Starting phenix.real_space_refine on Sat Dec 28 22:36:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ty8_26169/12_2024/7ty8_26169.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ty8_26169/12_2024/7ty8_26169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ty8_26169/12_2024/7ty8_26169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ty8_26169/12_2024/7ty8_26169.map" model { file = "/net/cci-nas-00/data/ceres_data/7ty8_26169/12_2024/7ty8_26169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ty8_26169/12_2024/7ty8_26169.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 36 5.16 5 C 5800 2.51 5 N 1314 2.21 5 O 1433 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8591 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4067 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 29, 'TRANS': 485} Chain breaks: 1 Chain: "B" Number of atoms: 4067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4067 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 29, 'TRANS': 485} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 186 Unusual residues: {'CLR': 4, 'NFL': 1, 'PC1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 186 Unusual residues: {'CLR': 4, 'NFL': 1, 'PC1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Time building chain proxies: 6.07, per 1000 atoms: 0.71 Number of scatterers: 8591 At special positions: 0 Unit cell: (125.892, 85.004, 83.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 2 15.00 F 6 9.00 O 1433 8.00 N 1314 7.00 C 5800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 642 " " NAG D 1 " - " ASN B 642 " Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 948.3 milliseconds 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 74.4% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 402 through 432 removed outlier: 3.882A pdb=" N LEU A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 436 through 455 Processing helix chain 'A' and resid 465 through 483 removed outlier: 3.711A pdb=" N THR A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 507 removed outlier: 4.143A pdb=" N VAL A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 502 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 516 removed outlier: 3.527A pdb=" N VAL A 513 " --> pdb=" O SER A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 547 removed outlier: 3.901A pdb=" N ILE A 543 " --> pdb=" O LYS A 539 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 593 removed outlier: 3.572A pdb=" N LEU A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 removed outlier: 3.737A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 623 removed outlier: 3.526A pdb=" N MET A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 621 " --> pdb=" O MET A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 667 removed outlier: 3.595A pdb=" N MET A 664 " --> pdb=" O PRO A 660 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 665 " --> pdb=" O ILE A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 690 removed outlier: 3.741A pdb=" N ILE A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 719 removed outlier: 3.966A pdb=" N LEU A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE A 719 " --> pdb=" O VAL A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 738 Processing helix chain 'A' and resid 760 through 773 removed outlier: 3.584A pdb=" N ALA A 767 " --> pdb=" O GLY A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 784 through 799 removed outlier: 3.564A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 791 " --> pdb=" O VAL A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 810 Processing helix chain 'A' and resid 811 through 813 No H-bonds generated for 'chain 'A' and resid 811 through 813' Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.737A pdb=" N HIS A 819 " --> pdb=" O PRO A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 829 through 853 removed outlier: 3.604A pdb=" N LEU A 835 " --> pdb=" O TRP A 831 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 852 " --> pdb=" O TRP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 864 Processing helix chain 'A' and resid 865 through 872 removed outlier: 3.559A pdb=" N LEU A 869 " --> pdb=" O LEU A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 878 Processing helix chain 'A' and resid 879 through 887 