Starting phenix.real_space_refine on Thu Aug 6 08:37:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g7u_29824/08_2026/8g7u_29824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7u_29824/08_2026/8g7u_29824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8g7u_29824/08_2026/8g7u_29824.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g7u_29824/08_2026/8g7u_29824.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g7u_29824/08_2026/8g7u_29824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7u_29824/08_2026/8g7u_29824.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7u_29824/08_2026/8g7u_29824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7u_29824/08_2026/8g7u_29824.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 Zn 2 6.06 5 P 52 5.49 5 S 80 5.16 5 C 8895 2.51 5 N 2424 2.21 5 O 2776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14229 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5234 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 619} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1424 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5115 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 27, 'TRANS': 603} Chain breaks: 3 Chain: "D" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1415 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 523 Unusual residues: {'GTP': 1} Classifications: {'RNAv2': 23, 'undetermined': 1} Modifications used: {'rna3p_pur': 12, 'rna3p_pyr': 11} Link IDs: {'rna3p': 22, None: 1} Not linked: pdbres="GTP X 1 " pdbres=" G X 2 " Chain: "Y" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 516 Unusual residues: {'UTP': 1} Classifications: {'RNAv2': 23, 'undetermined': 1} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 12} Link IDs: {'rna3p': 22, None: 1} Not linked: pdbres="UTP Y 1 " pdbres=" C Y 2 " Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4328 SG CYS A 813 90.632 21.520 41.450 1.00 83.84 S ATOM 4741 SG CYS A 864 87.352 22.632 37.635 1.00106.15 S ATOM 10849 SG CYS C 810 103.431 77.672 58.361 1.00 20.23 S ATOM 11288 SG CYS C 864 105.544 81.022 58.252 1.00 52.52 S ATOM 11327 SG CYS C 869 102.103 80.659 56.989 1.00 44.16 S Time building chain proxies: 2.69, per 1000 atoms: 0.19 Number of scatterers: 14229 At special positions: 0 Unit cell: (130.045, 117.46, 127.528, 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) Zn 2 29.99 S 80 16.00 P 52 15.00 O 2776 8.00 N 2424 7.00 C 8895 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 347 " - pdb=" SG CYS B 402 " distance=2.04 Simple disulfide: pdb=" SG CYS D 347 " - pdb=" SG CYS D 402 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 578.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 813 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 869 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 810 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 864 " 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3128 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 15 sheets defined 38.6% alpha, 11.3% beta 13 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 244 through 255 removed outlier: 5.188A pdb=" N LEU A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 267 through 284 Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 333 through 340 removed outlier: 4.008A pdb=" N ILE A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.723A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.748A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 381 through 395 Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 445 through 452 removed outlier: 3.907A pdb=" N VAL A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 487 removed outlier: 3.542A pdb=" N LYS A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 497 Processing helix chain 'A' and resid 506 through 521 Processing helix chain 'A' and resid 529 through 558 Processing helix chain 'A' and resid 559 through 578 removed outlier: 3.663A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 601 removed outlier: 4.155A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 607 removed outlier: 6.118A pdb=" N SER A 605 " --> pdb=" O ARG A 602 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 607 " --> pdb=" O PRO A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 637 through 648 removed outlier: 4.064A pdb=" N ASP A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 769 removed outlier: 4.322A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 794 Processing helix chain 'A' and resid 837 through 840 Processing helix chain 'A' and resid 889 through 892 Processing helix chain 'A' and resid 907 through 911 Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 251 through 256 Processing helix chain 'C' and resid 268 through 283 removed outlier: 3.836A pdb=" N LEU C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 315 removed outlier: 3.576A pdb=" N PHE C 314 " --> pdb=" O PHE C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 338 Processing helix chain 'C' and resid 348 through 357 Processing helix chain 'C' and resid 362 through 366 removed outlier: 3.861A pdb=" N ILE C 365 " --> pdb=" O SER C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 377 Processing helix chain 'C' and resid 381 through 395 Processing helix chain 'C' and resid 419 through 434 Processing helix chain 'C' and resid 445 through 450 Processing helix chain 'C' and resid 469 through 491 Processing helix chain 'C' and resid 492 through 496 Processing helix chain 'C' and resid 506 through 521 removed outlier: 3.900A pdb=" N GLU C 510 " --> pdb=" O THR C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 556 removed outlier: 3.890A pdb=" N ARG C 533 " --> pdb=" O ASP C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 576 removed outlier: 4.041A pdb=" N ALA C 563 " --> pdb=" O ARG C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 602 removed outlier: 3.905A pdb=" N LYS C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLN C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU C 596 " --> pdb=" O GLU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 625 removed outlier: 3.717A pdb=" N LEU C 624 " --> pdb=" O GLU C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 649 Processing helix chain 'C' and resid 746 through 769 Processing helix chain 'C' and resid 772 through 792 Processing helix chain 'C' and resid 836 through 840 removed outlier: 3.732A pdb=" N GLU C 840 " --> pdb=" O ALA C 837 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 261 through 263 removed outlier: 6.129A pdb=" N ILE A 262 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU A 408 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N PHE A 371 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL A 294 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ASP A 372 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE A 296 " --> pdb=" O ASP A 372 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 344 " --> pdb=" O VAL A 293 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 459 through 462 removed outlier: 6.495A pdb=" N VAL A 712 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU A 741 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU A 714 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 634 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 816 through 819 removed outlier: 3.942A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 831 through 833 removed outlier: 4.630A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 842 through 846 removed outlier: 4.174A pdb=" N ILE A 862 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A 874 " --> pdb=" O ILE A 862 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 280 through 282 removed outlier: 3.777A pdb=" N ILE B 426 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 301 through 302 removed outlier: 3.670A pdb=" N GLY B 328 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N TRP B 325 " --> pdb=" O TRP B 351 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TRP B 351 " --> pdb=" O TRP B 325 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 327 " --> pdb=" O VAL B 349 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 261 through 262 removed outlier: 6.552A pdb=" N VAL C 294 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ASP C 372 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE C 296 " --> pdb=" O ASP C 372 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 457 through 458 removed outlier: 6.822A pdb=" N GLN C 457 " --> pdb=" O CYS C 738 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 461 through 462 removed outlier: 3.915A pdb=" N THR C 742 " --> pdb=" O ARG C 461 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU C 714 " --> pdb=" O LEU C 741 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 659 through 660 removed outlier: 6.847A pdb=" N GLY C 659 " --> pdb=" O ILE C 695 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 816 through 819 removed outlier: 6.723A pdb=" N LEU C 808 " --> pdb=" O ALA C 817 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR C 819 " --> pdb=" O LYS C 806 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS C 806 " --> pdb=" O TYR C 819 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 809 " --> pdb=" O VAL C 893 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 823 through 825 removed outlier: 4.527A pdb=" N TYR C 831 " --> pdb=" O ILE C 887 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 833 " --> pdb=" O PRO C 885 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ASP C 872 " --> pdb=" O CYS C 864 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N CYS C 864 " --> pdb=" O ASP C 872 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY C 874 " --> pdb=" O ILE C 862 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS C 878 " --> pdb=" O LYS C 858 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LYS C 858 " --> pdb=" O LYS C 878 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 861 " --> pdb=" O ARG C 845 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 280 through 282 Processing sheet with id=AB6, first strand: chain 'D' and resid 301 through 303 removed outlier: 4.271A pdb=" N TRP D 325 " --> pdb=" O TRP D 351 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS D 347 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS D 348 " --> pdb=" O TRP D 360 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2223 1.29 - 1.43: 4050 1.43 - 1.56: 8152 1.56 - 1.69: 106 1.69 - 1.82: 108 Bond restraints: 14639 Sorted by residual: bond pdb=" C1' GTP X 1 " pdb=" C2' GTP X 1 " ideal model delta sigma weight residual 1.524 1.286 0.238 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C3' UTP Y 1 " pdb=" C4' UTP Y 1 " ideal model delta sigma weight residual 1.527 1.303 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C1' GTP X 1 " pdb=" O4' GTP X 1 " ideal model delta sigma weight residual 1.410 1.613 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C1' UTP Y 1 " pdb=" C2' UTP Y 1 " ideal model delta sigma weight residual 1.525 1.333 0.192 2.00e-02 2.50e+03 9.22e+01 bond pdb=" C5 GTP X 1 " pdb=" C6 GTP X 1 " ideal model delta sigma weight residual 1.390 1.544 -0.154 2.00e-02 2.50e+03 5.96e+01 ... (remaining 14634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 19299 2.39 - 4.78: 615 4.78 - 7.17: 72 7.17 - 9.57: 13 9.57 - 11.96: 8 Bond angle restraints: 20007 Sorted by residual: angle pdb=" CA VAL C 332 " pdb=" CB VAL C 332 " pdb=" CG1 VAL C 332 " ideal model delta sigma weight residual 110.40 117.42 -7.02 1.70e+00 3.46e-01 1.70e+01 angle pdb=" C ASP A 527 " pdb=" N LYS A 528 " pdb=" CA LYS A 528 " ideal model delta sigma weight residual 121.54 129.33 -7.79 1.91e+00 2.74e-01 1.66e+01 angle pdb=" O1A UTP Y 1 " pdb=" PA UTP Y 1 " pdb=" O2A UTP Y 1 " ideal model delta sigma weight residual 121.55 109.59 11.96 3.00e+00 1.11e-01 1.59e+01 angle pdb=" C GLN B 395 " pdb=" N GLU B 