Starting phenix.real_space_refine on Mon Mar 11 00:05:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg1_33804/03_2024/7yg1_33804_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg1_33804/03_2024/7yg1_33804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg1_33804/03_2024/7yg1_33804.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg1_33804/03_2024/7yg1_33804.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg1_33804/03_2024/7yg1_33804_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg1_33804/03_2024/7yg1_33804_neut.pdb" } resolution = 3.77 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= 0.023 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: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 3961 2.51 5 N 1117 2.21 5 O 1092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 635": "OE1" <-> "OE2" Residue "A ASP 660": "OD1" <-> "OD2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 815": "OE1" <-> "OE2" Residue "A PHE 822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A ASP 838": "OD1" <-> "OD2" Residue "A ASP 839": "OD1" <-> "OD2" Residue "A TYR 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 852": "NH1" <-> "NH2" Residue "A PHE 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 892": "OE1" <-> "OE2" Residue "A PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 934": "NH1" <-> "NH2" Residue "A ASP 936": "OD1" <-> "OD2" Residue "A ASP 943": "OD1" <-> "OD2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "A TYR 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 968": "NH1" <-> "NH2" Residue "A GLU 1013": "OE1" <-> "OE2" Residue "A TYR 1019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 635": "OE1" <-> "OE2" Residue "B TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 755": "OE1" <-> "OE2" Residue "B ASP 756": "OD1" <-> "OD2" Residue "B TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 778": "OE1" <-> "OE2" Residue "B GLU 815": "OE1" <-> "OE2" Residue "B GLU 825": "OE1" <-> "OE2" Residue "B PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 887": "NH1" <-> "NH2" Residue "B ASP 898": "OD1" <-> "OD2" Residue "B GLU 912": "OE1" <-> "OE2" Residue "B PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 944": "OE1" <-> "OE2" Residue "B GLU 945": "OE1" <-> "OE2" Residue "B GLU 1013": "OE1" <-> "OE2" Residue "B TYR 1019": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6208 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3109 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 18, 'TRANS': 366} Chain breaks: 1 Chain: "B" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3099 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 3.88, per 1000 atoms: 0.63 Number of scatterers: 6208 At special positions: 0 Unit cell: (77.404, 82.634, 107.738, 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 38 16.00 O 1092 8.00 N 1117 7.00 C 3961 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 1.3 seconds 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 2 sheets defined 45.5% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.878A pdb=" N ALA A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 655 through 665 removed outlier: 4.194A pdb=" N VAL A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE A 665 " --> pdb=" O PHE A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 703 removed outlier: 4.686A pdb=" N GLN A 690 " --> pdb=" O MET A 686 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU A 691 " --> pdb=" O PRO A 687 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE A 692 " --> pdb=" O GLU A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 726 removed outlier: 3.518A pdb=" N LEU A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A 726 " --> pdb=" O GLN A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 767 removed outlier: 3.987A pdb=" N ASP A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 5.315A pdb=" N PHE A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN A 823 " --> pdb=" O THR A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 844 removed outlier: 3.507A pdb=" N THR A 843 " --> pdb=" O GLY A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 854 through 858 removed outlier: 3.792A pdb=" N LYS A 858 " --> pdb=" O ARG A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 884 removed outlier: 3.743A pdb=" N SER A 884 " --> pdb=" O ILE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 901 removed outlier: 4.274A pdb=" N ASN A 900 " --> pdb=" O PRO A 897 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN A 901 " --> pdb=" O ASP A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 914 removed outlier: 3.518A pdb=" N THR A 908 " --> pdb=" O ARG A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 923 No H-bonds generated for 'chain 'A' and resid 921 through 923' Processing helix chain 'A' and resid 924 through 934 Processing helix chain 'A' and resid 949 through 966 removed outlier: 3.677A pdb=" N SER A 953 " --> pdb=" O ASN A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 998 removed outlier: 4.378A pdb=" N SER A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 628 removed outlier: 3.785A pdb=" N SER B 626 " --> pdb=" O ASN B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 665 removed outlier: 3.749A pdb=" N VAL B 659 " --> pdb=" O ARG B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 703 Processing helix chain 'B' and resid 717 through 728 removed outlier: 4.089A pdb=" N LEU B 724 " --> pdb=" O GLY B 720 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN B 726 " --> pdb=" O GLN B 722 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 727 " --> pdb=" O ILE B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 734 Processing helix chain 'B' and resid 750 through 767 removed outlier: 4.266A pdb=" N VAL B 754 " --> pdb=" O HIS B 750 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 761 " --> pdb=" O TYR B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 820 Processing helix chain 'B' and resid 821 through 824 Processing helix chain 'B' and resid 841 through 852 Proline residue: B 847 - end of helix Processing helix chain 'B' and resid 853 through 859 removed outlier: 3.997A pdb=" N LYS B 858 " --> pdb=" O ARG B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 886 removed outlier: 4.325A pdb=" N ALA B 878 " --> pdb=" O GLN B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 900 removed outlier: 3.901A pdb=" N ILE B 899 " --> pdb=" O LEU B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 914 Processing helix chain 'B' and resid 924 through 935 Processing helix chain 'B' and resid 949 through 965 Processing helix chain 'B' and resid 986 through 998 Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 713 removed outlier: 4.337A pdb=" N GLY A 741 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG A 775 " --> pdb=" O VAL A1005 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.760A pdb=" N PHE B 708 " --> pdb=" O MET B 672 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS B 645 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLY B 675 " --> pdb=" O CYS B 645 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 647 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B 646 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N MET B 774 " --> pdb=" O VAL B 740 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE B 973 " --> pdb=" O ILE B1006 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE B1008 " --> pdb=" O ILE B 973 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE B 975 " --> pdb=" O ILE B1008 " (cutoff:3.500A) 224 hydrogen bonds defined for protein. 636 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: 1.42 Time building geometry restraints manager: 2.74 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: 2041 1.34 - 1.46: 1079 1.46 - 1.58: 3153 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 6335 Sorted by residual: bond pdb=" CA TYR B 621 " pdb=" C TYR B 621 " ideal model delta sigma weight residual 1.524 1.478 0.046 1.28e-02 6.10e+03 1.30e+01 bond pdb=" CA HIS A 750 " pdb=" C HIS A 750 " ideal model delta sigma weight residual 1.524 1.484 0.040 1.26e-02 6.30e+03 9.84e+00 bond pdb=" N PRO A 751 " pdb=" CD PRO A 751 " ideal model delta sigma weight residual 1.473 1.514 -0.041 1.40e-02 5.10e+03 8.61e+00 bond pdb=" N HIS A 750 " pdb=" CA HIS A 750 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.41e-02 5.03e+03 8.05e+00 bond pdb=" N ILE A 880 " pdb=" CA ILE A 880 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.30e-02 5.92e+03 7.81e+00 ... (remaining 6330 not shown) Histogram of bond angle deviations from ideal: 98.56 - 105.64: 164 105.64 - 112.73: 3282 112.73 - 119.81: 2052 119.81 - 126.89: 2969 126.89 - 133.98: 80 Bond angle restraints: 8547 Sorted by residual: angle pdb=" N LEU A 836 " pdb=" CA LEU A 836 " pdb=" C LEU A 836 " ideal model delta sigma weight residual 113.97 101.34 12.63 1.28e+00 6.10e-01 9.74e+01 angle pdb=" N ALA A 878 " pdb=" CA ALA A 878 " pdb=" C ALA A 878 " ideal model delta sigma weight residual 111.28 102.13 9.15 1.09e+00 8.42e-01 7.04e+01 angle pdb=" N ASP B 943 " pdb=" CA ASP B 943 " pdb=" C ASP B 943 " ideal model delta sigma weight residual 112.87 103.14 9.73 1.20e+00 6.94e-01 6.57e+01 angle pdb=" N LEU B 780 " pdb=" CA LEU B 780 " pdb=" C LEU B 780 " ideal model delta sigma weight residual 111.07 103.10 7.97 1.07e+00 8.73e-01 5.55e+01 angle pdb=" C LEU A1016 " pdb=" CA LEU A1016 " pdb=" CB LEU A1016 " ideal model delta sigma weight residual 111.89 101.99 9.90 1.42e+00 4.96e-01 4.86e+01 ... (remaining 8542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 3441 17.59 - 35.18: 357 35.18 - 52.76: 54 52.76 - 70.35: 8 70.35 - 87.94: 5 Dihedral angle restraints: 3865 sinusoidal: 1638 harmonic: 2227 Sorted by residual: dihedral pdb=" N ILE A 880 " pdb=" C ILE A 880 " pdb=" CA ILE A 880 " pdb=" CB ILE A 880 " ideal model delta harmonic sigma weight residual 123.40 135.03 -11.63 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" C ILE A 880 " pdb=" N ILE A 880 " pdb=" CA ILE A 880 " pdb=" CB ILE A 880 " ideal model delta harmonic sigma weight residual -122.00 -132.69 10.69 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" CA VAL B 629 " pdb=" C VAL B 629 " pdb=" N GLY B 630 " pdb=" CA GLY B 630 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 3862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 832 0.085 - 0.169: 92 0.169 - 0.254: 13 0.254 - 0.338: 3 0.338 - 0.423: 2 Chirality restraints: 942 Sorted by residual: chirality pdb=" CA LYS A 784 " pdb=" N LYS A 784 " pdb=" C LYS A 784 " pdb=" CB LYS A 784 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CA HIS A 750 " pdb=" N HIS A 750 " pdb=" C HIS A 750 " pdb=" CB HIS A 750 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA ILE A 880 " pdb=" N ILE A 880 " pdb=" C ILE A 880 " pdb=" CB ILE A 880 " both_signs ideal model delta sigma weight residual False 2.43 2.10 0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 939 not shown) Planarity restraints: 1098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B1002 " 0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO B1003 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B1003 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B1003 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 939 " -0.014 2.00e-02 2.50e+03 1.37e-02 4.66e+00 pdb=" CG TRP B 939 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 939 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 939 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 939 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 939 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 939 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 939 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 939 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 939 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 655 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO B 656 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 656 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 656 " 0.028 5.00e-02 4.00e+02 ... (remaining 1095 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1506 2.76 - 3.30: 6961 3.30 - 3.83: 10805 3.83 - 4.37: 13336 4.37 - 4.90: 19879 Nonbonded interactions: 52487 Sorted by model distance: nonbonded pdb=" OE2 GLU B 755 " pdb=" OG SER B 987 " model vdw 2.230 2.440 nonbonded pdb=" O ASN B 768 " pdb=" ND2 ASN B1011 " model vdw 2.256 2.520 nonbonded pdb=" NH2 ARG B 667 " pdb=" O LYS B 704 " model vdw 2.298 2.520 nonbonded pdb=" O ALA B 878 " pdb=" OG SER B 881 " model vdw 2.310 2.440 nonbonded pdb=" OE1 GLN B 722 " pdb=" NE2 GLN B 726 " model vdw 