Processing helix chain 'B' and resid 379 through 390 Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 394 through 399 Processing helix chain 'B' and resid 402 through 432 removed outlier: 3.882A pdb=" N LEU B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 436 through 455 Processing helix chain 'B' and resid 465 through 483 removed outlier: 3.711A pdb=" N THR B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 507 removed outlier: 4.157A pdb=" N VAL B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 502 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 516 removed outlier: 3.528A pdb=" N VAL B 513 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 547 removed outlier: 3.903A pdb=" N ILE B 543 " --> pdb=" O LYS B 539 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 593 removed outlier: 3.565A pdb=" N LEU B 573 " --> pdb=" O ASN B 569 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 removed outlier: 3.737A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 623 removed outlier: 3.525A pdb=" N MET B 617 " --> pdb=" O SER B 613 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B 621 " --> pdb=" O MET B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 667 removed outlier: 3.595A pdb=" N MET B 664 " --> pdb=" O PRO B 660 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 665 " --> pdb=" O ILE B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 690 removed outlier: 3.743A pdb=" N ILE B 684 " --> pdb=" O LEU B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 719 removed outlier: 3.964A pdb=" N LEU B 718 " --> pdb=" O GLY B 714 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE B 719 " --> pdb=" O VAL B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 738 Processing helix chain 'B' and resid 760 through 773 removed outlier: 3.583A pdb=" N ALA B 767 " --> pdb=" O GLY B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 784 through 799 removed outlier: 3.564A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 791 " --> pdb=" O VAL B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 810 Processing helix chain 'B' and resid 811 through 813 No H-bonds generated for 'chain 'B' and resid 811 through 813' Processing helix chain 'B' and resid 815 through 819 removed outlier: 3.734A pdb=" N HIS B 819 " --> pdb=" O PRO B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 827 Processing helix chain 'B' and resid 829 through 853 removed outlier: 3.605A pdb=" N LEU B 835 " --> pdb=" O TRP B 831 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 852 " --> pdb=" O TRP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 864 Processing helix chain 'B' and resid 865 through 872 removed outlier: 3.556A pdb=" N LEU B 869 " --> pdb=" O LEU B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 878 Processing helix chain 'B' and resid 879 through 887 Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AA2, first strand: chain 'A' and resid 739 through 742 removed outlier: 7.592A pdb=" N VAL A 740 " --> pdb=" O GLN A 754 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN A 754 " --> pdb=" O VAL A 740 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AA4, first strand: chain 'B' and resid 739 through 742 removed outlier: 7.591A pdb=" N VAL B 740 " --> pdb=" O GLN B 754 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN B 754 " --> pdb=" O VAL B 740 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1392 1.33 - 1.45: 2156 1.45 - 1.58: 5174 1.58 - 1.70: 4 1.70 - 1.83: 66 Bond restraints: 8792 Sorted by residual: bond pdb=" N ILE B 783 " pdb=" CA ILE B 783 " ideal model delta sigma weight residual 1.460 1.497 -0.037 7.60e-03 1.73e+04 2.36e+01 bond pdb=" N ILE A 783 " pdb=" CA ILE A 783 " ideal model delta sigma weight residual 1.460 1.496 -0.036 7.60e-03 1.73e+04 2.24e+01 bond pdb=" N VAL B 634 " pdb=" CA VAL B 634 " ideal model delta sigma weight residual 1.461 1.496 -0.035 8.70e-03 1.32e+04 1.60e+01 bond pdb=" N VAL A 634 " pdb=" CA VAL A 634 " ideal model delta sigma weight residual 1.461 1.496 -0.035 8.70e-03 1.32e+04 1.60e+01 bond pdb=" N LEU A 669 " pdb=" CA LEU A 669 " ideal model delta sigma weight residual 1.462 1.492 -0.030 8.50e-03 1.38e+04 1.27e+01 ... (remaining 8787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 7968 1.64 - 3.28: 3171 3.28 - 4.91: 728 4.91 - 