396 " pdb=" CA GLU B 396 " ideal model delta sigma weight residual 122.46 127.73 -5.27 1.41e+00 5.03e-01 1.40e+01 angle pdb=" O3A UTP Y 1 " pdb=" PB UTP Y 1 " pdb=" O3B UTP Y 1 " ideal model delta sigma weight residual 98.89 109.60 -10.71 3.00e+00 1.11e-01 1.27e+01 ... (remaining 20002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7598 17.94 - 35.88: 921 35.88 - 53.82: 206 53.82 - 71.76: 33 71.76 - 89.71: 16 Dihedral angle restraints: 8774 sinusoidal: 3968 harmonic: 4806 Sorted by residual: dihedral pdb=" O5' C Y 5 " pdb=" C5' C Y 5 " pdb=" C4' C Y 5 " pdb=" C3' C Y 5 " ideal model delta sinusoidal sigma weight residual 60.00 107.06 -47.06 3 6.40e+00 2.44e-02 4.63e+01 dihedral pdb=" O5' C Y 23 " pdb=" C5' C Y 23 " pdb=" C4' C Y 23 " pdb=" C3' C Y 23 " ideal model delta sinusoidal sigma weight residual 60.00 106.96 -46.96 3 6.40e+00 2.44e-02 4.62e+01 dihedral pdb=" O5' G Y 12 " pdb=" C5' G Y 12 " pdb=" C4' G Y 12 " pdb=" C3' G Y 12 " ideal model delta sinusoidal sigma weight residual 180.00 135.10 44.90 3 6.40e+00 2.44e-02 4.44e+01 ... (remaining 8771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1604 0.057 - 0.115: 462 0.115 - 0.172: 107 0.172 - 0.230: 54 0.230 - 0.287: 17 Chirality restraints: 2244 Sorted by residual: chirality pdb=" CB VAL A 522 " pdb=" CA VAL A 522 " pdb=" CG1 VAL A 522 " pdb=" CG2 VAL A 522 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB VAL C 332 " pdb=" CA VAL C 332 " pdb=" CG1 VAL C 332 " pdb=" CG2 VAL C 332 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" P G Y 21 " pdb=" OP1 G Y 21 " pdb=" OP2 G Y 21 " pdb=" O5' G Y 21 " both_signs ideal model delta sigma weight residual True 2.17 -2.44 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2241 not shown) Planarity restraints: 2362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 261 " 0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C ILE A 261 " -0.065 2.00e-02 2.50e+03 pdb=" O ILE A 261 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE A 262 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 381 " 0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO C 382 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 382 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 382 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 286 " -0.044 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO D 287 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 287 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 287 " -0.036 5.00e-02 4.00e+02 ... (remaining 2359 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 189 2.62 - 3.19: 11819 3.19 - 3.76: 22936 3.76 - 4.33: 29317 4.33 - 4.90: 47100 Nonbonded interactions: 111361 Sorted by model distance: nonbonded pdb=" O2' UTP Y 1 " pdb=" OP2 C Y 2 " model vdw 2.056 3.040 nonbonded pdb=" C3' GTP X 1 " pdb=" OP2 G X 2 " model vdw 2.058 2.776 nonbonded pdb=" O2' UTP Y 1 " pdb=" P C Y 2 " model vdw 2.068 3.400 nonbonded pdb=" OG SER C 698 " pdb=" OH TYR C 717 " model vdw 2.234 3.040 nonbonded pdb=" O SER C 855 " pdb=" OG SER C 855 " model vdw 2.288 3.040 ... (remaining 111356 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 241 through 661 or resid 690 through 699 or resid 709 thro \ ugh 718 or resid 734 through 922 or resid 1001)) selection = (chain 'C' and resid 241 through 1001) } ncs_group { reference = (chain 'B' and (resid 252 through 343 or (resid 344 and (name N or name CA or na \ me C or name O or name CB )) or resid 345 through 360 or resid 364 through 430)) \ selection = (chain 'D' and (resid 252 through 360 or resid 364 through 430)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 13.960 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 0.400 14648 Z= 0.429 Angle : 0.996 11.958 20011 Z= 0.515 Chirality : 0.065 0.287 2244 Planarity : 0.007 0.083 2362 Dihedral : 16.296 89.706 5640 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.61 % Allowed : 12.24 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.99 (0.17), residues: 1610 helix: -1.95 (0.16), residues: 584 sheet: -2.69 (0.29), residues: 288 loop : -3.18 (0.19), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 559 TYR 0.019 0.002 TYR D 400 PHE 0.029 0.003 PHE A 842 TRP 0.017 0.002 TRP C 908 HIS 0.012 0.002 HIS C 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00843 / 0.40 (14639) covalent geometry : angle 0.99623 / 0.51 (20007) SS BOND : bond 0.00935 / 0.45 ( 2) SS BOND : angle 0.93874 / 0.53 ( 4) hydrogen bonds : bond 0.16225 / 10.73 ( 563) hydrogen bonds : angle 7.39294 / 5.07 ( 1592) metal coordination : bond 0.24235 / 11.95 ( 5) Misc. bond : bond 0.05378 / 2.71 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 216 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 713 ILE cc_start: 0.7695 (mp) cc_final: 0.7262 (mp) REVERT: A 760 MET cc_start: 0.4704 (ppp) cc_final: 0.3432 (ppp) REVERT: B 324 HIS cc_start: 0.6566 (m-70) cc_final: 0.6107 (m-70) REVERT: D 277 ASP cc_start: 0.8343 (p0) cc_final: 0.8142 (p0) REVERT: D 379 TRP cc_start: 0.7373 (t60) cc_final: 0.6871 (t60) REVERT: D 411 TYR cc_start: 0.8320 (m-80) cc_final: 0.8074 (m-80) outliers start: 9 outliers final: 5 residues processed: 224 average time/residue: 0.1229 time to fit residues: 38.8974 Evaluate side-chains 142 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain D residue 363 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 40.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 GLN A 305 GLN A 389 ASN A 606 ASN A 752 GLN B 256 GLN B 324 HIS B 429 GLN C 259 ASN C 287 GLN C 306 GLN ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 GLN C 619 GLN C 769 GLN C 830 HIS D 264 ASN D 381 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.137680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.113949 restraints weight = 37922.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.114712 restraints weight = 46771.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.115190 restraints weight = 38891.