2.311 2.520 ... (remaining 52482 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' and (resid 617 through 959 or (resid 960 and (name N or name CA or na \ me C or name O or name CB )) or resid 961 through 989 or (resid 990 and (name N \ or name CA or name C or name O or name CB )) or resid 991 through 1020)) selection = chain 'B' } 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.850 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.690 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 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 : 0.005 0.052 6335 Z= 0.309 Angle : 1.151 12.634 8547 Z= 0.753 Chirality : 0.059 0.423 942 Planarity : 0.005 0.059 1098 Dihedral : 14.003 87.938 2425 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 42.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 1.33 % Allowed : 17.85 % Favored : 80.83 % Cbeta Deviations : 0.14 % 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: -3.77 (0.27), residues: 762 helix: -1.54 (0.29), residues: 281 sheet: -1.64 (0.56), residues: 71 loop : -3.53 (0.26), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 939 HIS 0.003 0.001 HIS B 907 PHE 0.016 0.001 PHE B 665 TYR 0.023 0.002 TYR B 627 ARG 0.005 0.001 ARG A 719 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 198 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 LEU cc_start: 0.6959 (tp) cc_final: 0.6590 (tp) REVERT: A 710 SER cc_start: 0.9087 (t) cc_final: 0.8809 (m) REVERT: A 785 MET cc_start: 0.5182 (mpp) cc_final: 0.4601 (mpp) REVERT: A 843 THR cc_start: 0.7276 (p) cc_final: 0.7020 (p) REVERT: A 909 LYS cc_start: 0.5995 (tmtt) cc_final: 0.5785 (tptp) REVERT: A 914 MET cc_start: 0.2879 (ttt) cc_final: 0.2143 (ttt) REVERT: A 926 ASP cc_start: 0.8195 (m-30) cc_final: 0.7658 (p0) REVERT: A 931 ASN cc_start: 0.6945 (m-40) cc_final: 0.6738 (m110) REVERT: A 991 MET cc_start: 0.7301 (tmm) cc_final: 0.6140 (mmm) REVERT: B 621 TYR cc_start: 0.7661 (t80) cc_final: 0.6541 (t80) REVERT: B 642 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6740 (mmp80) REVERT: B 655 ARG cc_start: 0.4581 (mtt180) cc_final: 0.4355 (mtt-85) REVERT: B 712 VAL cc_start: 0.8947 (t) cc_final: 0.8406 (t) REVERT: B 782 VAL cc_start: 0.7480 (OUTLIER) cc_final: 0.7085 (p) REVERT: B 839 ASP cc_start: 0.4554 (t0) cc_final: 0.3829 (p0) REVERT: B 939 TRP cc_start: 0.7722 (p90) cc_final: 0.6834 (m-10) REVERT: B 955 ARG cc_start: 0.8935 (mtt-85) cc_final: 0.8497 (mtt90) outliers start: 9 outliers final: 3 residues processed: 203 average time/residue: 0.2425 time to fit residues: 60.1678 Evaluate side-chains 151 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 821 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN A1014 ASN ** B 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 6335 Z= 0.378 Angle : 0.885 8.940 8547 Z= 0.461 Chirality : 0.052 0.157 942 Planarity : 0.007 0.088 1098 Dihedral : 6.466 44.364 857 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 32.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 6.93 % Allowed : 19.32 % Favored : 73.75 % 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: -3.00 (0.28), residues: 762 helix: -0.81 (0.29), residues: 288 sheet: -1.70 (0.57), residues: 72 loop : -3.06 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP A 939 HIS 0.009 0.002 HIS B 750 PHE 0.028 0.003 PHE A1018 TYR 0.027 0.003 TYR B 834 ARG 0.010 0.001 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 138 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 711 ASP cc_start: 0.8087 (m-30) cc_final: 0.7593 (p0) REVERT: A 785 MET cc_start: 0.5197 (mpp) cc_final: 0.4642 (mpp) REVERT: B 955 ARG cc_start: 0.8975 (mtt-85) cc_final: 0.8693 (mtm180) REVERT: B 1008 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8312 (mm) REVERT: B 1018 PHE cc_start: 0.8209 (t80) cc_final: 0.7971 (t80) outliers start: 47 outliers final: 25 residues processed: 173 average time/residue: 0.1915 time to fit residues: 42.9040 Evaluate side-chains 143 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 668 ASN Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 891 HIS Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 870 ASN Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain B residue 1008 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 55 optimal weight: 0.0040 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6335 Z= 0.233 Angle : 0.791 11.472 8547 Z= 0.395 Chirality : 0.049 0.170 942 Planarity : 0.005 0.055 1098 Dihedral : 5.758 26.531 850 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 26.