6.55: 108 6.55 - 8.19: 5 Bond angle restraints: 11980 Sorted by residual: angle pdb=" C PRO B 598 " pdb=" N GLY B 599 " pdb=" CA GLY B 599 " ideal model delta sigma weight residual 120.03 125.80 -5.77 1.12e+00 7.97e-01 2.65e+01 angle pdb=" C PRO A 598 " pdb=" N GLY A 599 " pdb=" CA GLY A 599 " ideal model delta sigma weight residual 120.03 125.79 -5.76 1.12e+00 7.97e-01 2.65e+01 angle pdb=" C GLY B 380 " pdb=" N GLY B 381 " pdb=" CA GLY B 381 " ideal model delta sigma weight residual 120.00 125.62 -5.62 1.10e+00 8.26e-01 2.61e+01 angle pdb=" C GLY A 380 " pdb=" N GLY A 381 " pdb=" CA GLY A 381 " ideal model delta sigma weight residual 120.00 125.61 -5.61 1.10e+00 8.26e-01 2.60e+01 angle pdb=" N LEU A 873 " pdb=" CA LEU A 873 " pdb=" C LEU A 873 " ideal model delta sigma weight residual 111.07 116.05 -4.98 1.07e+00 8.73e-01 2.17e+01 ... (remaining 11975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 5094 17.32 - 34.64: 380 34.64 - 51.96: 106 51.96 - 69.28: 33 69.28 - 86.61: 13 Dihedral angle restraints: 5626 sinusoidal: 2656 harmonic: 2970 Sorted by residual: dihedral pdb=" CA ARG A 388 " pdb=" C ARG A 388 " pdb=" N ARG A 389 " pdb=" CA ARG A 389 " ideal model delta harmonic sigma weight residual -180.00 -160.60 -19.40 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ARG B 388 " pdb=" C ARG B 388 " pdb=" N ARG B 389 " pdb=" CA ARG B 389 " ideal model delta harmonic sigma weight residual -180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA TYR A 628 " pdb=" C TYR A 628 " pdb=" N THR A 629 " pdb=" CA THR A 629 " ideal model delta harmonic sigma weight residual 180.00 163.42 16.58 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 5623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 488 0.043 - 0.086: 398 0.086 - 0.129: 366 0.129 - 0.172: 163 0.172 - 0.215: 19 Chirality restraints: 1434 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.16e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 7.08e+00 chirality pdb=" CA LEU B 484 " pdb=" N LEU B 484 " pdb=" C LEU B 484 " pdb=" CB LEU B 484 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1431 not shown) Planarity restraints: 1404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.305 2.00e-02 2.50e+03 2.57e-01 8.25e+02 pdb=" C7 NAG D 1 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.441 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.304 2.00e-02 2.50e+03 2.56e-01 8.21e+02 pdb=" C7 NAG C 1 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.439 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " -0.072 2.00e-02 2.50e+03 5.89e-02 4.33e+01 pdb=" C7 NAG C 2 " 0.019 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " -0.054 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " 0.093 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.014 2.00e-02 2.50e+03 ... (remaining 1401 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 2694 2.91 - 3.40: 9413 3.40 - 3.90: 15126 3.90 - 4.40: 17228 4.40 - 4.90: 28434 Nonbonded interactions: 72895 Sorted by model distance: nonbonded pdb=" CD1 LEU B 874 " pdb=" CD2 PHE B 878 " model vdw 2.407 3.760 nonbonded pdb=" CD1 LEU A 874 " pdb=" CD2 PHE A 878 " model vdw 2.430 3.760 nonbonded pdb=" OH TYR A 555 " pdb=" OH TYR B 555 " model vdw 2.441 3.040 nonbonded pdb=" O VAL B 729 " pdb=" OG1 THR B 733 " model vdw 2.486 3.040 nonbonded pdb=" O VAL A 729 " pdb=" OG1 THR A 733 " model vdw 2.486 3.040 ... (remaining 72890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.250 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 : 0.013 0.049 8792 Z= 0.854 Angle : 1.782 8.189 11980 Z= 1.347 Chirality : 0.085 0.215 1434 Planarity : 0.010 0.257 1402 Dihedral : 14.152 86.606 3710 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.78 % Allowed : 7.37 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.22), residues: 1022 helix: -2.25 (0.16), residues: 676 sheet: None (None), residues: 0 loop : -1.83 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 662 HIS 0.004 0.001 HIS A 819 PHE 0.016 0.002 PHE A 495 TYR 0.014 0.002 TYR B 628 ARG 0.004 0.001 ARG B 514 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 201 time to evaluate : 1.030 Fit side-chains REVERT: A 641 SER cc_start: 0.7642 (OUTLIER) cc_final: 0.7207 (p) REVERT: A 696 MET cc_start: 0.7845 (mmm) cc_final: 0.7568 (mmt) REVERT: A 833 MET