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.115808 restraints weight = 24308.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.116330 restraints weight = 21414.175| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14648 Z= 0.148 Angle : 0.675 11.681 20011 Z= 0.331 Chirality : 0.047 0.480 2244 Planarity : 0.005 0.061 2362 Dihedral : 9.799 85.110 2350 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.52 % Allowed : 16.79 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.20), residues: 1610 helix: 0.00 (0.20), residues: 585 sheet: -2.51 (0.29), residues: 275 loop : -2.85 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 502 TYR 0.017 0.001 TYR C 426 PHE 0.013 0.001 PHE A 853 TRP 0.014 0.001 TRP C 512 HIS 0.004 0.001 HIS D 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (14639) covalent geometry : angle 0.67454 / 0.33 (20007) SS BOND : bond 0.00231 / 0.12 ( 2) SS BOND : angle 1.08562 / 0.84 ( 4) hydrogen bonds : bond 0.04563 / 3.01 ( 563) hydrogen bonds : angle 5.28245 / 3.62 ( 1592) metal coordination : bond 0.00156 / 0.08 ( 5) Misc. bond : bond 0.00098 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 LYS cc_start: 0.2659 (OUTLIER) cc_final: 0.2049 (tptp) REVERT: A 525 MET cc_start: 0.5823 (ttt) cc_final: 0.5564 (tmm) REVERT: A 755 MET cc_start: 0.4290 (tmm) cc_final: 0.3116 (tpt) REVERT: A 760 MET cc_start: 0.4771 (ppp) cc_final: 0.3757 (ppp) REVERT: B 324 HIS cc_start: 0.6758 (m90) cc_final: 0.6500 (m90) REVERT: C 457 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7752 (pt0) REVERT: C 698 SER cc_start: 0.8113 (m) cc_final: 0.7818 (p) REVERT: D 277 ASP cc_start: 0.8553 (p0) cc_final: 0.8303 (p0) REVERT: D 297 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.6928 (m-10) REVERT: D 316 GLU cc_start: 0.6620 (tt0) cc_final: 0.6244 (tt0) REVERT: D 379 TRP cc_start: 0.7623 (t60) cc_final: 0.7213 (t60) REVERT: D 428 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6674 (pptt) outliers start: 37 outliers final: 23 residues processed: 197 average time/residue: 0.1068 time to fit residues: 31.1754 Evaluate side-chains 161 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 525 MET Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 297 PHE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 428 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 96 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 429 GLN C 281 HIS ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 868 ASN D 338 GLN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.137837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.116384 restraints weight = 38012.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.116669 restraints weight = 45429.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.117070 restraints weight = 41474.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.117691 restraints weight = 25735.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.118095 restraints weight = 22246.472| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14648 Z= 0.133 Angle : 0.625 11.021 20011 Z= 0.305 Chirality : 0.046 0.461 2244 Planarity : 0.004 0.054 2362 Dihedral : 9.485 87.091 2350 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.47 % Allowed : 17.81 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.20), residues: 1610 helix: 0.78 (0.21), residues: 589 sheet: -2.27 (0.30), residues: 263 loop : -2.65 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 811 TYR 0.012 0.001 TYR D 424 PHE 0.030 0.001 PHE C 892 TRP 0.012 0.001 TRP C 512 HIS 0.004 0.001 HIS D 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (14639) covalent geometry : angle 0.62437 / 0.30 (20007) SS BOND : bond 0.00678 / 0.32 ( 2) SS BOND : angle 1.54552 / 1.24 ( 4) hydrogen bonds : bond 0.04137 / 2.70 ( 563) hydrogen bonds : angle 4.85215 / 3.33 ( 1592) metal coordination : bond 0.00365 / 0.18 ( 5) Misc. bond : bond 0.00035 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 0.331 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: A 262 ILE cc_start: 0.5567 (OUTLIER) cc_final: 0.5251 (tp) REVERT: A 369 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7735 (mtt) REVERT: A 434 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8859 (tt) REVERT: A 462 LYS cc_start: 0.2776 (OUTLIER) cc_final: 0.2084 (tptp) REVERT: A 521 MET cc_start: 0.7064 (mtp) cc_final: 0.6678 (mtp) REVERT: A 760 MET cc_start: 0.4825 (ppp) cc_final: 0.3889 (ppp) REVERT: B 324 HIS cc_start: 0.6711 (m90) cc_final: 0.6442 (m90) REVERT: B 420 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.7012 (t-90) REVERT: C 282 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8664 (mm) REVERT: C 372 ASP cc_start: 0.8692 (t0) cc_final: 0.8397 (t0) REVERT: C 457 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7803 (pt0) REVERT: C 523 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.7031 (m-80) REVERT: C 611 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8910 (mp) REVERT: C 857 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6793 (mm-30) REVERT: D 277 ASP cc_start: 0.8437 (p0) cc_final: 0.8208 (p0) REVERT: D 297 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.6795 (m-80) REVERT: D 301 GLN cc_start: 0.8550 (mt0) cc_final: 0.7655 (pt0) REVERT: D 316 GLU cc_start: 0.6797 (tt0) cc_final: 0.6242 (tt0) REVERT: D 338 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8452 (mm110) REVERT: D 379 TRP cc_start: 0.7562 (t60) cc_final: 0.6764 (t60) REVERT: D 404 ILE cc_start: 0.4799 (OUTLIER) cc_final: 0.4481 (tp) REVERT: D 428 LYS cc_start: 0.7401 (pptt) cc_final: 0.6801 (pptt) outliers start: 51 outliers final: 30 residues processed: 202 average time/residue: 0.1018 time to fit residues: 30.9088 Evaluate side-chains 186 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 297 PHE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 416 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 45 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 155 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.137039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.115569 restraints weight = 37883.