Starting phenix.real_space_refine on Sun Dec 29 00:19:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ty4_26165/12_2024/7ty4_26165.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ty4_26165/12_2024/7ty4_26165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ty4_26165/12_2024/7ty4_26165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ty4_26165/12_2024/7ty4_26165.map" model { file = "/net/cci-nas-00/data/ceres_data/7ty4_26165/12_2024/7ty4_26165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ty4_26165/12_2024/7ty4_26165.cif" } resolution = 2.99 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= 0.043 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 36 5.16 5 C 5798 2.51 5 N 1310 2.21 5 O 1490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8636 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: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 187 Unusual residues: {'CLR': 1, 'PC1': 1, 'Y01': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 187 Unusual residues: {'CLR': 1, 'PC1': 1, 'Y01': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Time building chain proxies: 6.33, per 1000 atoms: 0.73 Number of scatterers: 8636 At special positions: 0 Unit cell: (112.98, 97.916, 83.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 2 15.00 O 1490 8.00 N 1310 7.00 C 5798 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 1.0 seconds 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: 54 helices and 4 sheets defined 74.6% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 402 through 432 removed outlier: 3.501A pdb=" N LEU A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.626A pdb=" N GLY A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 455 Processing helix chain 'A' and resid 465 through 483 Processing helix chain 'A' and resid 485 through 507 removed outlier: 3.859A pdb=" N VAL A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 515 Processing helix chain 'A' and resid 517 through 547 removed outlier: 3.511A pdb=" N LEU A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 543 " --> pdb=" O LYS A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 593 Processing helix chain 'A' and resid 598 through 608 Processing helix chain 'A' and resid 608 through 623 removed outlier: 3.509A pdb=" N MET A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 646 Processing helix chain 'A' and resid 660 through 667 removed outlier: 4.022A pdb=" N MET A 664 " --> pdb=" O PRO A 660 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 665 " --> pdb=" O ILE A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 690 Processing helix chain 'A' and resid 701 through 719 removed outlier: 3.756A pdb=" N LEU A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 719 " --> pdb=" O VAL A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 738 Processing helix chain 'A' and resid 760 through 773 Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 784 through 799 removed outlier: 3.722A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 812 removed outlier: 3.535A pdb=" N LEU A 811 " --> pdb=" O ASP A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.824A 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 Processing helix chain 'A' and resid 858 through 865 removed outlier: 3.605A pdb=" N LEU A 865 " --> pdb=" O PHE A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'A' and resid 873 through 878 removed outlier: 3.606A pdb=" N ILE A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 887 Processing helix chain 'B' and resid 379 through 390 Processing helix chain 'B' and resid 392 through 399 Processing helix chain 'B' and resid 402 through 432 removed outlier: 3.501A pdb=" N LEU B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 3.626A pdb=" N GLY B 424 " --> pdb=" O ALA B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 455 Processing helix chain 'B' and resid 465 through 483 Processing helix chain 'B' and resid 485 through 507 removed outlier: 3.859A pdb=" N VAL B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 493 " --> pdb=" O GLY B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 515 Processing helix chain 'B' and resid 517 through 547 removed outlier: 3.509A pdb=" N LEU B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 543 " --> pdb=" O LYS B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 593 Processing helix chain 'B' and resid 598 through 608 Processing helix chain 'B' and resid 608 through 623 removed outlier: 3.509A pdb=" N MET B 617 " --> pdb=" O SER B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 646 Processing helix chain 'B' and resid 660 through 667 removed outlier: 4.023A pdb=" N MET B 664 " --> pdb=" O PRO B 660 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 665 " --> pdb=" O ILE B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 690 Processing helix chain 'B' and resid 701 through 719 removed outlier: 3.757A pdb=" N LEU B 718 " --> pdb=" O GLY B 714 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 719 " --> pdb=" O VAL B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 738 Processing helix chain 'B' and resid 760 through 773 Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 784 through 799 removed outlier: 3.724A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 812 removed outlier: 3.534A pdb=" N LEU B 811 " --> pdb=" O ASP B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 819 removed outlier: 3.824A 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 Processing helix chain 'B' and resid 858 through 865 removed outlier: 3.605A pdb=" N LEU B 865 " --> pdb=" O PHE B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'B' and resid 873 through 878 removed outlier: 3.607A pdb=" N ILE B 877 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 887 Processing sheet with id=AA1, first strand: chain 'A' and resid 461 through 463 removed outlier: 4.792A pdb=" N VAL A 461 " --> pdb=" O THR A 727 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 739 through 742 removed outlier: 7.659A pdb=" N VAL A 740 " --> pdb=" O GLN A 754 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN A 754 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 752 " --> pdb=" O GLY A 742 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 461 through 463 removed outlier: 4.792A pdb=" N VAL B 461 " --> pdb=" O THR B 727 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 739 through 742 removed outlier: 7.661A pdb=" N VAL B 740 " --> pdb=" O GLN B 754 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN B 754 " --> pdb=" O VAL B 740 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN B 752 " --> pdb=" O GLY B 742 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1518 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: 2.35 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 - 1.32: 1254 1.32 - 1.45: 2267 1.45 - 1.57: 5201 1.57 - 1.69: 4 1.69 - 1.82: 66 Bond restraints: 8792 Sorted by residual: bond pdb=" N LEU B 669 " pdb=" CA LEU B 669 " ideal model delta sigma weight residual 1.463 1.491 -0.027 6.90e-03 2.10e+04 1.58e+01 bond pdb=" N LEU A 669 " pdb=" CA LEU A 669 " ideal model delta sigma weight residual 1.463 1.491 -0.027 6.90e-03 2.10e+04 1.57e+01 bond pdb=" N LEU B 874 " pdb=" CA LEU B 874 " ideal model delta sigma weight residual 1.462 1.495 -0.033 8.50e-03 1.38e+04 1.53e+01 bond pdb=" N THR A 431 " pdb=" CA THR A 431 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.16e-02 7.43e+03 1.49e+01 bond pdb=" N THR B 431 " pdb=" CA THR B 431 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.16e-02 7.43e+03 1.49e+01 ... (remaining 8787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 9035 2.13 - 4.26: 2548 4.26 - 6.39: 383 6.39 - 8.53: 6 8.53 - 10.66: 2 Bond angle restraints: 11974 Sorted by residual: angle pdb=" N VAL A 825 " pdb=" CA VAL A 825 " pdb=" C VAL A 825 " ideal model delta sigma weight residual 111.00 105.19 5.81 1.09e+00 8.42e-01 2.84e+01 angle pdb=" C PRO B 598 " pdb=" N GLY B 599 " pdb=" CA GLY B 599 " ideal model delta sigma weight residual 120.03 125.79 -5.76 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 