Starting phenix.real_space_refine on Wed Feb 14 04:43:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty4_26165/02_2024/7ty4_26165.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty4_26165/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty4_26165/02_2024/7ty4_26165.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty4_26165/02_2024/7ty4_26165.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty4_26165/02_2024/7ty4_26165.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty4_26165/02_2024/7ty4_26165.pdb" } 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 Residue "A GLU 485": "OE1" <-> "OE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A GLU 758": "OE1" <-> "OE2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B GLU 522": "OE1" <-> "OE2" Residue "B GLU 758": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.30, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 3.57 Conformation dependent library (CDL) restraints added in 1.5 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: 0.80 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: 2.37 Time building geometry restraints manager: 3.76 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: 98.01 - 105.27: 291 105.27 - 112.53: 4427 112.53 - 119.80: 3921 119.80 - 127.06: 3284 127.06 - 134.32: 51 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 2.440 nonbonded pdb=" O ASP B 607 " pdb=" O HOH B2301 " model vdw 2.222 2.440 nonbonded pdb=" OE1 GLN A 447 " pdb=" O HOH A2301 " model vdw 2.422 2.440 nonbonded pdb=" OE1 GLN B 447 " pdb=" O HOH B2302 " model vdw 2.423 2.440 nonbonded pdb=" NH2 ARG A 490 " pdb=" O MET A 721 " model vdw 2.450 2.520 ... (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 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: 1.880 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: 0.000 Extract box with map and model: 8.040 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.340 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 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:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.250 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 0.941 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: 0.9617 time to fit residues: 135.6756 Evaluate side-chains 73 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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: 2.9990 chunk 77 optimal weight: 0.0000 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 overall best weight: 0.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 ASN A 447 GLN A 457 GLN A 545 GLN A 683 GLN B 447 GLN B 457 GLN B 545 GLN B 564 GLN B 683 GLN B 834 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 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 0.041 8792 Z= 0.196 Angle : 0.650 9.907 11974 Z= 0.308 Chirality : 0.039 0.143 1434 Planarity : 0.005 0.044 1408 Dihedral : 10.090 67.328 1840 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.34 % Allowed : 10.71 % Favored : 86.94 % 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: 0.75 (0.25), residues: 1022 helix: 1.36 (0.19), residues: 688 sheet: None (None), residues: 0 loop : -1.33 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 662 HIS 0.003 0.001 HIS A 734 PHE 0.020 0.001 PHE B 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 fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8920 (pp) REVERT: A 681 GLU cc_start: 0.8989 (tt0) cc_final: 0.8426 (tm-30) REVERT: A 696 MET cc_start: 0.8426 (mmm) cc_final: 0.8171 (mmm) REVERT: B 386 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8914 (pp) REVERT: B 681 GLU cc_start: 0.8977 (tt0) cc_final: 0.8426 (tm-30) REVERT: B 721 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8522 (mtp) outliers start: 21 outliers final: 0 residues processed: 97 average time/residue: 0.7507 time to fit residues: 80.9934 Evaluate side-chains 70 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 721 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 7.9990 chunk 28 optimal weight: 0.0060 chunk 77 optimal weight: 0.1980 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN B 447 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2493 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= 0.167 Angle : 0.592 8.918 11974 Z= 0.280 Chirality : 0.039 0.145 1434 Planarity : 0.005 0.048 1408 Dihedral : 9.484 62.178 1836 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.12 % Allowed : 11.94 % Favored : 85.94 % 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: 1.48 (0.26), residues: 1022 helix: 1.91 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -1.05 (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 B 834 PHE 0.013 0.001 PHE A 471 TYR 0.012 0.001 TYR A 824 ARG 0.005 0.000 ARG B 603 *********************** 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 95 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8893 (pp) REVERT: A 559 MET cc_start: 0.8790 (mtm) cc_final: 0.8458 (mtt) REVERT: A 696 MET cc_start: 0.8485 (mmm) cc_final: 0.8024 (mmm) REVERT: B 386 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8892 (pp) REVERT: B 433 ASN cc_start: 0.9456 (m110) cc_final: 0.9240 (m110) REVERT: B 559 MET cc_start: 0.8722 (mtm) cc_final: 0.8467 (mtt) REVERT: B 681 GLU cc_start: 0.8943 (tt0) cc_final: 0.8386 (tm-30) outliers start: 19 outliers final: 3 residues processed: 87 average time/residue: 0.8740 time to fit residues: 83.7080 Evaluate side-chains 71 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 386 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: 0.4980 chunk 48 