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.116003 restraints weight = 45141.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.116556 restraints weight = 39155.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.116890 restraints weight = 26509.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.117451 restraints weight = 22965.730| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14648 Z= 0.152 Angle : 0.647 11.676 20011 Z= 0.312 Chirality : 0.046 0.424 2244 Planarity : 0.004 0.053 2362 Dihedral : 9.331 86.406 2350 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 4.01 % Allowed : 19.17 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.21), residues: 1610 helix: 1.04 (0.21), residues: 592 sheet: -2.18 (0.30), residues: 262 loop : -2.46 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 811 TYR 0.014 0.001 TYR C 548 PHE 0.019 0.001 PHE C 892 TRP 0.010 0.001 TRP C 512 HIS 0.005 0.001 HIS D 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (14639) covalent geometry : angle 0.64722 / 0.31 (20007) SS BOND : bond 0.00434 / 0.21 ( 2) SS BOND : angle 1.33015 / 1.05 ( 4) hydrogen bonds : bond 0.04066 / 2.65 ( 563) hydrogen bonds : angle 4.74027 / 3.24 ( 1592) metal coordination : bond 0.00329 / 0.17 ( 5) Misc. bond : bond 0.00028 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 154 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7654 (mtt) REVERT: A 462 LYS cc_start: 0.2840 (OUTLIER) cc_final: 0.2144 (tptp) REVERT: A 755 MET cc_start: 0.4020 (tmm) cc_final: 0.3072 (ptp) REVERT: A 760 MET cc_start: 0.4740 (ppp) cc_final: 0.3858 (ppp) REVERT: B 324 HIS cc_start: 0.6573 (m90) cc_final: 0.6291 (m90) REVERT: B 420 HIS cc_start: 0.7643 (OUTLIER) cc_final: 0.7088 (t-90) REVERT: C 372 ASP cc_start: 0.8727 (t0) cc_final: 0.8488 (t0) REVERT: C 434 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9217 (mp) REVERT: C 457 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7768 (pt0) REVERT: C 611 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8930 (mp) REVERT: C 612 GLU cc_start: 0.7242 (tm-30) cc_final: 0.7019 (tm-30) REVERT: D 277 ASP cc_start: 0.8364 (p0) cc_final: 0.8138 (p0) REVERT: D 297 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.7139 (m-10) REVERT: D 338 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8649 (tp40) REVERT: D 379 TRP cc_start: 0.7640 (t60) cc_final: 0.6758 (t60) outliers start: 59 outliers final: 40 residues processed: 198 average time/residue: 0.0979 time to fit residues: 28.8752 Evaluate side-chains 188 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 297 PHE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 428 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 115 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 557 HIS ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 GLN ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.135796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.112573 restraints weight = 37726.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.112646 restraints weight = 49173.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.113307 restraints weight = 43769.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.114069 restraints weight = 28206.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.114370 restraints weight = 25557.124| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14648 Z= 0.188 Angle : 0.678 10.596 20011 Z= 0.326 Chirality : 0.047 0.413 2244 Planarity : 0.004 0.052 2362 Dihedral : 9.328 84.771 2350 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 5.03 % Allowed : 18.42 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.21), residues: 1610 helix: 1.12 (0.21), residues: 591 sheet: -1.97 (0.32), residues: 249 loop : -2.43 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 811 TYR 0.013 0.001 TYR C 548 PHE 0.018 0.002 PHE A 633 TRP 0.008 0.001 TRP C 908 HIS 0.004 0.001 HIS D 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (14639) covalent geometry : angle 0.67762 / 0.33 (20007) SS BOND : bond 0.00508 / 0.24 ( 2) SS BOND : angle 1.37341 / 1.17 ( 4) hydrogen bonds : bond 0.04219 / 2.75 ( 563) hydrogen bonds : angle 4.81015 / 3.28 ( 1592) metal coordination : bond 0.00434 / 0.22 ( 5) Misc. bond : bond 0.00031 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 149 time to evaluate : 0.351 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 262 ILE cc_start: 0.5560 (OUTLIER) cc_final: 0.5234 (tp) REVERT: A 369 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7570 (mtt) REVERT: A 462 LYS cc_start: 0.2668 (OUTLIER) cc_final: 0.1929 (tptp) REVERT: A 760 MET cc_start: 0.4716 (ppp) cc_final: 0.3844 (ppp) REVERT: A 853 PHE cc_start: 0.5801 (OUTLIER) cc_final: 0.5440 (p90) REVERT: B 324 HIS cc_start: 0.6737 (m90) cc_final: 0.6502 (m90) REVERT: B 420 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.7167 (t-90) REVERT: C 434 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9230 (mp) REVERT: C 457 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7737 (pt0) REVERT: C 611 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8988 (mp) REVERT: C 612 GLU cc_start: 0.7351 (tm-30) cc_final: 0.7120 (tm-30) REVERT: D 277 ASP cc_start: 0.8453 (p0) cc_final: 0.8229 (p0) REVERT: D 299 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8957 (m) REVERT: D 338 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8665 (tp40) REVERT: D 379 TRP cc_start: 0.7814 (t60) cc_final: 0.6823 (t60) REVERT: D 404 ILE cc_start: 0.4853 (OUTLIER) cc_final: 0.4641 (tp) outliers start: 74 outliers final: 50 residues processed: 210 average time/residue: 0.0987 time to fit residues: 31.0350 Evaluate side-chains 197 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 137 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 428 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 130 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 134 optimal weight: 0.2980 chunk 121 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 30.0000 chunk 20 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 507 GLN A 549 ASN ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 GLN D 301 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.138932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.114410 restraints weight = 37781.