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 5.01 % Allowed : 21.98 % Favored : 73.01 % 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: -2.47 (0.29), residues: 762 helix: -0.37 (0.30), residues: 293 sheet: -2.19 (0.50), residues: 86 loop : -2.59 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 939 HIS 0.006 0.001 HIS B 750 PHE 0.019 0.002 PHE B 661 TYR 0.018 0.002 TYR B 621 ARG 0.007 0.000 ARG B 642 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 141 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 TRP cc_start: 0.6522 (t60) cc_final: 0.6139 (t60) REVERT: A 711 ASP cc_start: 0.8005 (m-30) cc_final: 0.7492 (p0) REVERT: A 785 MET cc_start: 0.5221 (mpp) cc_final: 0.4837 (mpp) REVERT: B 686 MET cc_start: 0.8156 (ttm) cc_final: 0.7801 (tmm) REVERT: B 856 TRP cc_start: 0.7544 (m100) cc_final: 0.7023 (m-90) REVERT: B 886 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6742 (t80) REVERT: B 939 TRP cc_start: 0.7506 (p90) cc_final: 0.6498 (m-10) REVERT: B 955 ARG cc_start: 0.8947 (mtt-85) cc_final: 0.8501 (mtt90) REVERT: B 1018 PHE cc_start: 0.8230 (t80) cc_final: 0.7796 (t80) outliers start: 34 outliers final: 23 residues processed: 162 average time/residue: 0.1936 time to fit residues: 40.8098 Evaluate side-chains 147 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 668 ASN Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 891 HIS Chi-restraints excluded: chain A residue 907 HIS Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 886 PHE Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 1005 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 0.0270 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6335 Z= 0.209 Angle : 0.754 12.397 8547 Z= 0.372 Chirality : 0.049 0.199 942 Planarity : 0.005 0.044 1098 Dihedral : 5.587 24.835 850 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 23.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 6.64 % Allowed : 21.39 % Favored : 71.98 % 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: -2.17 (0.30), residues: 762 helix: -0.27 (0.30), residues: 298 sheet: -2.06 (0.49), residues: 91 loop : -2.27 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 699 HIS 0.005 0.001 HIS B 750 PHE 0.023 0.002 PHE B 924 TYR 0.019 0.001 TYR B 621 ARG 0.010 0.000 ARG B 667 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 141 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 686 MET cc_start: 0.6544 (ptt) cc_final: 0.6249 (ptt) REVERT: A 699 TRP cc_start: 0.6489 (t60) cc_final: 0.6233 (t60) REVERT: A 711 ASP cc_start: 0.8021 (m-30) cc_final: 0.7475 (p0) REVERT: A 776 MET cc_start: 0.4208 (pmm) cc_final: 0.3707 (pmm) REVERT: A 785 MET cc_start: 0.5157 (mpp) cc_final: 0.4830 (mpp) REVERT: A 1018 PHE cc_start: 0.6548 (OUTLIER) cc_final: 0.6264 (m-80) REVERT: B 686 MET cc_start: 0.8451 (ttm) cc_final: 0.8251 (tmm) REVERT: B 856 TRP cc_start: 0.7384 (m100) cc_final: 0.6893 (m-90) REVERT: B 886 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6777 (t80) REVERT: B 933 MET cc_start: 0.8014 (ppp) cc_final: 0.7672 (ppp) REVERT: B 955 ARG cc_start: 0.8882 (mtt-85) cc_final: 0.8468 (mtm-85) REVERT: B 1018 PHE cc_start: 0.8346 (t80) cc_final: 0.8092 (t80) outliers start: 45 outliers final: 29 residues processed: 169 average time/residue: 0.1716 time to fit residues: 38.3940 Evaluate side-chains 158 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 668 ASN Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 891 HIS Chi-restraints excluded: chain A residue 907 HIS Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 1018 PHE Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 870 ASN Chi-restraints excluded: chain B residue 886 PHE Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 1005 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.3980 chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 GLN B 668 ASN ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6335 Z= 0.224 Angle : 0.738 10.243 8547 Z= 0.364 Chirality : 0.049 0.209 942 Planarity : 0.005 0.077 1098 Dihedral : 5.604 25.626 850 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 25.