Starting phenix.real_space_refine on Sat Mar 16 06:40:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi8_23842/03_2024/7mi8_23842.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi8_23842/03_2024/7mi8_23842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi8_23842/03_2024/7mi8_23842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi8_23842/03_2024/7mi8_23842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi8_23842/03_2024/7mi8_23842.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi8_23842/03_2024/7mi8_23842.pdb" } resolution = 3.7 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6930 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 4542 2.51 5 N 1146 2.21 5 O 1316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 1536": "NH1" <-> "NH2" Residue "A PHE 1537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1543": "OD1" <-> "OD2" Residue "A ASP 1544": "OD1" <-> "OD2" Residue "A PHE 1578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1594": "OE1" <-> "OE2" Residue "A ASP 1600": "OD1" <-> "OD2" Residue "A ASP 1612": "OD1" <-> "OD2" Residue "A GLU 1614": "OE1" <-> "OE2" Residue "A ASP 1635": "OD1" <-> "OD2" Residue "A ASP 1677": "OD1" <-> "OD2" Residue "A ASP 1692": "OD1" <-> "OD2" Residue "A ASP 1742": "OD1" <-> "OD2" Residue "A TYR 1758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1824": "OD1" <-> "OD2" Residue "A PHE 1826": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1827": "OD1" <-> "OD2" Residue "A GLU 1855": "OE1" <-> "OE2" Residue "A GLU 1884": "OE1" <-> "OE2" Residue "A GLU 1910": "OE1" <-> "OE2" Residue "A PHE 3638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3672": "OD1" <-> "OD2" Residue "A TYR 3679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3717": "OE1" <-> "OE2" Residue "A ASP 3731": "OD1" <-> "OD2" Residue "A ASP 3739": "OD1" <-> "OD2" Residue "A ASP 3742": "OD1" <-> "OD2" Residue "A TYR 3746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3770": "OD1" <-> "OD2" Residue "A GLU 3771": "OE1" <-> "OE2" Residue "A ASP 3776": "OD1" <-> "OD2" Residue "A GLU 3782": "OE1" <-> "OE2" Residue "A GLU 3791": "OE1" <-> "OE2" Residue "A ARG 3792": "NH1" <-> "NH2" Residue "A ASP 3795": "OD1" <-> "OD2" Residue "A GLU 3802": "OE1" <-> "OE2" Residue "A TYR 3854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3860": "OE1" <-> "OE2" Residue "A GLU 3898": "OE1" <-> "OE2" Residue "A ASP 3905": "OD1" <-> "OD2" Residue "A ASP 3909": "OD1" <-> "OD2" Residue "A PHE 3916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4000": "OE1" <-> "OE2" Residue "A GLU 4005": "OE1" <-> "OE2" Residue "A ASP 4019": "OD1" <-> "OD2" Residue "A ARG 4028": "NH1" <-> "NH2" Residue "A GLU 4041": "OE1" <-> "OE2" Residue "A GLU 4054": "OE1" <-> "OE2" Residue "A GLU 4068": "OE1" <-> "OE2" Residue "A GLU 4074": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7034 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 7034 Classifications: {'peptide': 868} Link IDs: {'PTRANS': 21, 'TRANS': 846} Chain breaks: 2 Time building chain proxies: 4.42, per 1000 atoms: 0.63 Number of scatterers: 7034 At special positions: 0 Unit cell: (105.672, 117.586, 91.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1316 8.00 N 1146 7.00 C 4542 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 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.2 seconds 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1642 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 5 sheets defined 63.4% alpha, 7.4% 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 1524 through 1534 Processing helix chain 'A' and resid 1535 through 1539 removed outlier: 3.530A pdb=" N TYR A1538 " --> pdb=" O PRO A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1551 removed outlier: 3.535A pdb=" N LYS A1547 " --> pdb=" O ASP A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1558 through 1567 removed outlier: 4.395A pdb=" N LYS A1563 " --> pdb=" O SER A1559 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LYS A1564 " --> pdb=" O LYS A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1632 removed outlier: 3.811A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A1616 " --> pdb=" O ASP A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1641 removed outlier: 3.965A pdb=" N SER A1641 " --> pdb=" O GLU A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1667 removed outlier: 3.775A pdb=" N LYS A1662 " --> pdb=" O GLU A1658 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A1665 " --> pdb=" O GLU A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1689 removed outlier: 3.581A pdb=" N TYR A1672 " --> pdb=" O GLN A1668 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A1675 " --> pdb=" O LYS A1671 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A1689 " --> pdb=" O ASP A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1717 removed outlier: 4.108A pdb=" N LYS A1696 " --> pdb=" O ASP A1692 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A1697 " --> pdb=" O ASN A1693 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU A1704 " --> pdb=" O ALA A1700 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A1717 " --> pdb=" O GLY A1713 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1731 removed outlier: 4.098A pdb=" N LYS A1730 " --> pdb=" O LEU A1726 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A1731 " --> pdb=" O LEU A1727 " (cutoff:3.500A) Processing helix chain 'A' and resid 1742 through 1745 Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 3.949A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1813 removed outlier: 3.570A pdb=" N LEU A1813 " --> pdb=" O PHE A1809 " (cutoff:3.500A) Processing helix chain 'A' and resid 1827 through 1842 removed outlier: 3.683A pdb=" N LEU A1831 " --> pdb=" O ASP A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1854 through 1875 Processing helix chain 'A' and resid 1909 through 1913 removed outlier: 3.525A pdb=" N LYS A1913 " --> pdb=" O GLU A1910 " (cutoff:3.500A) Processing helix chain 'A' and resid 3617 through 3639 removed outlier: 3.618A pdb=" N HIS A3624 " --> pdb=" O ILE A3620 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A3627 " --> pdb=" O LYS A3623 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS A3639 " --> pdb=" O PHE A3635 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3655 removed outlier: 3.679A pdb=" N PHE A3649 " --> pdb=" O SER A3645 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A3655 " --> pdb=" O SER A3651 " (cutoff:3.500A) Processing helix chain 'A' and resid 3670 through 3687 removed outlier: 3.944A pdb=" N TRP A3676 " --> pdb=" O ASP A3672 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER A3687 " --> pdb=" O TYR A3683 " (cutoff:3.500A) Processing helix chain 'A' and resid 3688 through 3690 No H-bonds generated for 'chain 'A' and resid 3688 through 3690' Processing helix chain 'A' and resid 3691 through 3711 removed outlier: 4.425A pdb=" N ASP A3709 " --> pdb=" O LEU A3705 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A3710 " --> pdb=" O TYR A3706 " (cutoff:3.500A) Processing helix chain 'A' and resid 3712 through 3727 removed outlier: 3.595A pdb=" N LYS A3716 " --> pdb=" O SER A3712 " (cutoff:3.500A) Processing helix chain 'A' and resid 3745 through 3753 removed outlier: 3.546A pdb=" N THR A3753 " --> pdb=" O ASP A3749 " (cutoff:3.500A) Processing helix chain 'A' and resid 3756 through 3768 removed outlier: 4.409A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS A3764 " --> pdb=" O LEU A3760 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE A3767 " --> pdb=" O PHE A3763 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A3768 " --> pdb=" O LYS A3764 " (cutoff:3.500A) Processing helix chain 'A' and resid 3773 through 3781 Processing helix chain 'A' and resid 3796 through 3808 removed outlier: 3.524A pdb=" N GLU A3802 " --> pdb=" O PHE A3798 " (cutoff:3.500A) Processing helix chain 'A' and resid 3818 through 3836 removed outlier: 4.471A pdb=" N ILE A3834 " --> pdb=" O SER A3830 " (cutoff:3.500A) Processing helix chain 'A' and resid 3847 through 3854 removed outlier: 3.633A pdb=" N THR A3853 " --> pdb=" O SER A3849 " (cutoff:3.500A) Processing helix chain 'A' and resid 3854 through 3861 removed outlier: 4.641A pdb=" N GLU A3861 " --> pdb=" O LYS A3857 " (cutoff:3.500A) Processing helix chain 'A' and resid 3864 through 3870 removed outlier: 3.917A pdb=" N HIS A3868 " --> pdb=" O ALA A3864 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS A3870 " --> pdb=" O GLU A3866 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3892 Processing helix chain 'A' and resid 3902 through 3913 removed outlier: 3.664A pdb=" N SER A3913 " --> pdb=" O ASP A3909 " (cutoff:3.500A) Processing helix chain 'A' and resid 3922 through 3944 removed outlier: 3.899A pdb=" N VAL A3926 " --> pdb=" O GLY A3922 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A3927 " --> pdb=" O VAL A3923 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG A3944 " --> pdb=" O THR A3940 " (cutoff:3.500A) Processing helix chain 'A' and resid 3957 through 3974 removed outlier: 4.058A pdb=" N PHE A3961 " --> pdb=" O ASN A3957 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A3974 " --> pdb=" O ASN A3970 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3992 removed outlier: 4.116A pdb=" N ARG A3986 " --> pdb=" O TRP A3982 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP A3987 " --> pdb=" O ALA A3983 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS A3988 " --> pdb=" O GLN A3984 " (cutoff:3.500A) Processing helix chain 'A' and resid 4000 through 4015 removed outlier: 3.524A pdb=" N HIS A4013 " --> pdb=" O LYS A4009 " (cutoff:3.500A) Processing helix chain 'A' and resid 4037 through 4051 Processing helix chain 'A' and resid 4057 through 4062 Processing helix chain 'A' and resid 4066 through 4091 removed outlier: 3.692A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1569 through 1574 removed outlier: 6.819A pdb=" N ARG A1583 " --> pdb=" O GLU A1570 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE A1572 " --> pdb=" O GLY