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.116178 restraints weight = 36506.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.116166 restraints weight = 30369.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.116800 restraints weight = 19398.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.117206 restraints weight = 17083.493| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14648 Z= 0.110 Angle : 0.617 10.992 20011 Z= 0.296 Chirality : 0.045 0.412 2244 Planarity : 0.004 0.051 2362 Dihedral : 9.151 85.880 2350 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.35 % Allowed : 19.78 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.21), residues: 1610 helix: 1.42 (0.21), residues: 591 sheet: -1.98 (0.31), residues: 261 loop : -2.32 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 811 TYR 0.017 0.001 TYR C 548 PHE 0.016 0.001 PHE C 892 TRP 0.016 0.001 TRP C 512 HIS 0.003 0.001 HIS D 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (14639) covalent geometry : angle 0.61717 / 0.30 (20007) SS BOND : bond 0.00328 / 0.16 ( 2) SS BOND : angle 0.99770 / 0.73 ( 4) hydrogen bonds : bond 0.03769 / 2.44 ( 563) hydrogen bonds : angle 4.46722 / 3.04 ( 1592) metal coordination : bond 0.00246 / 0.12 ( 5) Misc. bond : bond 0.00025 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 163 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ILE cc_start: 0.5555 (OUTLIER) cc_final: 0.5231 (tp) REVERT: A 266 THR cc_start: 0.5720 (OUTLIER) cc_final: 0.5196 (p) REVERT: A 369 MET cc_start: 0.8250 (mmm) cc_final: 0.7595 (mtt) REVERT: A 462 LYS cc_start: 0.2521 (OUTLIER) cc_final: 0.1962 (tptp) REVERT: A 525 MET cc_start: 0.5216 (tmm) cc_final: 0.4929 (tmm) REVERT: A 711 LEU cc_start: 0.5897 (mt) cc_final: 0.5640 (mt) REVERT: A 760 MET cc_start: 0.4597 (ppp) cc_final: 0.3780 (ppp) REVERT: A 772 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7020 (m-30) REVERT: B 387 LEU cc_start: 0.5222 (mt) cc_final: 0.5001 (mt) REVERT: B 420 HIS cc_start: 0.7722 (OUTLIER) cc_final: 0.7209 (t-90) REVERT: C 434 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9229 (mp) REVERT: C 612 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7250 (tm-30) REVERT: D 303 LEU cc_start: 0.8778 (mm) cc_final: 0.8558 (mm) REVERT: D 338 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8558 (mm110) outliers start: 64 outliers final: 41 residues processed: 211 average time/residue: 0.0853 time to fit residues: 27.3414 Evaluate side-chains 192 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 145 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 416 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 15 optimal weight: 0.0470 chunk 152 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.138669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.113871 restraints weight = 37594.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.114701 restraints weight = 35089.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.115278 restraints weight = 27975.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.115405 restraints weight = 19615.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.115859 restraints weight = 17636.561| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14648 Z= 0.128 Angle : 0.632 12.822 20011 Z= 0.304 Chirality : 0.045 0.389 2244 Planarity : 0.004 0.048 2362 Dihedral : 9.092 83.781 2349 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 4.08 % Allowed : 20.26 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.21), residues: 1610 helix: 1.48 (0.21), residues: 590 sheet: -1.81 (0.32), residues: 249 loop : -2.28 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 824 TYR 0.017 0.001 TYR C 548 PHE 0.015 0.001 PHE C 892 TRP 0.014 0.001 TRP D 257 HIS 0.004 0.001 HIS D 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (14639) covalent geometry : angle 0.63238 / 0.30 (20007) SS BOND : bond 0.00365 / 0.18 ( 2) SS BOND : angle 1.03781 / 0.78 ( 4) hydrogen bonds : bond 0.03819 / 2.49 ( 563) hydrogen bonds : angle 4.47191 / 3.05 ( 1592) metal coordination : bond 0.00310 / 0.16 ( 5) Misc. bond : bond 0.00020 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 156 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ILE cc_start: 0.5607 (OUTLIER) cc_final: 0.5290 (tp) REVERT: A 266 THR cc_start: 0.5767 (OUTLIER) cc_final: 0.5243 (p) REVERT: A 369 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7805 (mtt) REVERT: A 517 GLN cc_start: 0.7371 (tm-30) cc_final: 0.7125 (tm-30) REVERT: A 525 MET cc_start: 0.5286 (tmm) cc_final: 0.4968 (tmm) REVERT: A 711 LEU cc_start: 0.5905 (mt) cc_final: 0.5570 (mt) REVERT: A 760 MET cc_start: 0.4762 (ppp) cc_final: 0.3978 (ppp) REVERT: A 772 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7054 (m-30) REVERT: A 853 PHE cc_start: 0.5786 (OUTLIER) cc_final: 0.5579 (p90) REVERT: B 266 LYS cc_start: 0.7085 (mmmt) cc_final: 0.6547 (tptt) REVERT: B 420 HIS cc_start: 0.7744 (OUTLIER) cc_final: 0.7249 (t-90) REVERT: C 434 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9266 (mp) REVERT: C 457 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7835 (pt0) REVERT: C 612 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7232 (tm-30) REVERT: D 338 GLN cc_start: 0.8953 (mm-40) cc_final: 0.8571 (mm110) outliers start: 60 outliers final: 46 residues processed: 203 average time/residue: 0.1174 time to fit residues: 36.1154 Evaluate side-chains 198 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 144 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 428 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 106 optimal weight: 0.2980 chunk 90 optimal weight: 0.0770 chunk 64 optimal weight: 30.0000 chunk 71 optimal weight: 40.0000 chunk 32 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 overall best weight: 1.