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 6.64 % Allowed : 23.89 % Favored : 69.47 % 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: -2.02 (0.30), residues: 762 helix: -0.07 (0.31), residues: 294 sheet: -2.27 (0.47), residues: 101 loop : -2.14 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 939 HIS 0.005 0.001 HIS B 750 PHE 0.021 0.002 PHE B 924 TYR 0.012 0.001 TYR B 621 ARG 0.010 0.000 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 137 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 686 MET cc_start: 0.6439 (ptt) cc_final: 0.6184 (ptt) REVERT: A 699 TRP cc_start: 0.6596 (t60) cc_final: 0.6363 (t60) REVERT: A 711 ASP cc_start: 0.8098 (m-30) cc_final: 0.7625 (p0) REVERT: A 776 MET cc_start: 0.4610 (pmm) cc_final: 0.4380 (pmm) REVERT: A 785 MET cc_start: 0.5251 (mpp) cc_final: 0.4932 (mpp) REVERT: A 926 ASP cc_start: 0.8323 (m-30) cc_final: 0.7603 (p0) REVERT: A 1018 PHE cc_start: 0.5751 (OUTLIER) cc_final: 0.5409 (m-10) REVERT: B 856 TRP cc_start: 0.7335 (m100) cc_final: 0.7026 (m100) REVERT: B 886 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6776 (t80) REVERT: B 944 GLU cc_start: 0.5243 (OUTLIER) cc_final: 0.4868 (pt0) REVERT: B 955 ARG cc_start: 0.8893 (mtt-85) cc_final: 0.8456 (mtm-85) REVERT: B 1018 PHE cc_start: 0.8270 (t80) cc_final: 0.8066 (t80) outliers start: 45 outliers final: 36 residues processed: 165 average time/residue: 0.1695 time to fit residues: 37.2888 Evaluate side-chains 165 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 126 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 668 ASN Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 891 HIS Chi-restraints excluded: chain A residue 907 HIS Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1018 PHE Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 769 TYR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain B residue 870 ASN Chi-restraints excluded: chain B residue 886 PHE Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 944 GLU Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1005 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 0.0370 chunk 14 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6335 Z= 0.208 Angle : 0.778 16.628 8547 Z= 0.372 Chirality : 0.050 0.249 942 Planarity : 0.004 0.043 1098 Dihedral : 5.582 25.260 850 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 24.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 6.64 % Allowed : 24.78 % Favored : 68.58 % 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: -2.03 (0.30), residues: 762 helix: -0.14 (0.31), residues: 297 sheet: -2.11 (0.48), residues: 101 loop : -2.15 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 939 HIS 0.004 0.001 HIS B 750 PHE 0.021 0.002 PHE B 924 TYR 0.015 0.001 TYR B 621 ARG 0.009 0.000 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 129 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 711 ASP cc_start: 0.8103 (m-30) cc_final: 0.7585 (p0) REVERT: A 785 MET cc_start: 0.5249 (mpp) cc_final: 0.4958 (mpp) REVERT: A 926 ASP cc_start: 0.8221 (m-30) cc_final: 0.7551 (p0) REVERT: A 1018 PHE cc_start: 0.5786 (OUTLIER) cc_final: 0.5349 (m-10) REVERT: B 730 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6311 (pt) REVERT: B 856 TRP cc_start: 0.7311 (m100) cc_final: 0.7070 (m100) REVERT: B 886 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6820 (t80) REVERT: B 933 MET cc_start: 0.8059 (ppp) cc_final: 0.7701 (ppp) REVERT: B 944 GLU cc_start: 0.5390 (OUTLIER) cc_final: 0.4966 (pt0) REVERT: B 955 ARG cc_start: 0.8886 (mtt-85) cc_final: 0.8500 (mtm-85) outliers start: 45 outliers final: 34 residues processed: 156 average time/residue: 0.1706 time to fit residues: 35.4833 Evaluate side-chains 163 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 125 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 668 ASN Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 891 HIS Chi-restraints excluded: chain A residue 907 HIS Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1018 PHE Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 769 TYR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 786 MET Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 886 PHE Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 944 GLU Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 1005 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 HIS ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6335 Z= 0.213 Angle : 0.773 13.753 8547 Z= 0.371 Chirality : 0.049 0.231 942 Planarity : 0.004 0.039 1098 Dihedral : 5.511 25.932 850 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 24.