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 98 optimal weight: 0.0040 chunk 88 optimal weight: 0.0170 chunk 26 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 overall best weight: 0.2748 ------------------------------------------------------------------------------- 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: 0.8693 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8792 Z= 0.150 Angle : 0.567 9.663 11974 Z= 0.265 Chirality : 0.038 0.135 1434 Planarity : 0.005 0.050 1408 Dihedral : 9.082 58.427 1836 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.23 % Allowed : 13.28 % 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: 1.76 (0.27), residues: 1022 helix: 2.09 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -0.85 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 662 HIS 0.002 0.001 HIS B 834 PHE 0.014 0.001 PHE A 526 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 89 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 MET cc_start: 0.8749 (mtm) cc_final: 0.8443 (mtt) REVERT: B 433 ASN cc_start: 0.9378 (m110) cc_final: 0.9110 (m110) REVERT: B 559 MET cc_start: 0.8703 (mtm) cc_final: 0.8406 (mtt) REVERT: B 681 GLU cc_start: 0.8930 (tt0) cc_final: 0.8370 (tm-30) outliers start: 11 outliers final: 6 residues processed: 86 average time/residue: 0.7743 time to fit residues: 74.0851 Evaluate side-chains 70 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 0.0030 chunk 84 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- 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: 0.8751 moved from start: 0.3036 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= 0.241 Angle : 0.597 8.523 11974 Z= 0.277 Chirality : 0.039 0.137 1434 Planarity : 0.005 0.047 1408 Dihedral : 9.012 59.806 1836 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.67 % Allowed : 13.50 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.17 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -0.77 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 662 HIS 0.002 0.001 HIS A 651 PHE 0.012 0.001 PHE A 471 TYR 0.016 0.001 TYR B 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 81 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 559 MET cc_start: 0.8776 (mtm) cc_final: 0.8408 (mtt) REVERT: A 705 ASP cc_start: 0.9152 (m-30) cc_final: 0.8843 (m-30) REVERT: B 433 ASN cc_start: 0.9383 (m110) cc_final: 0.9118 (m110) REVERT: B 559 MET cc_start: 0.8734 (mtm) cc_final: 0.8395 (mtt) REVERT: B 681 GLU cc_start: 0.8958 (tt0) cc_final: 0.8437 (tt0) REVERT: B 705 ASP cc_start: 0.9139 (m-30) cc_final: 0.8825 (m-30) outliers start: 15 outliers final: 6 residues processed: 76 average time/residue: 0.7835 time to fit residues: 66.3213 Evaluate side-chains 70 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 24 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 95 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.3199 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= 0.191 Angle : 0.576 9.167 11974 Z= 0.267 Chirality : 0.039 0.145 1434 Planarity : 0.004 0.048 1408 Dihedral : 8.814 59.862 1836 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.90 % Allowed : 13.39 % Favored : 84.71 % 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: 1.83 (0.27), residues: 1022 helix: 2.06 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.73 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 492 HIS 0.001 0.001 HIS B 834 PHE 0.012 0.001 PHE A 471 TYR 0.015 0.001 TYR B 824 ARG 0.004 0.000 ARG A 490 *********************** 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 87 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 559 MET cc_start: 0.8792 (mtm) cc_final: 0.8415 (mtt) REVERT: A 721 MET cc_start: 0.8777 (mmm) cc_final: 0.8458 (mpp) REVERT: B 433 ASN cc_start: 0.9398 (m110) cc_final: 0.9089 (m110) REVERT: B 559 MET cc_start: 0.8757 (mtm) cc_final: 0.8395 (mtt) outliers start: 17 outliers final: 8 residues processed: 84 average time/residue: 0.6952 time to fit residues: 65.8342 Evaluate side-chains 70 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 98 optimal weight: 0.0270 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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: 0.8737 moved from start: 0.3337 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= 0.174 Angle : 0.602 10.190 11974 Z= 0.277 Chirality : 0.039 0.166 1434 Planarity : 0.005 0.047 1408 Dihedral : 8.661 59.634 1836 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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: 1.81 (0.27), residues: 1022 helix: 2.03 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.70 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 492 HIS 0.001 0.001 HIS A 703 PHE 0.012 0.001 PHE A 471 TYR 0.015 0.001 TYR B 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 76 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 559 MET cc_start: 0.8789 (mtm) cc_final: 0.8480 (mtt) REVERT: A 705 ASP cc_start: 0.9117 (m-30) cc_final: 0.8851 (m-30) REVERT: B 433 ASN cc_start: 0.9356 (m110) cc_final: 0.8990 (m110) REVERT: B 559 MET cc_start: 0.8777 (mtm) cc_final: 0.8415 (mtt) REVERT: B 601 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8529 (tm) REVERT: B 705 ASP cc_start: 0.9116 (m-30) cc_final: 0.8858 (m-30) outliers start: 10 outliers final: 6 residues processed: 75 average time/residue: 0.8369 time to fit residues: 69.9560 Evaluate side-chains 70 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 85 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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: 0.8739 moved