A1581 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLY A1581 " --> pdb=" O ILE A1572 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N PHE A1574 " --> pdb=" O ILE A1579 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE A1579 " --> pdb=" O PHE A1574 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1733 through 1736 Processing sheet with id=AA3, first strand: chain 'A' and resid 1818 through 1820 removed outlier: 7.009A pdb=" N GLY A1792 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N LEU A1898 " --> pdb=" O GLY A1792 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE A1794 " --> pdb=" O LEU A1898 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY A1791 " --> pdb=" O ARG A1917 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE A1919 " --> pdb=" O GLY A1791 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N CYS A1793 " --> pdb=" O PHE A1919 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id=AA5, first strand: chain 'A' and resid 3812 through 3815 removed outlier: 3.840A pdb=" N GLN A3842 " --> pdb=" O ILE A3814 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N THR A3876 " --> pdb=" O ILE A3839 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU A3841 " --> pdb=" O THR A3876 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N HIS A3878 " --> pdb=" O LEU A3841 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS A3877 " --> pdb=" O MET A3788 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR A3785 " --> pdb=" O ASP A3893 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL A3895 " --> pdb=" O TYR A3785 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N THR A3787 " --> pdb=" O VAL A3895 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1092 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: 2.26 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2215 1.34 - 1.46: 1502 1.46 - 1.58: 3424 1.58 - 1.70: 0 1.70 - 1.81: 46 Bond restraints: 7187 Sorted by residual: bond pdb=" CB ASP A4019 " pdb=" CG ASP A4019 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.89e+00 bond pdb=" CG LEU A1702 " pdb=" CD2 LEU A1702 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.66e+00 bond pdb=" CB MET A3788 " pdb=" CG MET A3788 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.06e+00 bond pdb=" CG LEU A1545 " pdb=" CD1 LEU A1545 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.86e+00 bond pdb=" CA THR A3737 " pdb=" CB THR A3737 " ideal model delta sigma weight residual 1.530 1.553 -0.023 1.69e-02 3.50e+03 1.79e+00 ... (remaining 7182 not shown) Histogram of bond angle deviations from ideal: 97.04 - 104.46: 73 104.46 - 111.88: 3306 111.88 - 119.30: 2680 119.30 - 126.72: 3553 126.72 - 134.14: 100 Bond angle restraints: 9712 Sorted by residual: angle pdb=" C LEU A3736 " pdb=" N THR A3737 " pdb=" CA THR A3737 " ideal model delta sigma weight residual 121.54 132.65 -11.11 1.91e+00 2.74e-01 3.38e+01 angle pdb=" N THR A3737 " pdb=" CA THR A3737 " pdb=" C THR A3737 " ideal model delta sigma weight residual 110.80 100.37 10.43 2.13e+00 2.20e-01 2.40e+01 angle pdb=" CA LEU A1882 " pdb=" CB LEU A1882 " pdb=" CG LEU A1882 " ideal model delta sigma weight residual 116.30 132.64 -16.34 3.50e+00 8.16e-02 2.18e+01 angle pdb=" CA LEU A1741 " pdb=" CB LEU A1741 " pdb=" CG LEU A1741 " ideal model delta sigma weight residual 116.30 131.52 -15.22 3.50e+00 8.16e-02 1.89e+01 angle pdb=" CA LEU A4033 " pdb=" CB LEU A4033 " pdb=" CG LEU A4033 " ideal model delta sigma weight residual 116.30 130.64 -14.34 3.50e+00 8.16e-02 1.68e+01 ... (remaining 9707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3923 17.89 - 35.79: 272 35.79 - 53.68: 59 53.68 - 71.57: 14 71.57 - 89.46: 12 Dihedral angle restraints: 4280 sinusoidal: 1742 harmonic: 2538 Sorted by residual: dihedral pdb=" CA GLU A3809 " pdb=" C GLU A3809 " pdb=" N SER A3810 " pdb=" CA SER A3810 " ideal model delta harmonic sigma weight residual 180.00 160.61 19.39 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CB GLU A4068 " pdb=" CG GLU A4068 " pdb=" CD GLU A4068 " pdb=" OE1 GLU A4068 " ideal model delta sinusoidal sigma weight residual 0.00 88.58 -88.58 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA ASP A1742 " pdb=" C ASP A1742 " pdb=" N ASP A1743 " pdb=" CA ASP A1743 " ideal model delta harmonic sigma weight residual 180.00 -164.24 -15.76 0 5.00e+00 4.00e-02 9.94e+00 ... (remaining 4277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 706 0.046 - 0.092: 268 0.092 - 0.137: 89 0.137 - 0.183: 13 0.183 - 0.229: 6 Chirality restraints: 1082 Sorted by residual: chirality pdb=" CA ASP A4019 " pdb=" N ASP A4019 " pdb=" C ASP A4019 " pdb=" CB ASP A4019 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA PHE A1794 " pdb=" N PHE A1794 " pdb=" C PHE A1794 " pdb=" CB PHE A1794 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB THR A1740 " pdb=" CA THR A1740 " pdb=" OG1 THR A1740 " pdb=" CG2 THR A1740 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.82e-01 ... (remaining 1079 not shown) Planarity restraints: 