cc_start: 0.8496 (tmm) cc_final: 0.8162 (tmm) REVERT: B 696 MET cc_start: 0.7842 (mmm) cc_final: 0.7557 (mmt) REVERT: B 833 MET cc_start: 0.8457 (tmm) cc_final: 0.8101 (tmm) outliers start: 7 outliers final: 2 residues processed: 208 average time/residue: 0.2202 time to fit residues: 62.4669 Evaluate side-chains 115 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain B residue 650 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 683 GLN B 550 GLN B 683 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8792 Z= 0.237 Angle : 0.656 7.021 11980 Z= 0.325 Chirality : 0.042 0.160 1434 Planarity : 0.005 0.042 1402 Dihedral : 10.323 88.605 1813 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.12 % Allowed : 12.61 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.25), residues: 1022 helix: 0.37 (0.18), residues: 700 sheet: None (None), residues: 0 loop : -1.35 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 492 HIS 0.004 0.001 HIS B 651 PHE 0.024 0.002 PHE A 411 TYR 0.010 0.001 TYR A 486 ARG 0.006 0.001 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.963 Fit side-chains REVERT: A 399 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8177 (t0) REVERT: A 812 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8873 (mp) REVERT: B 399 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8187 (t0) outliers start: 19 outliers final: 6 residues processed: 143 average time/residue: 0.1728 time to fit residues: 38.1477 Evaluate side-chains 111 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 681 GLU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 614 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 77 optimal weight: 0.0570 chunk 63 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 100 optimal weight: 0.0570 chunk 82 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 834 HIS B 834 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8792 Z= 0.193 Angle : 0.595 7.480 11980 Z= 0.291 Chirality : 0.039 0.165 1434 Planarity : 0.005 0.046 1402 Dihedral : 9.986 85.599 1808 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.46 % Allowed : 13.84 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1022 helix: 0.97 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -1.05 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 662 HIS 0.002 0.001 HIS B 734 PHE 0.016 0.001 PHE B 411 TYR 0.015 0.001 TYR B 486 ARG 0.005 0.001 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.099 Fit side-chains REVERT: A 664 MET cc_start: 0.7967 (mtm) cc_final: 0.7642 (mtp) REVERT: A 812 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8829 (mp) REVERT: B 399 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8312 (t0) REVERT: B 664 MET cc_start: 0.8000 (mtm) cc_final: 0.7674 (mtp) outliers start: 22 outliers final: 9 residues processed: 127 average time/residue: 0.1518 time to fit residues: 29.7980 Evaluate side-chains 113 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 614 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 93 optimal weight: 0.0270 chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 0.0270 chunk 26 optimal weight: 0.0070 chunk 82 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 overall best weight: 0.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 GLN A 884 GLN B 457 GLN B 884 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8792 Z= 0.162 Angle : 0.590 8.569 11980 Z= 0.283 Chirality : 0.039 0.166 1434 Planarity : 0.005 0.049 1402 Dihedral : 9.605 83.606 1808 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.23 % Allowed : 15.29 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1022 helix: 1.19 (0.19), residues: 694 sheet: None (None), residues: 0 loop : -0.89 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 662 HIS 0.002 0.001 HIS A 834 PHE 0.015 0.001 PHE A 524 TYR 0.024 0.001 TYR B 486 ARG 0.004 0.001 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.903 Fit side-chains REVERT: A 399 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8394 (t70) REVERT: A 664 MET cc_start: 0.7746 (mtm) cc_final: 0.7417 (mtp) REVERT: A 820 PRO cc_start: 0.8708 (Cg_exo) cc_final: 0.8465 (Cg_endo) REVERT: B 399 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8437 (t70) REVERT: B 664 MET cc_start: 0.7746 (mtm) cc_final: 0.7417 (mtp) outliers start: 20 outliers