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 6.49 % Allowed : 26.11 % Favored : 67.40 % 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: -1.92 (0.31), residues: 762 helix: -0.05 (0.31), residues: 297 sheet: -1.86 (0.51), residues: 95 loop : -2.16 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 939 HIS 0.004 0.001 HIS B 750 PHE 0.020 0.002 PHE B 924 TYR 0.015 0.001 TYR B 621 ARG 0.009 0.000 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 133 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 711 ASP cc_start: 0.8068 (m-30) cc_final: 0.7605 (p0) REVERT: A 774 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.6398 (tmm) REVERT: A 785 MET cc_start: 0.5346 (mpp) cc_final: 0.5063 (mpp) REVERT: A 926 ASP cc_start: 0.8193 (m-30) cc_final: 0.7467 (p0) REVERT: B 886 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6797 (t80) REVERT: B 944 GLU cc_start: 0.5271 (OUTLIER) cc_final: 0.4885 (pt0) REVERT: B 955 ARG cc_start: 0.8896 (mtt-85) cc_final: 0.8513 (mtm-85) outliers start: 44 outliers final: 38 residues processed: 159 average time/residue: 0.1823 time to fit residues: 38.3816 Evaluate side-chains 163 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 122 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 668 ASN Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 682 HIS Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 891 HIS Chi-restraints excluded: chain A residue 907 HIS Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 769 TYR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 870 ASN Chi-restraints excluded: chain B residue 886 PHE Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 944 GLU Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1005 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 0.0030 chunk 70 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 HIS ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6335 Z= 0.207 Angle : 0.769 12.389 8547 Z= 0.369 Chirality : 0.049 0.229 942 Planarity : 0.004 0.038 1098 Dihedral : 5.493 25.812 850 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 24.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 6.05 % Allowed : 26.99 % Favored : 66.96 % 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: -1.80 (0.31), residues: 762 helix: 0.01 (0.32), residues: 301 sheet: -1.74 (0.51), residues: 95 loop : -2.09 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 939 HIS 0.008 0.001 HIS A 682 PHE 0.021 0.002 PHE B 924 TYR 0.015 0.001 TYR B 627 ARG 0.010 0.000 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 131 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 711 ASP cc_start: 0.8045 (m-30) cc_final: 0.7567 (p0) REVERT: A 774 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6367 (tmm) REVERT: A 785 MET cc_start: 0.5350 (mpp) cc_final: 0.5065 (mpp) REVERT: A 926 ASP cc_start: 0.8225 (m-30) cc_final: 0.7542 (p0) REVERT: A 991 MET cc_start: 0.7585 (tpt) cc_final: 0.7151 (mmm) REVERT: B 698 LYS cc_start: 0.9142 (tptt) cc_final: 0.8834 (pttt) REVERT: B 886 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.6760 (t80) REVERT: B 944 GLU cc_start: 0.5202 (OUTLIER) cc_final: 0.4923 (pt0) REVERT: B 954 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8157 (mm) REVERT: B 955 ARG cc_start: 0.8870 (mtt-85) cc_final: 0.8507 (mtm-85) outliers start: 41 outliers final: 34 residues processed: 156 average time/residue: 0.1792 time to fit residues: 36.9253 Evaluate side-chains 160 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 122 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 668 ASN Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 891 HIS Chi-restraints excluded: chain A residue 907 HIS Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 769 TYR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 886 PHE Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 944 GLU Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1005 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6335 Z= 0.218 Angle : 0.763 11.367 8547 Z= 0.371 Chirality : 0.049 0.224 942 Planarity : 0.004 0.039 1098 Dihedral : 5.426 27.008 850 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 24.