1225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A3801 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ILE A3801 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE A3801 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A3802 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A1562 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.95e+00 pdb=" C MET A1562 " 0.055 2.00e-02 2.50e+03 pdb=" O MET A1562 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS A1563 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A1554 " 0.018 2.00e-02 2.50e+03 2.49e-02 9.32e+00 pdb=" CG HIS A1554 " -0.053 2.00e-02 2.50e+03 pdb=" ND1 HIS A1554 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS A1554 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 HIS A1554 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A1554 " -0.001 2.00e-02 2.50e+03 ... (remaining 1222 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1217 2.76 - 3.30: 6889 3.30 - 3.83: 11188 3.83 - 4.37: 13130 4.37 - 4.90: 22444 Nonbonded interactions: 54868 Sorted by model distance: nonbonded pdb=" O LEU A1687 " pdb=" OG SER A1690 " model vdw 2.226 2.440 nonbonded pdb=" O LEU A3736 " pdb=" OG1 THR A3737 " model vdw 2.251 2.440 nonbonded pdb=" O ASN A3761 " pdb=" ND2 ASN A3765 " model vdw 2.282 2.520 nonbonded pdb=" O LYS A3805 " pdb=" NZ LYS A3808 " model vdw 2.300 2.520 nonbonded pdb=" NZ LYS A3735 " pdb=" O THR A3737 " model vdw 2.338 2.520 ... (remaining 54863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 11.110 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.210 Find NCS groups from input model: 0.160 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:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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 : 0.006 0.054 7187 Z= 0.384 Angle : 0.967 16.338 9712 Z= 0.524 Chirality : 0.054 0.229 1082 Planarity : 0.007 0.033 1225 Dihedral : 14.131 89.462 2638 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.44 % Favored : 97.45 % Rotamer: Outliers : 0.38 % Allowed : 4.22 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.21), residues: 862 helix: -2.18 (0.15), residues: 481 sheet: -0.68 (0.68), residues: 61 loop : -1.86 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A3934 HIS 0.032 0.003 HIS A1554 PHE 0.030 0.003 PHE A1794 TYR 0.022 0.002 TYR A1705 ARG 0.003 0.001 ARG A1768 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 179 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1556 ASP cc_start: 0.7787 (p0) cc_final: 0.7108 (p0) REVERT: A 1708 PHE cc_start: 0.8719 (m-10) cc_final: 0.8413 (m-10) REVERT: A 1738 ASN cc_start: 0.8885 (p0) cc_final: 0.8627 (p0) REVERT: A 1878 HIS cc_start: 0.8491 (m90) cc_final: 0.8013 (m-70) REVERT: A 3627 LYS cc_start: 0.8511 (mttt) cc_final: 0.8140 (mtmt) REVERT: A 3711 GLU cc_start: 0.7502 (mp0) cc_final: 0.6469 (tp30) REVERT: A 3776 ASP cc_start: 0.8939 (m-30) cc_final: 0.8602 (m-30) REVERT: A 3798 PHE cc_start: 0.8907 (m-80) cc_final: 0.8571 (m-80) REVERT: A 3984 GLN cc_start: 0.8847 (pm20) cc_final: 0.8622 (pm20) outliers start: 3 outliers final: 1 residues processed: 181 average time/residue: 0.2394 time to fit residues: 55.5035 Evaluate side-chains 101 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1793 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.0370 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1554 HIS A1555 HIS A1646 GLN A1693 ASN A1869 GLN ** A1899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3856 HIS A3948 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7187 Z= 0.161 Angle : 0.588 12.274 9712 Z= 0.304 Chirality : 0.040 0.171 1082 Planarity : 0.004 0.031 1225 Dihedral : 4.036 21.086 924 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.92 % Allowed : 11.64 % Favored : 86.45 % 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: -0.53 (0.26), residues: 862 helix: 0.41 (0.22), residues: 478 sheet: -0.28 (0.70), residues: 61 loop : -1.45 (0.30), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1607 HIS 0.011 0.001 HIS A1554 PHE 0.026 0.002 PHE A3703 TYR 0.015 0.001 TYR A1672 ARG 0.005 0.000 ARG A1529 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1710 ASN cc_start: 0.8506 (t0) cc_final: 0.8094 (t0) REVERT: A 1878 HIS cc_start: 0.8435 (m90) cc_final: 0.7958 (m-70) REVERT: A 3627 LYS cc_start: 0.8295 (mttt) cc_final: 0.8034 (mttp) REVERT: A 3678 LEU cc_start: 0.9051 (tt) cc_final: 0.8830 (tt) REVERT: A 3681 GLU cc_start: 0.8588 (tp30) cc_final: 0.8210 (tp30) REVERT: A 3795 ASP cc_start: 0.8343 (p0) cc_final: 0.8136 (p0) REVERT: A 3798 PHE cc_start: 0.8939 (m-80) cc_final: 0.8544 (m-80) REVERT: A 3883 LYS cc_start: 0.9060 (tttp) cc_final: 0.8600 (ttmm) REVERT: A 4074 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8483 (mt-10) outliers start: 15 outliers final: 4 residues processed: 121 average time/residue: 0.1720 time to fit residues: 28.6899 Evaluate side-chains 94 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1568 SER Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 3882 ASP