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 GLN ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 ASN ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.139184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.114258 restraints weight = 37604.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.117309 restraints weight = 34406.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.116602 restraints weight = 25208.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.116792 restraints weight = 17810.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.117088 restraints weight = 15643.821| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14648 Z= 0.123 Angle : 0.638 14.274 20011 Z= 0.306 Chirality : 0.045 0.377 2244 Planarity : 0.004 0.048 2362 Dihedral : 9.002 83.677 2349 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.28 % Allowed : 20.67 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.21), residues: 1610 helix: 1.55 (0.21), residues: 591 sheet: -1.85 (0.32), residues: 255 loop : -2.19 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 824 TYR 0.022 0.001 TYR C 548 PHE 0.016 0.001 PHE C 892 TRP 0.012 0.001 TRP C 512 HIS 0.003 0.001 HIS D 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (14639) covalent geometry : angle 0.63820 / 0.31 (20007) SS BOND : bond 0.00341 / 0.17 ( 2) SS BOND : angle 1.02706 / 0.74 ( 4) hydrogen bonds : bond 0.03812 / 2.47 ( 563) hydrogen bonds : angle 4.42091 / 3.01 ( 1592) metal coordination : bond 0.00268 / 0.13 ( 5) Misc. bond : bond 0.00023 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 152 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ILE cc_start: 0.5598 (OUTLIER) cc_final: 0.5277 (tp) REVERT: A 266 THR cc_start: 0.5751 (OUTLIER) cc_final: 0.5249 (p) REVERT: A 369 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7804 (mtt) REVERT: A 465 SER cc_start: 0.9024 (t) cc_final: 0.8343 (m) REVERT: A 517 GLN cc_start: 0.7488 (tm-30) cc_final: 0.7235 (tm-30) REVERT: A 711 LEU cc_start: 0.5857 (mt) cc_final: 0.5534 (mt) REVERT: A 760 MET cc_start: 0.4799 (ppp) cc_final: 0.4156 (ppp) REVERT: A 772 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7075 (m-30) REVERT: B 266 LYS cc_start: 0.7041 (mmmt) cc_final: 0.6510 (tptt) REVERT: B 357 LEU cc_start: 0.6819 (tp) cc_final: 0.5549 (mp) REVERT: B 420 HIS cc_start: 0.7710 (OUTLIER) cc_final: 0.7261 (t-90) REVERT: C 434 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9257 (mp) REVERT: C 457 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7850 (pt0) REVERT: C 479 MET cc_start: 0.8679 (ttm) cc_final: 0.8459 (mmm) REVERT: C 612 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7291 (tm-30) REVERT: D 303 LEU cc_start: 0.8819 (mm) cc_final: 0.8580 (mm) REVERT: D 316 GLU cc_start: 0.6964 (tt0) cc_final: 0.6604 (tt0) REVERT: D 338 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8529 (mm110) REVERT: D 428 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6823 (pptt) outliers start: 63 outliers final: 45 residues processed: 201 average time/residue: 0.1060 time to fit residues: 33.2303 Evaluate side-chains 197 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 428 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 12 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 46 optimal weight: 0.2980 chunk 146 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 137 optimal weight: 0.3980 chunk 142 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 30.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 GLN C 619 GLN D 288 GLN D 301 GLN D 356 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.140418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.115299 restraints weight = 37483.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.117090 restraints weight = 35655.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.117172 restraints weight = 29733.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.118116 restraints weight = 19371.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.118291 restraints weight = 16817.699| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14648 Z= 0.107 Angle : 0.630 10.595 20011 Z= 0.303 Chirality : 0.045 0.375 2244 Planarity : 0.004 0.047 2362 Dihedral : 8.899 84.023 2349 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.74 % Allowed : 21.21 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.22), residues: 1610 helix: 1.69 (0.21), residues: 585 sheet: -1.63 (0.32), residues: 261 loop : -2.08 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 824 TYR 0.023 0.001 TYR C 548 PHE 0.016 0.001 PHE C 892 TRP 0.015 0.001 TRP C 512 HIS 0.003 0.001 HIS D 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (14639) covalent geometry : angle 0.63008 / 0.30 (20007) SS BOND : bond 0.00283 / 0.14 ( 2) SS BOND : angle 0.98802 / 0.69 ( 4) hydrogen bonds : bond 0.03712 / 2.40 ( 563) hydrogen bonds : angle 4.34652 / 2.96 ( 1592) metal coordination : bond 0.00229 / 0.11 ( 5) Misc. bond : bond 0.00023 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 159 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ILE cc_start: 0.5516 (OUTLIER) cc_final: 0.5183 (tp) REVERT: A 266 THR cc_start: 0.5552 (OUTLIER) cc_final: 0.5067 (p) REVERT: A 369 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7527 (mtt) REVERT: A 465 SER cc_start: 0.8984 (t) cc_final: 0.8314 (m) REVERT: A 525 MET cc_start: 0.5268 (tmm) cc_final: 0.5038 (tmm) REVERT: A 711 LEU cc_start: 0.5756 (mt) cc_final: 0.5509 (mt) REVERT: A 760 MET cc_start: 0.4806 (ppp) cc_final: 0.4147 (ppp) REVERT: A 772 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7016 (m-30) REVERT: B 357 LEU cc_start: 0.6660 (tp) cc_final: 0.5509 (mp) REVERT: B 420 HIS