from start: 0.3462 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= 0.182 Angle : 0.621 11.930 11974 Z= 0.282 Chirality : 0.040 0.227 1434 Planarity : 0.004 0.047 1408 Dihedral : 8.498 59.061 1836 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.34 % Allowed : 15.07 % Favored : 83.59 % 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: 2.04 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.65 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 492 HIS 0.002 0.001 HIS B 703 PHE 0.012 0.001 PHE A 471 TYR 0.014 0.001 TYR B 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 82 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 559 MET cc_start: 0.8759 (mtm) cc_final: 0.8469 (mtt) REVERT: A 705 ASP cc_start: 0.9119 (m-30) cc_final: 0.8820 (m-30) REVERT: B 433 ASN cc_start: 0.9364 (m110) cc_final: 0.9006 (m110) REVERT: B 559 MET cc_start: 0.8804 (mtm) cc_final: 0.8482 (mtt) REVERT: B 601 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8530 (tm) REVERT: B 705 ASP cc_start: 0.9118 (m-30) cc_final: 0.8825 (m-30) outliers start: 12 outliers final: 8 residues processed: 78 average time/residue: 0.7973 time to fit residues: 69.3142 Evaluate side-chains 74 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 889 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 0.0270 chunk 59 optimal weight: 0.0370 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 880 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3556 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= 0.178 Angle : 0.641 12.780 11974 Z= 0.292 Chirality : 0.041 0.317 1434 Planarity : 0.004 0.047 1408 Dihedral : 8.380 58.628 1836 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.23 % Allowed : 15.51 % Favored : 83.26 % 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: 1.83 (0.27), residues: 1022 helix: 2.03 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.66 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 492 HIS 0.002 0.001 HIS B 703 PHE 0.012 0.001 PHE A 471 TYR 0.013 0.001 TYR A 824 ARG 0.003 0.000 ARG B 827 *********************** 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 78 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 559 MET cc_start: 0.8711 (mtm) cc_final: 0.8450 (mtt) REVERT: A 601 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8531 (tm) REVERT: A 705 ASP cc_start: 0.9112 (m-30) cc_final: 0.8802 (m-30) REVERT: B 433 ASN cc_start: 0.9346 (m110) cc_final: 0.8992 (m110) REVERT: B 559 MET cc_start: 0.8795 (mtm) cc_final: 0.8478 (mtt) REVERT: B 601 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8488 (tm) REVERT: B 705 ASP cc_start: 0.9116 (m-30) cc_final: 0.8815 (m-30) outliers start: 11 outliers final: 8 residues processed: 77 average time/residue: 0.7700 time to fit residues: 66.4604 Evaluate side-chains 75 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 653 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 653 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: 0.0870 chunk 93 optimal weight: 4.9990 chunk 80 optimal weight: 0.0060 chunk 8 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.5174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 880 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3666 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= 0.182 Angle : 0.683 14.062 11974 Z= 0.307 Chirality : 0.041 0.313 1434 Planarity : 0.004 0.045 1408 Dihedral : 8.283 59.126 1836 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.34 % Allowed : 15.29 % Favored : 83.37 % 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: 1.74 (0.27), residues: 1022 helix: 1.96 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.69 (0.34), residues: 318 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 0.012 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 79 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 559 MET cc_start: 0.8699 (mtm) cc_final: 0.8440 (mtt) REVERT: A 601 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8533 (tm) REVERT: A 705 ASP cc_start: 0.9093 (m-30) cc_final: 0.8786 (m-30) REVERT: B 433 ASN cc_start: 0.9313 (m110) cc_final: 0.8934 (m110) REVERT: B 559 MET cc_start: 0.8790 (mtm) cc_final: 0.8496 (mtt) REVERT: B 601 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8499 (tm) REVERT: B 705 ASP cc_start: 0.9097 (m-30) cc_final: 0.8796 (m-30) outliers start: 12 outliers final: 9 residues processed: 77 average time/residue: 0.7438 time to fit residues: 64.0576 Evaluate side-chains 76 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 653 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 653 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: 0.6980 chunk 33 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.058656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.049937 restraints weight = 29874.404| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.29 r_work: 0.2682 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8792 Z= 0.218 Angle : 0.725 17.132 11974 Z= 0.321 Chirality : 0.042 0.301 1434 Planarity : 0.004 0.040 1408 Dihedral : 8.235 59.209 1836 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.34 % Allowed : 15.51 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.27), residues: 1022 helix: 1.92 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.66 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 492 HIS 0.002 0.001 HIS B 834 PHE 0.011 0.001 PHE A 471 TYR 0.013 0.001 TYR A 824 ARG 0.003 0.000 ARG A 656 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2412.56 seconds wall clock time: 45 minutes 43.83 seconds (2743.83 seconds total)