final: 11 residues processed: 134 average time/residue: 0.1673 time to fit residues: 34.2027 Evaluate side-chains 117 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 874 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 chunk 84 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 0.4980 chunk 88 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8792 Z= 0.179 Angle : 0.596 8.925 11980 Z= 0.282 Chirality : 0.039 0.165 1434 Planarity : 0.005 0.049 1402 Dihedral : 9.418 80.165 1808 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.46 % Allowed : 16.52 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.26), residues: 1022 helix: 1.35 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -0.65 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 662 HIS 0.001 0.000 HIS A 651 PHE 0.012 0.001 PHE A 524 TYR 0.024 0.002 TYR A 486 ARG 0.003 0.000 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 399 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8438 (t70) REVERT: A 664 MET cc_start: 0.7669 (mtm) cc_final: 0.7349 (mtp) REVERT: A 820 PRO cc_start: 0.8619 (Cg_exo) cc_final: 0.8399 (Cg_endo) REVERT: B 664 MET cc_start: 0.7675 (mtm) cc_final: 0.7348 (mtp) outliers start: 22 outliers final: 15 residues processed: 122 average time/residue: 0.1586 time to fit residues: 29.5805 Evaluate side-chains 121 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 874 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 98 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 chunk 51 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8792 Z= 0.184 Angle : 0.587 9.763 11980 Z= 0.277 Chirality : 0.039 0.165 1434 Planarity : 0.005 0.047 1402 Dihedral : 9.238 80.152 1808 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.34 % Allowed : 16.85 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1022 helix: 1.45 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -0.52 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 662 HIS 0.002 0.000 HIS A 834 PHE 0.017 0.001 PHE B 451 TYR 0.024 0.002 TYR A 486 ARG 0.002 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 399 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.8492 (t70) REVERT: A 664 MET cc_start: 0.7631 (mtm) cc_final: 0.7292 (mtp) REVERT: A 820 PRO cc_start: 0.8652 (Cg_exo) cc_final: 0.8439 (Cg_endo) REVERT: B 664 MET cc_start: 0.7650 (mtm) cc_final: 0.7324 (mtp) REVERT: B 820 PRO cc_start: 0.8745 (Cg_exo) cc_final: 0.8520 (Cg_endo) outliers start: 21 outliers final: 13 residues processed: 129 average time/residue: 0.1628 time to fit residues: 31.9324 Evaluate side-chains 119 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 831 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8792 Z= 0.232 Angle : 0.625 11.748 11980 Z= 0.293 Chirality : 0.040 0.165 1434 Planarity : 0.005 0.047 1402 Dihedral : 9.000 81.306 1808 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.23 % Allowed : 18.08 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.26), residues: 1022 helix: 1.42 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -0.34 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 662 HIS 0.004 0.001 HIS B 834 PHE 0.012 0.001 PHE A 836 TYR 0.026 0.002 TYR A 486 ARG 0.002 0.000 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 399 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8540 (t70) REVERT: A 664 MET cc_start: 0.7629 (mtm) cc_final: 0.7271 (mtp) REVERT: A 820 PRO cc_start: 0.8693 (Cg_exo) cc_final: 0.8481 (Cg_endo) REVERT: B 664 MET cc_start: 0.7639 (mtm) cc_final: 0.7280 (mtp) REVERT: B 820 PRO cc_start: 0.8688 (Cg_exo) cc_final: 0.8466 (Cg_endo) outliers start: 20 outliers final: 14 residues processed: 126 average time/residue: 0.1515 time to fit residues: 30.1853 Evaluate side-chains 121 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 831 TRP Chi-restraints excluded: chain B residue 874 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.0670 chunk 89 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8792 Z= 0.175 Angle : 0.611 12.018 11980 Z= 0.286 Chirality : 0.039 0.176 1434 Planarity : 0.005 0.047 1402 Dihedral : 8.728 81.359 1808 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.12 % Allowed : 18.86 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.26), residues: 1022 helix: 1.47 