Chi-restraints excluded: chain A residue 3951 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 84 optimal weight: 0.0870 chunk 69 optimal weight: 8.9990 chunk 77 optimal weight: 0.3980 chunk 26 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1788 GLN A1869 GLN ** A1899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3773 ASN ** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3856 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7187 Z= 0.205 Angle : 0.571 11.607 9712 Z= 0.296 Chirality : 0.041 0.294 1082 Planarity : 0.003 0.027 1225 Dihedral : 4.005 21.456 923 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.30 % Allowed : 13.94 % Favored : 83.76 % 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: 0.33 (0.28), residues: 862 helix: 1.21 (0.23), residues: 483 sheet: 0.07 (0.71), residues: 61 loop : -1.28 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1607 HIS 0.009 0.001 HIS A1555 PHE 0.024 0.002 PHE A3786 TYR 0.022 0.001 TYR A1672 ARG 0.003 0.000 ARG A1529 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1710 ASN cc_start: 0.8639 (t0) cc_final: 0.8137 (t0) REVERT: A 1878 HIS cc_start: 0.8465 (m90) cc_final: 0.7993 (m-70) REVERT: A 3627 LYS cc_start: 0.8366 (mttt) cc_final: 0.8123 (mttp) REVERT: A 3637 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7832 (mp10) REVERT: A 3681 GLU cc_start: 0.8478 (tp30) cc_final: 0.8050 (tp30) REVERT: A 3795 ASP cc_start: 0.8404 (p0) cc_final: 0.8203 (p0) REVERT: A 3798 PHE cc_start: 0.8955 (m-80) cc_final: 0.8519 (m-80) REVERT: A 3800 LEU cc_start: 0.9719 (mt) cc_final: 0.9509 (mp) REVERT: A 3883 LYS cc_start: 0.9096 (tttp) cc_final: 0.8646 (ttmm) outliers start: 18 outliers final: 10 residues processed: 103 average time/residue: 0.1452 time to fit residues: 22.2420 Evaluate side-chains 96 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1883 GLU Chi-restraints excluded: chain A residue 3620 ILE Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3844 ILE Chi-restraints excluded: chain A residue 3882 ASP Chi-restraints excluded: chain A residue 3939 ILE Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3856 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7187 Z= 0.198 Angle : 0.549 10.047 9712 Z= 0.282 Chirality : 0.040 0.255 1082 Planarity : 0.003 0.026 1225 Dihedral : 3.966 21.702 923 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.69 % Allowed : 15.22 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.28), residues: 862 helix: 1.52 (0.23), residues: 486 sheet: -0.00 (0.69), residues: 61 loop : -1.20 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1607 HIS 0.007 0.001 HIS A1555 PHE 0.027 0.002 PHE A1708 TYR 0.022 0.001 TYR A1672 ARG 0.002 0.000 ARG A1529 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1573 ILE cc_start: 0.8818 (mt) cc_final: 0.8483 (pt) REVERT: A 1710 ASN cc_start: 0.8671 (t0) cc_final: 0.8214 (t0) REVERT: A 1878 HIS cc_start: 0.8490 (m90) cc_final: 0.8017 (m-70) REVERT: A 3637 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7936 (mp10) REVERT: A 3681 GLU cc_start: 0.8516 (tp30) cc_final: 0.8111 (tp30) REVERT: A 3795 ASP cc_start: 0.8450 (p0) cc_final: 0.8242 (p0) REVERT: A 3798 PHE cc_start: 0.8955 (m-80) cc_final: 0.8520 (m-80) REVERT: A 3800 LEU cc_start: 0.9713 (mt) cc_final: 0.9484 (mp) REVERT: A 3883 LYS cc_start: 0.9116 (tttp) cc_final: 0.8661 (ttmm) outliers start: 21 outliers final: 13 residues processed: 101 average time/residue: 0.1446 time to fit residues: 21.2774 Evaluate side-chains 100 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1568 SER Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1883 GLU Chi-restraints excluded: chain A residue 3620 ILE Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3736 LEU Chi-restraints excluded: chain A residue 3844 ILE Chi-restraints excluded: chain A residue 3939 ILE Chi-restraints excluded: chain A residue 3951 SER Chi-restraints excluded: chain A residue 3969 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1829 GLN A1840 GLN ** A1899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3856 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7187 Z= 0.319 Angle : 0.629 8.462 9712 Z= 0.326 Chirality : 0.043 0.269 1082 Planarity : 0.003 0.032 1225 Dihedral : 4.320 21.847 923 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.22 % Allowed : 14.96 % Favored : 80.82 % 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: 0.76 (0.27), residues: 862 helix: 1.58 (0.23), residues: 481 sheet: -0.31 (0.59), residues: 73 loop : -1.00 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1607 HIS 0.005 0.002 HIS A3856 PHE 0.023 0.002 PHE A1794 TYR 0.018 0.002 TYR A1705 ARG 0.003 0.000 ARG A1532 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 92 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 1706 LEU cc_start: 0.9151 (mp) cc_final: 0.8949 (mp) REVERT: A 1790 TYR cc_start: 0.8850 (m-80) cc_final: 0.8622 (m-10) REVERT: A 1878 HIS cc_start: 0.8604 (m90) cc_final: 0.8151 (m-70) REVERT: A 3627 LYS cc_start: 0.8501 (mttt) cc_final: 0.8172 (mtmt) REVERT: A 3637 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8142 (mp10) REVERT: A 3681 GLU cc_start: 0.8574 (tp30) cc_final: 0.8172 (tp30) REVERT: A 3795 ASP cc_start: 0.8539 (p0) cc_final: 0.8330 (p0) REVERT: A 3798 PHE cc_start: 0.8954 (m-80) cc_final: 0.8518 (m-80) REVERT: A 3800 LEU cc_start: 0.9735 (mt) cc_final: 0.9516 (mp) REVERT: A 3883 LYS cc_start: 0.9134 (tttp) cc_final: 0.8679 (ttmm) REVERT: A 4074 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8501 (mt-10) outliers start: 33 outliers final: 21 residues processed: 111 average time/residue: 0.1442 time to fit residues: 23.4601 Evaluate side-chains 102 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1568 SER Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1911 ASN Chi-restraints excluded: chain A residue 3620 ILE Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3736 LEU Chi-restraints excluded: chain A residue 3739 ASP Chi-restraints excluded: chain A residue 3742 ASP Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3780 ASN Chi-restraints excluded: chain A residue 3882 ASP Chi-restraints excluded: chain A residue 3939 ILE Chi-restraints excluded: chain A residue 3951 SER Chi-restraints excluded: chain A residue 3969 GLU Chi-restraints excluded: chain A residue 4065 LEU Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1533 GLN A3714 GLN ** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3856 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7187 Z= 0.258 Angle : 0.604 8.530 9712 Z= 0.309 Chirality : 0.041 0.267 1082 Planarity : 0.003 0.046 1225 Dihedral : 4.333 22.074 923 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.73 % Allowed : 16.37 % Favored : 78.90 % 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: 0.89 (0.28), residues: 862 helix: 1.78 (0.23), residues: 476 sheet: -0.44 (0.54), residues: 80 loop : -1.02 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1607 HIS 0.005 0.001 HIS A1555 PHE 0.025 0.002 PHE A1919 TYR 0.015 0.001 TYR A1672 ARG 0.002 0.000 ARG A1532 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 89 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 1722 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7808 (tm-30) REVERT: A 1738 ASN cc_start: 0.8794 (p0) cc_final: 0.8534 (p0) REVERT: A 1790 TYR cc_start: 0.8787 (m-80) cc_final: 0.8558 (m-10) REVERT: A 1878 HIS cc_start: 0.8617 (m90) cc_final: 0.8182 (m-70) REVERT: A 3627 LYS cc_start: 0.8463 (mttt) cc_final: 0.8176 (mtmt) REVERT: A 3637 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8099 (mp10) REVERT: A 3681 GLU cc_start: 0.8542 (tp30) cc_final: 0.8178 (tp30) REVERT: A 3702 MET cc_start: 0.8332 (mmm) cc_final: 0.7833 (tpp) REVERT: A 3757 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7897 (tp) REVERT: A 3795 ASP cc_start: 0.8540 (p0) cc_final: 0.8299 (p0) REVERT: A 3798 PHE cc_start: 0.8957 (m-80) cc_final: 0.8507 (m-80) REVERT: A 3800 LEU cc_start: 0.9737 (mt) cc_final: 0.9529 (mp) REVERT: A 3883 LYS cc_start: 0.9156 (tttp) cc_final: 0.8699 (ttmm) REVERT: A 4074 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8438 (mt-10) outliers start: 37 outliers final: 26 residues processed: 116 average time/residue: 0.1719 time to fit residues: 29.5881 Evaluate side-chains 112 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 84 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1568 SER Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1685 ASP Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1883 GLU Chi-restraints excluded: chain A residue 1911 ASN Chi-restraints excluded: chain A residue 3620 ILE Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3705 LEU Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3736 LEU Chi-restraints excluded: chain A residue 3742 ASP Chi-restraints excluded: chain A residue 3757 ILE Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3780 ASN Chi-restraints excluded: chain A residue 3882 ASP Chi-restraints excluded: chain A residue 3939 ILE Chi-restraints excluded: chain A residue 3951 SER Chi-restraints excluded: chain A residue 3969 GLU Chi-restraints excluded: chain A residue 4004 LEU Chi-restraints excluded: chain A residue 4065 LEU Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1668 GLN ** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3856 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7187 Z= 0.238 Angle : 0.603 8.870 9712 Z= 0.308 Chirality : 0.041 0.277 1082 Planarity : 0.003 0.056 1225 Dihedral : 4.274 21.988 923 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.60 % Allowed : 17.65 % Favored : 77.75 % 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: 0.87 (0.28), residues: 862 helix: 1.81 (0.23), residues: 479 sheet: -0.54 (0.54), residues: 87 loop : -1.14 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1607 HIS 0.005 0.001 HIS A1555 PHE 0.017 0.001 PHE A1919 TYR 0.014 0.001 TYR A1672 ARG 0.002 0.000 ARG A1532 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 88 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1738 ASN cc_start: 