120.03 125.76 -5.73 1.12e+00 7.97e-01 2.62e+01 angle pdb=" N TYR B 596 " pdb=" CA TYR B 596 " pdb=" C TYR B 596 " ideal model delta sigma weight residual 108.41 116.71 -8.30 1.63e+00 3.76e-01 2.59e+01 angle pdb=" N GLU A 429 " pdb=" CA GLU A 429 " pdb=" C GLU A 429 " ideal model delta sigma weight residual 111.82 106.03 5.79 1.16e+00 7.43e-01 2.49e+01 ... (remaining 11969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.46: 5185 19.46 - 38.93: 348 38.93 - 58.39: 94 58.39 - 77.85: 22 77.85 - 97.32: 5 Dihedral angle restraints: 5654 sinusoidal: 2684 harmonic: 2970 Sorted by residual: dihedral pdb=" CA TYR A 596 " pdb=" C TYR A 596 " pdb=" N PHE A 597 " pdb=" CA PHE A 597 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA TYR B 555 " pdb=" C TYR B 555 " pdb=" N ASN B 556 " pdb=" CA ASN B 556 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA TYR A 555 " pdb=" C TYR A 555 " pdb=" N ASN A 556 " pdb=" CA ASN A 556 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 775 0.077 - 0.154: 596 0.154 - 0.232: 61 0.232 - 0.309: 0 0.309 - 0.386: 2 Chirality restraints: 1434 Sorted by residual: 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 -2.24 -0.16 2.00e-02 2.50e+03 6.67e+01 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 1.29e+01 chirality pdb=" CA VAL A 825 " pdb=" N VAL A 825 " pdb=" C VAL A 825 " pdb=" CB VAL A 825 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.39 2.00e-01 2.50e+01 3.72e+00 ... (remaining 1431 not shown) Planarity restraints: 1410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.326 2.00e-02 2.50e+03 2.77e-01 9.58e+02 pdb=" C7 NAG C 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.483 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.291 2.00e-02 2.50e+03 2.44e-01 7.44e+02 pdb=" C7 NAG D 1 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.187 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.415 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " -0.221 2.00e-02 2.50e+03 1.83e-01 4.17e+02 pdb=" C7 NAG C 2 " 0.059 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " -0.157 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " 0.299 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.019 2.00e-02 2.50e+03 ... (remaining 1407 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 401 2.75 - 3.29: 9297 3.29 - 3.83: 13893 3.83 - 4.36: 18726 4.36 - 4.90: 30644 Nonbonded interactions: 72961 Sorted by model distance: nonbonded pdb=" OH TYR A 555 " pdb=" OH TYR B 555 " model vdw 2.215 3.040 nonbonded pdb=" O ASP B 607 " pdb=" O HOH B2301 " model vdw 2.222 3.040 nonbonded pdb=" OE1 GLN A 447 " pdb=" O HOH A2301 " model vdw 2.422 3.040 nonbonded pdb=" OE1 GLN B 447 " pdb=" O HOH B2302 " model vdw 2.423 3.040 nonbonded pdb=" NH2 ARG A 490 " pdb=" O MET A 721 " model vdw 2.450 3.120 ... (remaining 72956 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: 2.080 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: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 22.570 Find NCS groups from input model: 0.230 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:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 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 0.051 8792 Z= 0.854 Angle : 1.798 10.657 11974 Z= 1.370 Chirality : 0.087 0.386 1434 Planarity : 0.012 0.277 1408 Dihedral : 14.464 97.319 3738 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.87 % Favored : 94.03 % Rotamer: Outliers : 0.45 % Allowed : 5.47 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.22), residues: 1022 helix: -1.56 (0.16), residues: 670 sheet: None (None), residues: 0 loop : -1.93 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 492 HIS 0.005 0.002 HIS A 819 PHE 0.016 0.002 PHE B 451 TYR 0.013 0.002 TYR B 628 ARG 0.003 0.000 ARG B 730 *********************** 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 130 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 ASN cc_start: 0.8611 (m-40) cc_final: 0.8260 (m110) REVERT: A 498 ILE cc_start: 0.9632 (mt) cc_final: 0.9415 (mp) REVERT: A 681 GLU cc_start: 