cc_start: 0.7692 (OUTLIER) cc_final: 0.7263 (t-90) REVERT: C 434 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9265 (mp) REVERT: C 457 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7814 (pt0) REVERT: C 612 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7144 (tm-30) REVERT: D 303 LEU cc_start: 0.8763 (mm) cc_final: 0.8517 (mm) REVERT: D 316 GLU cc_start: 0.6852 (tt0) cc_final: 0.6587 (tt0) REVERT: D 320 ARG cc_start: 0.7908 (ttm110) cc_final: 0.7531 (mtm-85) REVERT: D 338 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8490 (mm110) REVERT: D 428 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6598 (pptt) outliers start: 55 outliers final: 41 residues processed: 197 average time/residue: 0.1054 time to fit residues: 32.3464 Evaluate side-chains 193 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 847 HIS Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 288 GLN Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 428 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 123 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 1 optimal weight: 0.0050 chunk 69 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 overall best weight: 3.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 GLN C 280 HIS C 619 GLN D 256 GLN ** D 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.136378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.114187 restraints weight = 37512.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.113902 restraints weight = 54052.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.114779 restraints weight = 43928.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.115816 restraints weight = 27307.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.116166 restraints weight = 23425.656| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14648 Z= 0.212 Angle : 0.736 12.120 20011 Z= 0.353 Chirality : 0.047 0.358 2244 Planarity : 0.004 0.047 2362 Dihedral : 9.055 80.792 2349 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 4.08 % Allowed : 21.62 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.22), residues: 1610 helix: 1.44 (0.21), residues: 590 sheet: -1.90 (0.31), residues: 268 loop : -2.13 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 824 TYR 0.016 0.002 TYR C 548 PHE 0.028 0.002 PHE D 254 TRP 0.012 0.001 TRP D 315 HIS 0.005 0.001 HIS D 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (14639) covalent geometry : angle 0.73542 / 0.35 (20007) SS BOND : bond 0.00578 / 0.28 ( 2) SS BOND : angle 1.40263 / 1.10 ( 4) hydrogen bonds : bond 0.04338 / 2.84 ( 563) hydrogen bonds : angle 4.68332 / 3.19 ( 1592) metal coordination : bond 0.00433 / 0.22 ( 5) Misc. bond : bond 0.00034 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 143 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ILE cc_start: 0.5685 (OUTLIER) cc_final: 0.5369 (tp) REVERT: A 266 THR cc_start: 0.5765 (OUTLIER) cc_final: 0.5212 (p) REVERT: A 369 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7439 (mtt) REVERT: A 525 MET cc_start: 0.5379 (tmm) cc_final: 0.5166 (tmm) REVERT: A 760 MET cc_start: 0.5018 (ppp) cc_final: 0.4246 (ppp) REVERT: B 266 LYS cc_start: 0.7170 (mmmt) cc_final: 0.6684 (tptt) REVERT: B 420 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7222 (t-90) REVERT: C 434 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9263 (mp) REVERT: C 457 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7880 (pt0) REVERT: C 503 GLU cc_start: 0.8161 (pm20) cc_final: 0.7943 (pm20) REVERT: D 316 GLU cc_start: 0.6778 (tt0) cc_final: 0.6566 (tt0) REVERT: D 320 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7660 (mtm-85) REVERT: D 338 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8523 (tp40) REVERT: D 428 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6752 (pptt) outliers start: 60 outliers final: 45 residues processed: 192 average time/residue: 0.1080 time to fit residues: 32.1417 Evaluate side-chains 192 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 140 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain D residue 256 GLN Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 428 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 138 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 GLN ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 423 ASN ** 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 = 0.4059 r_free = 0.4059 target = 0.136370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.115022 restraints weight = 37587.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.115283 restraints weight = 57166.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.115994 restraints weight = 44567.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.117186 restraints weight = 27676.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.117538 restraints weight = 22562.191| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.276 14648 Z= 0.342 Angle : 1.139 59.200 20011 Z= 0.660 Chirality : 0.051 0.762 2244 Planarity : 0.005 0.148 2362 Dihedral : 9.054 80.815 2349 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 3.74 % Allowed : 22.03 % Favored : 74.24 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.21), residues: 1610 helix: 1.42 (0.21), residues: 590 sheet: -1.85 (0.31), residues: 266 loop : -2.13 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 824 TYR 0.025 0.002 TYR C 548 PHE 0.023 0.002 PHE D 254 TRP 0.011 0.001 TRP D 315 HIS 0.004 0.001 HIS D 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00723 / 0.34 (14639) covalent geometry : angle 1.13941 / 0.66 (20007) SS BOND : bond 0.00572 / 0.27 ( 2) SS BOND : angle 1.38618 / 1.08 ( 4) hydrogen bonds : bond 0.04329 / 2.83 ( 563) hydrogen bonds : angle 4.68023 / 3.19 ( 1592) metal coordination : bond 0.00390 / 0.20 ( 5) Misc. bond : bond 0.00030 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1834.92 seconds wall clock time: 32 minutes 52.95 seconds (1972.95 seconds total)