7795 (tmm) cc_final: 0.7461 (tmm) REVERT: B 158 GLU cc_start: 0.6904 (pm20) cc_final: 0.6660 (pm20) REVERT: B 202 LEU cc_start: 0.8753 (mp) cc_final: 0.8534 (mt) REVERT: B 242 GLN cc_start: 0.8462 (mt0) cc_final: 0.8130 (mt0) REVERT: B 349 GLU cc_start: 0.6512 (mp0) cc_final: 0.6194 (mm-30) REVERT: B 370 MET cc_start: 0.7908 (mtm) cc_final: 0.7572 (mtp) REVERT: B 458 VAL cc_start: 0.8364 (t) cc_final: 0.8050 (t) REVERT: B 485 GLN cc_start: 0.8396 (mp10) cc_final: 0.8048 (mp10) REVERT: B 503 MET cc_start: 0.9122 (mtp) cc_final: 0.8784 (mtp) REVERT: B 598 MET cc_start: 0.7803 (tpt) cc_final: 0.7508 (tpt) REVERT: C 219 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7389 (mp) REVERT: C 357 TYR cc_start: 0.8643 (m-80) cc_final: 0.8392 (m-80) outliers start: 17 outliers final: 10 residues processed: 229 average time/residue: 0.4452 time to fit residues: 155.8596 Evaluate side-chains 215 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 204 time to evaluate : 1.852 ------------------------------------------------------------------------------- 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 C residue 149 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 19 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 143 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.146116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.111690 restraints weight = 41565.621| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.94 r_work: 0.3184 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2608 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 : 0.448 5.063 17229 Z= 0.237 Chirality : 0.034 0.150 1991 Planarity : 0.003 0.046 2089 Dihedral : 8.663 123.479 1827 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.44 % Allowed : 8.46 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.21), residues: 1593 helix: 2.73 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.41 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 316 HIS 0.002 0.000 HIS A 288 PHE 0.016 0.001 PHE C 413 TYR 0.010 0.001 TYR B 231 ARG 0.001 0.000 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 964) hydrogen bonds : angle 3.78132 ( 2850) covalent geometry : bond 0.00268 (12660) covalent geometry : angle 0.44810 (17229) *********************** 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 221 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TRP cc_start: 0.6658 (m100) cc_final: 0.6075 (m100) REVERT: A 264 LYS cc_start: 0.7800 (mttt) cc_final: 0.7520 (mtpt) REVERT: A 342 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8580 (m-40) REVERT: A 428 MET cc_start: 0.7572 (mmt) cc_final: 0.7338 (mmt) REVERT: A 480 MET cc_start: 0.8150 (mmt) cc_final: 0.7704 (mmt) REVERT: A 497 MET cc_start: 0.7944 (tmm) cc_final: 0.7660 (tmm) REVERT: B 157 TYR cc_start: 0.7265 (m-10) cc_final: 0.7028 (m-80) REVERT: B 158 GLU cc_start: 0.6873 (pm20) cc_final: 0.6534 (pm20) REVERT: B 370 MET cc_start: 0.7922 (mtm) cc_final: 0.7573 (mtp) REVERT: B 458 VAL cc_start: 0.8402 (t) cc_final: 0.8086 (t) REVERT: B 598 MET cc_start: 0.7812 (tpt) cc_final: 0.7459 (tpt) REVERT: C 219 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7489 (mp) REVERT: C 257 MET cc_start: 0.7255 (ptt) cc_final: 0.6841 (ptp) REVERT: C 357 TYR cc_start: 0.8630 (m-80) cc_final: 0.8419 (m-80) outliers start: 18 outliers final: 12 residues processed: 213 average time/residue: 0.4352 time to fit residues: 142.7704 Evaluate side-chains 205 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 1.917 ------------------------------------------------------------------------------- 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 342 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 620 ASN 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 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 126 optimal weight: 1.9990 chunk 142 optimal weight: 0.0070 chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 86 optimal weight: 0.0270 chunk 75 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.146757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.112218 restraints weight = 41943.374| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.96 r_work: 0.3190 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12660 Z= 0.110 Angle : 0.434 5.068 17229 Z= 0.228 Chirality : 0.034 0.184 1991 Planarity : 0.003 0.045 2089 Dihedral : 7.712 84.671 1827 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.04 % Allowed : 9.18 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.21), residues: 1593 helix: 2.86 (0.14), residues: 1316 sheet: None (None), residues: 0 loop : -0.41 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.002 0.000 HIS A 288 PHE 0.014 0.001 PHE C 413 TYR 0.009 0.001 TYR A 553 ARG 0.002 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 964) hydrogen bonds : angle 3.66365 ( 2850) covalent geometry : bond 0.00240 (12660) covalent geometry : angle 0.43357 (17229) *********************** 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 