0.8803 (tt0) cc_final: 0.8347 (tt0) REVERT: A 741 MET cc_start: 0.9316 (mmm) cc_final: 0.8973 (mmm) REVERT: A 880 ASN cc_start: 0.9250 (p0) cc_final: 0.9047 (t0) REVERT: B 433 ASN cc_start: 0.9395 (m-40) cc_final: 0.9174 (m-40) REVERT: B 482 ASN cc_start: 0.8615 (m-40) cc_final: 0.8244 (m110) REVERT: B 498 ILE cc_start: 0.9630 (mt) cc_final: 0.9424 (mp) REVERT: B 681 GLU cc_start: 0.8808 (tt0) cc_final: 0.8352 (tt0) REVERT: B 741 MET cc_start: 0.9318 (mmm) cc_final: 0.8974 (mmm) REVERT: B 880 ASN cc_start: 0.9252 (p0) cc_final: 0.9038 (t0) outliers start: 4 outliers final: 2 residues processed: 130 average time/residue: 0.9899 time to fit residues: 139.7938 Evaluate side-chains 73 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain B residue 511 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 0.0870 chunk 92 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 ASN A 457 GLN A 545 GLN A 683 GLN B 457 GLN B 545 GLN B 564 GLN B 683 GLN B 834 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8792 Z= 0.204 Angle : 0.650 8.528 11974 Z= 0.312 Chirality : 0.040 0.146 1434 Planarity : 0.005 0.042 1408 Dihedral : 10.134 67.469 1840 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.57 % Allowed : 10.27 % Favored : 87.17 % 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: 0.73 (0.25), residues: 1022 helix: 1.33 (0.19), residues: 688 sheet: None (None), residues: 0 loop : -1.31 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 662 HIS 0.002 0.001 HIS A 734 PHE 0.019 0.001 PHE A 411 TYR 0.009 0.001 TYR A 824 ARG 0.007 0.001 ARG B 603 *********************** 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 104 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8911 (pp) REVERT: A 554 ASN cc_start: 0.8483 (t0) cc_final: 0.8168 (t0) REVERT: A 681 GLU cc_start: 0.9029 (tt0) cc_final: 0.8460 (tm-30) REVERT: A 696 MET cc_start: 0.8356 (mmm) cc_final: 0.8086 (mmm) REVERT: A 721 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8553 (mtp) REVERT: A 759 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7960 (pm20) REVERT: B 386 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8892 (pp) REVERT: B 554 ASN cc_start: 0.8383 (t0) cc_final: 0.7970 (t0) REVERT: B 681 GLU cc_start: 0.9024 (tt0) cc_final: 0.8467 (tm-30) REVERT: B 721 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8546 (mtp) REVERT: B 759 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8069 (pm20) outliers start: 23 outliers final: 0 residues processed: 97 average time/residue: 0.9537 time to fit residues: 101.5017 Evaluate side-chains 73 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 759 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 25 optimal weight: 0.0870 chunk 92 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- 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: 0.8743 moved from start: 0.2573 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= 0.221 Angle : 0.595 7.615 11974 Z= 0.282 Chirality : 0.039 0.140 1434 Planarity : 0.005 0.047 1408 Dihedral : 9.479 61.005 1836 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.46 % Allowed : 11.38 % Favored : 86.16 % 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: 1.55 (0.26), residues: 1022 helix: 1.94 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.96 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 662 HIS 0.002 0.001 HIS A 651 PHE 0.012 0.001 PHE A 411 TYR 0.012 0.001 TYR A 824 ARG 0.005 0.001 ARG B 656 *********************** 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 96 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 554 ASN cc_start: 0.8797 (t0) cc_final: 0.8444 (t0) REVERT: A 681 GLU cc_start: 0.9012 (tt0) cc_final: 0.8431 (tm-30) REVERT: A 696 MET cc_start: 0.8469 (mmm) cc_final: 0.7981 (mmm) REVERT: B 554 ASN cc_start: 0.8829 (t0) cc_final: 0.8372 (t0) REVERT: B 681 GLU cc_start: 0.9011 (tt0) cc_final: 0.8428 (tm-30) outliers start: 22 outliers final: 4 residues processed: 86 average time/residue: 0.8424 time to fit residues: 80.1535 Evaluate side-chains 68 