0.8807 (p0) cc_final: 0.8549 (p0) REVERT: A 1790 TYR cc_start: 0.8750 (m-80) cc_final: 0.8521 (m-10) REVERT: A 1878 HIS cc_start: 0.8622 (m90) cc_final: 0.8203 (m-70) REVERT: A 3637 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8079 (mp10) REVERT: A 3681 GLU cc_start: 0.8543 (tp30) cc_final: 0.8191 (tp30) REVERT: A 3702 MET cc_start: 0.8337 (mmm) cc_final: 0.7912 (tpp) REVERT: A 3757 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7919 (tp) REVERT: A 3795 ASP cc_start: 0.8533 (p0) cc_final: 0.8273 (p0) REVERT: A 3798 PHE cc_start: 0.8949 (m-80) cc_final: 0.8497 (m-80) REVERT: A 3883 LYS cc_start: 0.9155 (tttp) cc_final: 0.8694 (ttmm) REVERT: A 4074 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8424 (mt-10) outliers start: 36 outliers final: 25 residues processed: 114 average time/residue: 0.1496 time to fit residues: 24.7153 Evaluate side-chains 110 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 83 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1568 SER Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1685 ASP Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1883 GLU Chi-restraints excluded: chain A residue 3620 ILE Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3705 LEU Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3736 LEU Chi-restraints excluded: chain A residue 3742 ASP Chi-restraints excluded: chain A residue 3757 ILE Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3780 ASN Chi-restraints excluded: chain A residue 3882 ASP Chi-restraints excluded: chain A residue 3939 ILE Chi-restraints excluded: chain A residue 3951 SER Chi-restraints excluded: chain A residue 3969 GLU Chi-restraints excluded: chain A residue 4065 LEU Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.0870 chunk 16 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 0.0570 chunk 7 optimal weight: 20.0000 chunk 65 optimal weight: 0.8980 chunk 75 optimal weight: 0.0970 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1557 GLN A1840 GLN ** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3856 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7187 Z= 0.147 Angle : 0.596 10.899 9712 Z= 0.294 Chirality : 0.040 0.305 1082 Planarity : 0.003 0.050 1225 Dihedral : 4.004 21.823 923 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.32 % Allowed : 19.31 % Favored : 77.37 % 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: 1.06 (0.28), residues: 862 helix: 1.91 (0.23), residues: 481 sheet: -0.22 (0.57), residues: 79 loop : -1.03 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1607 HIS 0.006 0.001 HIS A1555 PHE 0.041 0.001 PHE A1708 TYR 0.011 0.001 TYR A1672 ARG 0.002 0.000 ARG A1529 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1573 ILE cc_start: 0.8868 (mt) cc_final: 0.8654 (mp) REVERT: A 1643 TYR cc_start: 0.8077 (m-80) cc_final: 0.7705 (m-10) REVERT: A 1738 ASN cc_start: 0.8791 (p0) cc_final: 0.8571 (p0) REVERT: A 1762 TYR cc_start: 0.9049 (t80) cc_final: 0.8831 (t80) REVERT: A 1878 HIS cc_start: 0.8576 (m90) cc_final: 0.8127 (m-70) REVERT: A 3637 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7926 (mp10) REVERT: A 3681 GLU cc_start: 0.8491 (tp30) cc_final: 0.8180 (tp30) REVERT: A 3795 ASP cc_start: 0.8483 (p0) cc_final: 0.8257 (p0) REVERT: A 3798 PHE cc_start: 0.8921 (m-80) cc_final: 0.8477 (m-80) REVERT: A 3883 LYS cc_start: 0.9146 (tttp) cc_final: 0.8674 (ttmm) REVERT: A 4074 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8321 (mt-10) outliers start: 26 outliers final: 19 residues processed: 124 average time/residue: 0.1445 time to fit residues: 26.0124 Evaluate side-chains 111 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1568 SER Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1883 GLU Chi-restraints excluded: chain A residue 3620 ILE Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3705 LEU Chi-restraints excluded: chain A residue 3736 LEU Chi-restraints excluded: chain A residue 3742 ASP Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3882 ASP Chi-restraints excluded: chain A residue 3951 SER Chi-restraints excluded: chain A residue 3969 GLU Chi-restraints excluded: chain A residue 4004 LEU Chi-restraints excluded: chain A residue 4065 LEU Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3856 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7187 Z= 0.191 Angle : 0.632 10.431 9712 Z= 0.316 Chirality : 0.042 0.318 1082 Planarity : 0.003 0.050 1225 Dihedral : 4.040 21.745 923 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.32 % Allowed : 20.84 % Favored : 75.83 % 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: 1.13 (0.28), residues: 862 helix: 1.97 (0.23), residues: 479 sheet: -0.17 (0.58), residues: 79 loop : -1.00 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1656 HIS 0.005 0.001 HIS A1555 PHE 0.016 0.001 PHE A1708 TYR 0.011 0.001 TYR A1705 ARG 0.002 0.000 ARG A1529 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 93 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1570 GLU cc_start: 0.8404 (tp30) cc_final: 0.8189 (tp30) REVERT: A 1643 TYR cc_start: 0.8101 (m-80) cc_final: 0.7652 (m-10) REVERT: A 1738 ASN cc_start: 0.8783 (p0) cc_final: 0.8561 (p0) REVERT: A 1878 HIS cc_start: 0.8578 (m90) cc_final: 0.8136 (m-70) REVERT: A 3637 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8000 (mp10) REVERT: A 3681 GLU cc_start: 0.8513 (tp30) cc_final: 0.8192 (tp30) REVERT: A 3795 ASP cc_start: 0.8522 (p0) cc_final: 0.8302 (p0) REVERT: A 3798 PHE cc_start: 0.8944 (m-80) cc_final: 0.8541 (m-80) REVERT: A 3883 LYS cc_start: 0.9160 (tttp) cc_final: 0.8687 (ttmm) REVERT: A 4074 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8389 (mt-10) outliers start: 26 outliers final: 22 residues processed: 114 average time/residue: 0.1432 time to fit residues: 24.0749 Evaluate side-chains 111 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1568 SER Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1703 VAL Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1883 GLU Chi-restraints excluded: chain A residue 1911 ASN Chi-restraints excluded: chain A residue 3620 ILE Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3705 LEU Chi-restraints excluded: chain A residue 3736 LEU Chi-restraints excluded: chain A residue 3742 ASP Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3844 ILE Chi-restraints excluded: chain A residue 3882 ASP Chi-restraints excluded: chain A residue 3951 SER Chi-restraints excluded: chain A residue 3969 GLU Chi-restraints excluded: chain A residue 4004 LEU Chi-restraints excluded: chain A residue 4065 LEU Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3856 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7187 Z= 0.299 Angle : 0.672 10.967 9712 Z= 0.343 Chirality : 0.043 0.305 1082 Planarity : 0.003 0.047 1225 Dihedral : 4.265 22.015 923 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.32 % Allowed : 21.23 % Favored : 75.45 % 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: 1.01 (0.28), residues: 862 helix: 1.90 (0.23), residues: 481 sheet: -0.08 (0.58), residues: 82 loop : -1.17 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1607 HIS 0.005 0.001 HIS A3856 PHE 0.018 0.002 PHE A1794 TYR 0.011 0.001 TYR A1705 ARG 0.002 0.000 ARG A1532 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 87 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 1643 TYR cc_start: 0.8194 (m-80) cc_final: 0.7708 (m-10) REVERT: A 1738 ASN cc_start: 0.8787 (p0) cc_final: 0.8532 (p0) REVERT: A 1790 TYR cc_start: 0.8697 (m-80) cc_final: 0.8488 (m-10) REVERT: A 1878 HIS cc_start: 0.8639 (m90) cc_final: 0.8219 (m-70) REVERT: A 3627 LYS cc_start: 0.8424 (mttt) cc_final: 0.8166 (mtmt) REVERT: A 3637 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8049 (mp10) REVERT: A 3681 GLU cc_start: 0.8531 (tp30) cc_final: 0.8191 (tp30) REVERT: A 3795 ASP cc_start: 0.8584 (p0) cc_final: 0.8331 (p0) REVERT: A 3798 PHE cc_start: 0.8980 (m-80) cc_final: 0.8579 (m-80) REVERT: A 4074 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8452 (mt-10) outliers start: 26 outliers final: 23 residues processed: 109 average time/residue: 0.1386 time to fit residues: 22.1293 Evaluate side-chains 109 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1568 SER Chi-restraints excluded: chain A residue 1576 GLU Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1703 VAL Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1883 GLU Chi-restraints excluded: chain A residue 1911 ASN Chi-restraints excluded: chain A residue 3620 ILE Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3705 LEU Chi-restraints excluded: chain A residue 3736 LEU Chi-restraints excluded: chain A residue 3742 ASP Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3844 ILE Chi-restraints excluded: chain A residue 3882 ASP Chi-restraints excluded: chain A residue 3951 SER Chi-restraints excluded: chain A residue 3969 GLU Chi-restraints excluded: chain A residue 4004 LEU Chi-restraints excluded: chain A residue 4065 LEU Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3856 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.097860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.079023 restraints weight = 18981.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.081755 restraints weight = 10226.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.083583 restraints weight = 6880.599| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7187 Z= 0.180 Angle : 0.652 11.648 9712 Z= 0.321 Chirality : 0.042 0.298 1082 Planarity : 0.003 0.051 1225 Dihedral : 4.105 21.579 923 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.58 % Allowed : 21.23 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.29), residues: 862 helix: 1.95 (0.24), residues: 480 sheet: -0.05 (0.59), residues: 82 loop : -1.10 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1656 HIS 0.006 0.001 HIS A3856 PHE 0.019 0.001 PHE A3763 TYR 0.010 0.001 TYR A1705 ARG 0.002 0.000 ARG A1529 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1919.86 seconds wall clock time: 36 minutes 56.47 seconds (2216.47 seconds total)