214 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7786 (mttt) cc_final: 0.7509 (mtpt) REVERT: A 342 ASN cc_start: 0.8915 (t0) cc_final: 0.8648 (m-40) REVERT: A 428 MET cc_start: 0.7605 (mmt) cc_final: 0.7198 (mmt) REVERT: A 497 MET cc_start: 0.7978 (tmm) cc_final: 0.7715 (tmm) REVERT: A 613 CYS cc_start: 0.8126 (m) cc_final: 0.7734 (m) REVERT: B 157 TYR cc_start: 0.7356 (m-10) cc_final: 0.7150 (m-80) REVERT: B 158 GLU cc_start: 0.6988 (pm20) cc_final: 0.6459 (pm20) REVERT: B 370 MET cc_start: 0.7862 (mtm) cc_final: 0.7493 (mtp) REVERT: B 458 VAL cc_start: 0.8381 (t) cc_final: 0.8058 (t) REVERT: B 598 MET cc_start: 0.7803 (tpt) cc_final: 0.7386 (tpt) REVERT: C 219 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7595 (mp) REVERT: C 257 MET cc_start: 0.7193 (ptt) cc_final: 0.6805 (ptp) REVERT: C 485 GLN cc_start: 0.8325 (mp10) cc_final: 0.7892 (mp10) outliers start: 13 outliers final: 9 residues processed: 211 average time/residue: 0.4365 time to fit residues: 140.1606 Evaluate side-chains 204 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 583 THR 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 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 119 optimal weight: 0.4980 chunk 58 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.142428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107407 restraints weight = 42464.075| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.01 r_work: 0.3081 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12660 Z= 0.156 Angle : 0.468 5.095 17229 Z= 0.251 Chirality : 0.036 0.145 1991 Planarity : 0.004 0.047 2089 Dihedral : 7.883 88.390 1827 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.12 % Allowed : 9.74 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.21), residues: 1593 helix: 2.60 (0.14), residues: 1321 sheet: None (None), residues: 0 loop : -0.47 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 150 HIS 0.004 0.001 HIS A 288 PHE 0.020 0.001 PHE C 413 TYR 0.011 0.001 TYR A 357 ARG 0.002 0.000 ARG A 436 Details of bonding type rmsd hydrogen bonds : bond 0.04704 ( 964) hydrogen bonds : angle 3.81654 ( 2850) covalent geometry : bond 0.00364 (12660) covalent geometry : angle 0.46774 (17229) *********************** 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 214 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7784 (mttt) cc_final: 0.7468 (mtpt) REVERT: A 428 MET cc_start: 0.7534 (mmt) cc_final: 0.7143 (mmt) REVERT: B 158 GLU cc_start: 0.6965 (pm20) cc_final: 0.6362 (pm20) REVERT: B 370 MET cc_start: 0.7903 (mtm) cc_final: 0.7598 (mtp) REVERT: B 444 GLN cc_start: 0.7044 (mm-40) cc_final: 0.6473 (tt0) REVERT: B 503 MET cc_start: 0.9072 (mtp) cc_final: 0.8665 (mtp) REVERT: B 598 MET cc_start: 0.7910 (tpt) cc_final: 0.7498 (tpt) REVERT: C 219 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7526 (mp) REVERT: C 257 MET cc_start: 0.7270 (ptt) cc_final: 0.6882 (ptp) outliers start: 14 outliers final: 10 residues processed: 211 average time/residue: 0.4346 time to fit residues: 139.5261 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 : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 578 VAL Chi-restraints excluded: chain C residue 219 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 118 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.143066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.107564 restraints weight = 42566.608| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.06 r_work: 0.3071 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3396 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= 0.170 Angle : 0.480 5.153 17229 Z= 0.257 Chirality : 0.036 0.152 1991 Planarity : 0.004 0.047 2089 Dihedral : 7.684 87.462 1827 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.96 % Allowed : 10.93 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.21), residues: 1593 helix: 2.51 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -0.44 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 184 HIS 0.004 0.001 HIS A 288 PHE 0.018 0.001 PHE C 413 TYR 0.012 0.001 TYR A 357 ARG 0.003 0.000 ARG A 436 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 964) hydrogen bonds : angle 3.86897 ( 2850) covalent geometry : bond 0.00400 (12660) covalent geometry : angle 0.47961 (17229) *********************** 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 210 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 198 time to evaluate : 1.865 Fit side-chains revert: symmetry clash REVERT: A 132 HIS cc_start: 0.6549 (t70) cc_final: 0.5927 (m90) REVERT: A 264 LYS cc_start: 0.7908 (mttt) cc_final: 0.7594 (mtpt) REVERT: B 158 GLU cc_start: 0.7060 (pm20) cc_final: 0.6442 (pm20) REVERT: B 370 MET cc_start: 0.8017 (mtm) cc_final: 0.7758 (mtp) REVERT: B 444 GLN cc_start: 0.7204 (mm-40) cc_final: 0.6563 (tt0) REVERT: B 598 MET cc_start: 0.7918 (tpt) cc_final: 0.7549 (tpt) REVERT: C 219 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7535 (mp) REVERT: C 257 MET cc_start: 0.7282 (ptt) cc_final: 0.6896 (ptp) outliers start: 12 outliers final: 10 residues processed: 209 average time/residue: 0.4433 time to fit residues: 140.9986 Evaluate side-chains 201 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.143714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108405 restraints weight = 42278.055| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.05 r_work: 0.3091 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3515 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= 0.136 Angle : 0.455 5.280 17229 Z= 0.241 Chirality : 0.035 0.138 1991 Planarity : 0.004 0.049 2089 Dihedral : 7.429 82.422 1827 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.96 % Allowed : 11.49 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.21), residues: 1593 helix: 2.61 (0.15), residues: 1311 sheet: None (None), residues: 0 loop : -0.42 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 184 HIS 0.003 0.001 HIS A 288 PHE 0.014 0.001 PHE B 279 TYR 0.011 0.001 TYR A 357 ARG 0.001 0.000 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 964) hydrogen bonds : angle 3.76336 ( 2850) covalent geometry : bond 0.00312 (12660) covalent geometry : angle 0.45524 (17229) *********************** 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 205 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7822 (mttt) cc_final: 0.7509 (mtpt) REVERT: A 428 MET cc_start: 0.7416 (mmt) cc_final: 0.7128 (mmt) REVERT: B 158 GLU cc_start: 0.7145 (pm20) cc_final: 0.6512 (pm20) REVERT: B 370 MET cc_start: 0.7971 (mtm) cc_final: 0.7683 (mtp) REVERT: B 444 GLN cc_start: 0.7285 (mm-40) cc_final: 0.6717 (tt0) REVERT: B 598 MET cc_start: 0.7843 (tpt) cc_final: 0.7445 (tpt) REVERT: C 257 MET cc_start: 0.7428 (ptt) cc_final: 0.7065 (ptp) REVERT: C 485 GLN cc_start: 0.8571 (mp10) cc_final: 0.8158 (mp10) outliers start: 12 outliers final: 8 residues processed: 203 average time/residue: 0.4330 time to fit residues: 134.7533 Evaluate side-chains 198 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 190 time to evaluate : 1.836 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 112 optimal weight: 0.0030 chunk 158 optimal weight: 1.9990 chunk 24 optimal weight: 0.0370 chunk 10 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 155 optimal weight: 0.0980 chunk 70 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 overall best weight: 0.2868 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.147173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112611 restraints weight = 41708.044| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.00 r_work: 0.3155 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12660 Z= 0.088 Angle : 0.412 4.899 17229 Z= 0.214 Chirality : 0.034 0.131 1991 Planarity : 0.003 0.048 2089 Dihedral : 6.947 73.731 1827 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.64 % Allowed : 12.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.22), residues: 1593 helix: 2.95 (0.15), residues: 1318 sheet: None (None), residues: 0 loop : -0.46 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 184 HIS 0.002 0.000 HIS C 394 PHE 0.015 0.001 PHE B 279 TYR 0.010 0.001 TYR C 360 ARG 0.001 0.000 ARG C 251 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 964) hydrogen bonds : angle 3.48683 ( 2850) covalent geometry : bond 0.00184 (12660) covalent geometry : angle 0.41194 (17229) *********************** 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 206 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 198 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7738 (mttt) cc_final: 0.7464 (mtpt) REVERT: A 613 CYS cc_start: 0.7990 (m) cc_final: 0.7617 (m) REVERT: B 370 MET cc_start: 0.7737 (mtm) cc_final: 0.7373 (mtp) REVERT: B 598 MET cc_start: 0.7582 (tpt) cc_final: 0.7227 (tpt) REVERT: C 257 MET cc_start: 0.7254 (ptt) cc_final: 0.6882 (ptp) REVERT: C 485 GLN cc_start: 0.8300 (mp10) cc_final: 0.7938 (mp10) outliers start: 8 outliers final: 7 residues processed: 203 average time/residue: 0.4398 time to fit residues: 138.4746 Evaluate side-chains 194 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 187 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 178 TRP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 357 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain C residue 448 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3604 r_free = 0.3604 target = 0.138787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.104146 restraints weight = 42727.407| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.00 r_work: 0.3052 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12660 Z= 0.212 Angle : 0.522 6.623 17229 Z= 0.282 Chirality : 0.038 0.159 1991 Planarity : 0.004 0.048 2089 Dihedral : 7.692 86.821 1827 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.80 % Allowed : 12.69 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.21), residues: 1593 helix: 2.43 (0.14), residues: 1316 sheet: None (None), residues: 0 loop : -0.48 