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8749 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 : 0.003 0.032 8792 Z= 0.194 Angle : 0.584 9.043 11974 Z= 0.273 Chirality : 0.039 0.136 1434 Planarity : 0.005 0.048 1408 Dihedral : 9.184 59.606 1836 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.79 % Allowed : 12.05 % Favored : 86.16 % 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: 1.81 (0.26), residues: 1022 helix: 2.11 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.77 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 662 HIS 0.002 0.001 HIS B 834 PHE 0.013 0.001 PHE B 471 TYR 0.013 0.001 TYR A 824 ARG 0.006 0.001 ARG A 656 *********************** 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 83 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 554 ASN cc_start: 0.8880 (t0) cc_final: 0.8472 (t0) REVERT: A 759 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7992 (pm20) REVERT: B 433 ASN cc_start: 0.9401 (m110) cc_final: 0.9081 (m110) REVERT: B 554 ASN cc_start: 0.8927 (t0) cc_final: 0.8526 (t0) REVERT: B 559 MET cc_start: 0.8805 (mtm) cc_final: 0.8472 (mtt) REVERT: B 681 GLU cc_start: 0.9007 (tt0) cc_final: 0.8419 (tt0) outliers start: 16 outliers final: 6 residues processed: 80 average time/residue: 0.9358 time to fit residues: 82.3840 Evaluate side-chains 72 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 864 ILE 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: 2.9990 chunk 40 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8758 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8792 Z= 0.199 Angle : 0.594 8.596 11974 Z= 0.275 Chirality : 0.039 0.131 1434 Planarity : 0.005 0.047 1408 Dihedral : 9.058 59.674 1836 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.45 % Allowed : 12.50 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.93 (0.27), residues: 1022 helix: 2.15 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -0.61 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 492 HIS 0.001 0.001 HIS B 834 PHE 0.013 0.001 PHE B 471 TYR 0.013 0.001 TYR A 824 ARG 0.004 0.000 ARG A 656 *********************** 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 85 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 554 ASN cc_start: 0.8929 (t0) cc_final: 0.8516 (t0) REVERT: A 559 MET cc_start: 0.8842 (mtm) cc_final: 0.8401 (mtt) REVERT: A 681 GLU cc_start: 0.9015 (tt0) cc_final: 0.8680 (tm-30) REVERT: A 759 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8024 (pm20) REVERT: B 433 ASN cc_start: 0.9399 (m110) cc_final: 0.9065 (m110) REVERT: B 554 ASN cc_start: 0.8949 (t0) cc_final: 0.8515 (t0) REVERT: B 559 MET cc_start: 0.8811 (mtm) cc_final: 0.8400 (mtt) REVERT: B 681 GLU cc_start: 0.9020 (tt0) cc_final: 0.8684 (tm-30) outliers start: 13 outliers final: 7 residues processed: 82 average time/residue: 0.9048 time to fit residues: 81.9016 Evaluate side-chains 73 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 95 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8760 moved from start: 0.3214 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= 0.192 Angle : 0.597 9.912 11974 Z= 0.275 Chirality : 0.039 0.146 1434 Planarity : 0.005 0.048 1408 Dihedral : 8.874 59.820 1836 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.45 % Allowed : 13.06 % Favored : 85.49 % 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: 1.88 (0.27), residues: 1022 helix: 2.07 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -0.61 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 492 HIS 0.002 0.001 HIS B 834 PHE 0.013 0.001 PHE B 471 TYR 0.013 0.001 TYR A 824 ARG 0.004 0.000 ARG A 656 *********************** 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 84 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 433 ASN cc_start: 0.9491 (m-40) cc_final: 0.9208 (m-40) REVERT: A 554 ASN cc_start: 0.8964 (t0) cc_final: 0.8503 (t0) REVERT: A 559 MET cc_start: 0.8814 (mtm) cc_final: 0.8418 (mtt) REVERT: A 705 ASP cc_start: 0.9096 (m-30) cc_final: 0.8816 (m-30) REVERT: A 759 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: B 433 ASN cc_start: 0.9363 (m110) cc_final: 0.8961 (m110) REVERT: B 554 ASN cc_start: 0.8984 (t0) cc_final: 0.8571 (t0) REVERT: B 559 MET cc_start: 0.8818 (mtm) cc_final: 0.8406 (mtt) REVERT: B 681 GLU cc_start: 0.9013 (tt0) cc_final: 0.8683 (tm-30) REVERT: B 705 ASP cc_start: 0.9099 (m-30) cc_final: 0.8824 (m-30) outliers start: 13 outliers final: 7 residues processed: 82 average time/residue: 0.8139 time to fit residues: 74.5898 Evaluate side-chains 73 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 98 optimal weight: 0.0570 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 GLN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 819 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3373 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= 0.187 Angle : 0.603 9.587 11974 Z= 0.278 Chirality : 0.039 0.165 1434 Planarity : 0.005 0.048 1408 Dihedral : 8.706 59.971 1836 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.90 % Allowed : 13.17 % Favored : 84.93 % 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: 1.86 (0.27), residues: 1022 helix: 2.02 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -0.54 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 492 HIS 0.002 0.001 HIS B 834 PHE 0.012 0.001 PHE B 471 TYR 0.013 0.001 TYR A 824 ARG 0.003 0.000 ARG A 490 *********************** 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 87 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 433 ASN cc_start: 0.9433 (m-40) cc_final: 0.9133 (m-40) REVERT: A 554 ASN cc_start: 0.8994 (t0) cc_final: 0.8523 (t0) REVERT: A 559 MET cc_start: 0.8824 (mtm) cc_final: 0.8469 (mtt) REVERT: A 759 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8014 (pm20) REVERT: B 433 ASN cc_start: 0.9343 (m110) cc_final: 0.8937 (m110) REVERT: B 554 ASN cc_start: 0.9012 (t0) cc_final: 0.8571 (t0) REVERT: B 559 MET cc_start: 0.8843 (mtm) cc_final: 0.8462 (mtt) REVERT: B 681 GLU cc_start: 0.9019 (tt0) cc_final: 0.8693 (tm-30) outliers start: 17 outliers final: 9 residues processed: 82 average time/residue: 0.8258 time to fit residues: 75.1757 Evaluate side-chains 75 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8764 moved from start: 0.3495 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= 0.195 Angle : 0.621 12.090 11974 Z= 0.285 Chirality : 0.039 0.155 1434 Planarity : 0.004 0.047 1408 Dihedral : 8.553 59.105 1836 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.45 % Allowed : 14.29 % Favored : 84.26 % 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: 1.91 (0.27), residues: 1022 helix: 2.04 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -0.47 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 662 HIS 0.002 0.001 HIS B 834 PHE 0.012 0.001 PHE A 471 TYR 0.013 0.001 TYR A 824 ARG 0.003 0.000 ARG A 656 *********************** 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 79 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 433 ASN cc_start: 0.9431 (m-40) cc_final: 0.9133 (m-40) REVERT: A 554 ASN cc_start: 0.9028 (t0) cc_final: 0.8546 (t0) REVERT: A 559 MET cc_start: 0.8813 (mtm) cc_final: 0.8494 (mtt) REVERT: A 681 GLU cc_start: 0.9011 (tt0) cc_final: 0.8657 (tm-30) REVERT: B 433 ASN cc_start: 0.9345 (m110) cc_final: 0.8942 (m110) REVERT: B 554 ASN cc_start: 0.9015 (t0) cc_final: 0.8577 (t0) REVERT: B 559 MET cc_start: 0.8832 (mtm) cc_final: 0.8455 (mtt) REVERT: B 663 MET cc_start: 0.9204 (tpp) cc_final: 0.8969 (tpp) REVERT: B 681 GLU cc_start: 0.9021 (tt0) cc_final: 0.8666 (tm-30) outliers start: 13 outliers final: 7 residues processed: 76 average time/residue: 0.8598 time to fit residues: 72.4140 Evaluate side-chains 70 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.0364 ------------------------------------------------------------------------------- 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: 0.8777 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8792 Z= 0.238 Angle : 0.660 12.762 11974 Z= 0.305 Chirality : 0.040 0.164 1434 Planarity : 0.005 0.047 1408 Dihedral : 8.497 59.265 1836 