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -0.32 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 662 HIS 0.001 0.001 HIS A 547 PHE 0.012 0.001 PHE A 524 TYR 0.027 0.002 TYR B 486 ARG 0.003 0.000 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.804 Fit side-chains REVERT: A 399 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.7797 (t70) REVERT: A 664 MET cc_start: 0.7613 (mtm) cc_final: 0.7274 (mtp) REVERT: A 820 PRO cc_start: 0.8678 (Cg_exo) cc_final: 0.8466 (Cg_endo) REVERT: B 664 MET cc_start: 0.7622 (mtm) cc_final: 0.7284 (mtp) REVERT: B 820 PRO cc_start: 0.8640 (Cg_exo) cc_final: 0.8429 (Cg_endo) outliers start: 19 outliers final: 14 residues processed: 121 average time/residue: 0.1618 time to fit residues: 30.7589 Evaluate side-chains 118 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 831 TRP Chi-restraints excluded: chain B residue 841 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8792 Z= 0.213 Angle : 0.631 12.021 11980 Z= 0.297 Chirality : 0.040 0.200 1434 Planarity : 0.005 0.046 1402 Dihedral : 8.664 80.885 1808 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.01 % Allowed : 18.75 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.26), residues: 1022 helix: 1.47 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -0.27 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 662 HIS 0.002 0.001 HIS B 834 PHE 0.012 0.001 PHE B 836 TYR 0.026 0.002 TYR B 486 ARG 0.006 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.875 Fit side-chains REVERT: A 664 MET cc_start: 0.7459 (mtm) cc_final: 0.7134 (mtp) REVERT: A 820 PRO cc_start: 0.8708 (Cg_exo) cc_final: 0.8499 (Cg_endo) REVERT: B 664 MET cc_start: 0.7476 (mtm) cc_final: 0.7144 (mtp) REVERT: B 820 PRO cc_start: 0.8651 (Cg_exo) cc_final: 0.8434 (Cg_endo) outliers start: 18 outliers final: 13 residues processed: 115 average time/residue: 0.1419 time to fit residues: 25.4902 Evaluate side-chains 111 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 831 TRP Chi-restraints excluded: chain B residue 850 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.9990 chunk 93 optimal weight: 0.0370 chunk 80 optimal weight: 0.0970 chunk 8 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8792 Z= 0.185 Angle : 0.643 13.259 11980 Z= 0.301 Chirality : 0.039 0.171 1434 Planarity : 0.005 0.047 1402 Dihedral : 8.545 80.349 1808 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.45 % Allowed : 19.87 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.26), residues: 1022 helix: 1.46 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -0.30 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 662 HIS 0.002 0.001 HIS B 834 PHE 0.011 0.001 PHE A 524 TYR 0.025 0.002 TYR B 486 ARG 0.003 0.000 ARG A 694 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.999 Fit side-chains REVERT: A 664 MET cc_start: 0.7436 (mtm) cc_final: 0.7082 (mtp) REVERT: A 696 MET cc_start: 0.7972 (pmm) cc_final: 0.7720 (pmm) REVERT: A 820 PRO cc_start: 0.8698 (Cg_exo) cc_final: 0.8492 (Cg_endo) REVERT: B 664 MET cc_start: 0.7426 (mtm) cc_final: 0.7100 (mtp) REVERT: B 820 PRO cc_start: 0.8639 (Cg_exo) cc_final: 0.8424 (Cg_endo) outliers start: 13 outliers final: 13 residues processed: 113 average time/residue: 0.1454 time to fit residues: 26.0511 Evaluate side-chains 113 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 831 TRP Chi-restraints excluded: chain B residue 841 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.081982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.074050 restraints weight = 28117.481| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.38 r_work: 0.3228 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8792 Z= 0.212 Angle : 0.646 13.190 11980 Z= 0.302 Chirality : 0.040 0.186 1434 Planarity : 0.005 0.047 1402 Dihedral : 8.470 79.692 1808 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.79 % Allowed : 19.20 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.26), residues: 1022 helix: 1.46 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -0.31 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 662 HIS 0.002 0.001 HIS B 834 PHE 0.012 0.001 PHE B 836 TYR 0.026 0.002 TYR B 486 ARG 0.003 0.000 ARG B 694 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1919.63 seconds wall clock time: 36 minutes 55.43 seconds (2215.43 seconds total)