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 184 HIS 0.004 0.001 HIS C 288 PHE 0.023 0.002 PHE C 413 TYR 0.014 0.001 TYR A 357 ARG 0.003 0.001 ARG A 436 Details of bonding type rmsd hydrogen bonds : bond 0.05300 ( 964) hydrogen bonds : angle 3.94621 ( 2850) covalent geometry : bond 0.00506 (12660) covalent geometry : angle 0.52232 (17229) *********************** 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 203 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 193 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 HIS cc_start: 0.6540 (t70) cc_final: 0.5812 (m90) REVERT: A 264 LYS cc_start: 0.7950 (mttt) cc_final: 0.7630 (mtpt) REVERT: B 112 TRP cc_start: 0.5926 (t60) cc_final: 0.5524 (t-100) REVERT: B 158 GLU cc_start: 0.7287 (pm20) cc_final: 0.6677 (pm20) REVERT: B 370 MET cc_start: 0.8072 (mtm) cc_final: 0.7809 (mtp) REVERT: B 444 GLN cc_start: 0.7352 (mm-40) cc_final: 0.6774 (tt0) REVERT: B 503 MET cc_start: 0.9092 (mtp) cc_final: 0.8669 (mtp) REVERT: B 598 MET cc_start: 0.8013 (tpt) cc_final: 0.7650 (tpt) REVERT: C 257 MET cc_start: 0.7559 (ptt) cc_final: 0.7204 (ptp) outliers start: 10 outliers final: 10 residues processed: 201 average time/residue: 0.4246 time to fit residues: 130.6812 Evaluate side-chains 199 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 1.733 ------------------------------------------------------------------------------- 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 376 THR Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain B residue 578 VAL 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 78 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3631 r_free = 0.3631 target = 0.140835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106134 restraints weight = 42046.988| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.98 r_work: 0.3101 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12660 Z= 0.119 Angle : 0.450 5.715 17229 Z= 0.237 Chirality : 0.034 0.131 1991 Planarity : 0.003 0.047 2089 Dihedral : 7.282 78.889 1827 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.64 % Allowed : 13.09 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.21), residues: 1593 helix: 2.66 (0.15), residues: 1311 sheet: None (None), residues: 0 loop : -0.52 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 184 HIS 0.002 0.001 HIS A 288 PHE 0.015 0.001 PHE B 279 TYR 0.009 0.001 TYR A 357 ARG 0.001 0.000 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 964) hydrogen bonds : angle 3.70950 ( 2850) covalent geometry : bond 0.00267 (12660) covalent geometry : angle 0.45002 (17229) ********************** 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 203 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 195 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7866 (mttt) cc_final: 0.7564 (mtpt) REVERT: A 613 CYS cc_start: 0.8102 (m) cc_final: 0.7665 (m) REVERT: B 112 TRP cc_start: 0.5911 (t60) cc_final: 0.5570 (t-100) REVERT: B 158 GLU cc_start: 0.7356 (pm20) cc_final: 0.6746 (pm20) REVERT: B 370 MET cc_start: 0.7967 (mtm) cc_final: 0.7682 (mtp) REVERT: B 444 GLN cc_start: 0.7318 (mm-40) cc_final: 0.6790 (tt0) REVERT: B 598 MET cc_start: 0.7867 (tpt) cc_final: 0.7492 (tpt) REVERT: C 257 MET cc_start: 0.7466 (ptt) cc_final: 0.7110 (ptp) REVERT: C 485 GLN cc_start: 0.8526 (mp10) cc_final: 0.8153 (mp10) outliers start: 8 outliers final: 8 residues processed: 202 average time/residue: 0.4409 time to fit residues: 136.6721 Evaluate side-chains 199 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 191 time to evaluate : 1.892 ------------------------------------------------------------------------------- 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 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 154 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 106 optimal weight: 20.0000 chunk 133 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.139541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105225 restraints weight = 41991.005| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.96 r_work: 0.3093 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3811 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= 0.135 Angle : 0.461 6.295 17229 Z= 0.244 Chirality : 0.035 0.138 1991 Planarity : 0.003 0.049 2089 Dihedral : 7.280 79.135 1827 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.64 % Allowed : 13.17 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.21), residues: 1593 helix: 2.66 (0.15), residues: 1311 sheet: None (None), residues: 0 loop : -0.54 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 184 HIS 0.003 0.001 HIS A 288 PHE 0.017 0.001 PHE B 279 TYR 0.011 0.001 TYR A 357 ARG 0.001 0.000 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 964) hydrogen bonds : angle 3.72936 ( 2850) covalent geometry : bond 0.00309 (12660) covalent geometry : angle 0.46058 (17229) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11216.55 seconds wall clock time: 192 minutes 34.75 seconds (11554.75 seconds total)