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.23 % Allowed : 14.51 % Favored : 84.26 % 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: 1.89 (0.27), residues: 1022 helix: 2.03 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -0.48 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 662 HIS 0.002 0.001 HIS A 651 PHE 0.012 0.001 PHE B 471 TYR 0.013 0.001 TYR A 824 ARG 0.002 0.000 ARG A 656 *********************** 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 77 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 433 ASN cc_start: 0.9459 (m-40) cc_final: 0.9152 (m-40) REVERT: A 554 ASN cc_start: 0.9005 (t0) cc_final: 0.8514 (t0) REVERT: A 559 MET cc_start: 0.8760 (mtm) cc_final: 0.8466 (mtt) REVERT: A 681 GLU cc_start: 0.9018 (tt0) cc_final: 0.8505 (tt0) REVERT: B 433 ASN cc_start: 0.9306 (m110) cc_final: 0.8884 (m110) REVERT: B 554 ASN cc_start: 0.9002 (t0) cc_final: 0.8564 (t0) REVERT: B 559 MET cc_start: 0.8861 (mtm) cc_final: 0.8486 (mtt) REVERT: B 681 GLU cc_start: 0.9018 (tt0) cc_final: 0.8659 (tm-30) outliers start: 11 outliers final: 8 residues processed: 75 average time/residue: 0.8386 time to fit residues: 69.7324 Evaluate side-chains 72 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 0.0570 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 11 optimal weight: 0.0970 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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: 0.8752 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8792 Z= 0.182 Angle : 0.679 13.802 11974 Z= 0.307 Chirality : 0.039 0.159 1434 Planarity : 0.005 0.047 1408 Dihedral : 8.329 58.723 1836 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.89 % Allowed : 14.84 % Favored : 84.26 % 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: 1.88 (0.27), residues: 1022 helix: 1.99 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -0.43 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 492 HIS 0.002 0.001 HIS B 834 PHE 0.012 0.001 PHE A 471 TYR 0.013 0.001 TYR A 824 ARG 0.003 0.000 ARG A 656 ********************** 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 77 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 433 ASN cc_start: 0.9407 (m-40) cc_final: 0.9088 (m-40) REVERT: A 554 ASN cc_start: 0.9016 (t0) cc_final: 0.8518 (t0) REVERT: A 559 MET cc_start: 0.8742 (mtm) cc_final: 0.8417 (mtt) REVERT: A 663 MET cc_start: 0.9181 (tpp) cc_final: 0.8769 (tpp) REVERT: A 681 GLU cc_start: 0.9003 (tt0) cc_final: 0.8647 (tm-30) REVERT: A 721 MET cc_start: 0.8514 (mpp) cc_final: 0.8085 (mpp) REVERT: B 433 ASN cc_start: 0.9258 (m110) cc_final: 0.8817 (m110) REVERT: B 554 ASN cc_start: 0.9013 (t0) cc_final: 0.8552 (t0) REVERT: B 559 MET cc_start: 0.8846 (mtm) cc_final: 0.8478 (mtt) REVERT: B 601 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8562 (tm) REVERT: B 681 GLU cc_start: 0.9005 (tt0) cc_final: 0.8647 (tm-30) outliers start: 8 outliers final: 7 residues processed: 77 average time/residue: 0.8459 time to fit residues: 72.0882 Evaluate side-chains 72 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 880 ASN B 880 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.057439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.048785 restraints weight = 30280.118| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 3.27 r_work: 0.2661 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8792 Z= 0.220 Angle : 0.688 18.591 11974 Z= 0.312 Chirality : 0.040 0.235 1434 Planarity : 0.005 0.047 1408 Dihedral : 8.287 59.845 1836 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.12 % Allowed : 14.84 % Favored : 84.04 % 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: 1.84 (0.27), residues: 1022 helix: 1.97 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.47 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 496 HIS 0.002 0.001 HIS B 834 PHE 0.011 0.001 PHE B 471 TYR 0.013 0.001 TYR A 824 ARG 0.002 0.000 ARG A 656 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2369.18 seconds wall clock time: 43 minutes 55.29 seconds (2635.29 seconds total)