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.53 % Favored : 91.34 % Rotamer: Outliers : 5.75 % Allowed : 27.73 % Favored : 66.52 % 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: -1.85 (0.31), residues: 762 helix: 0.06 (0.31), residues: 301 sheet: -1.95 (0.50), residues: 95 loop : -2.15 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 939 HIS 0.004 0.001 HIS B 750 PHE 0.020 0.002 PHE B 924 TYR 0.022 0.002 TYR B 627 ARG 0.009 0.000 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 125 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 711 ASP cc_start: 0.8071 (m-30) cc_final: 0.7625 (p0) REVERT: A 774 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.6543 (tmm) REVERT: A 785 MET cc_start: 0.5379 (mpp) cc_final: 0.5089 (mpp) REVERT: A 926 ASP cc_start: 0.8334 (m-30) cc_final: 0.7615 (p0) REVERT: A 991 MET cc_start: 0.7387 (tpt) cc_final: 0.6975 (mmm) REVERT: B 686 MET cc_start: 0.8472 (ttm) cc_final: 0.8205 (tmm) REVERT: B 698 LYS cc_start: 0.9091 (tptt) cc_final: 0.8741 (pttt) REVERT: B 886 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6757 (t80) REVERT: B 944 GLU cc_start: 0.5265 (OUTLIER) cc_final: 0.5041 (pt0) REVERT: B 954 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8175 (mm) REVERT: B 955 ARG cc_start: 0.8892 (mtt-85) cc_final: 0.8517 (mtm-85) outliers start: 39 outliers final: 33 residues processed: 147 average time/residue: 0.1781 time to fit residues: 34.6628 Evaluate side-chains 159 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 122 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 668 ASN Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 891 HIS Chi-restraints excluded: chain A residue 907 HIS Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 769 TYR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 886 PHE Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 944 GLU Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1005 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 0.0070 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.6182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6335 Z= 0.209 Angle : 0.777 11.589 8547 Z= 0.373 Chirality : 0.049 0.206 942 Planarity : 0.004 0.053 1098 Dihedral : 5.390 25.727 850 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 23.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.92 % Favored : 90.94 % Rotamer: Outliers : 5.46 % Allowed : 28.47 % Favored : 66.08 % 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: -1.76 (0.31), residues: 762 helix: 0.14 (0.32), residues: 301 sheet: -1.86 (0.50), residues: 96 loop : -2.12 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 939 HIS 0.004 0.001 HIS B 750 PHE 0.022 0.002 PHE B 661 TYR 0.023 0.001 TYR B 627 ARG 0.016 0.000 ARG A1009 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 131 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 711 ASP cc_start: 0.8052 (m-30) cc_final: 0.7661 (p0) REVERT: A 774 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6973 (tpp) REVERT: A 785 MET cc_start: 0.5568 (mpp) cc_final: 0.5293 (mpp) REVERT: A 926 ASP cc_start: 0.8252 (m-30) cc_final: 0.7590 (p0) REVERT: A 991 MET cc_start: 0.7353 (tpt) cc_final: 0.6948 (mmm) REVERT: B 686 MET cc_start: 0.8415 (ttm) cc_final: 0.8185 (tmm) REVERT: B 698 LYS cc_start: 0.9061 (tptt) cc_final: 0.8733 (pttt) REVERT: B 886 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.6613 (t80) REVERT: B 944 GLU cc_start: 0.5392 (OUTLIER) cc_final: 0.5151 (pt0) REVERT: B 954 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8111 (mm) REVERT: B 955 ARG cc_start: 0.8870 (mtt-85) cc_final: 0.8484 (mtm-85) outliers start: 37 outliers final: 31 residues processed: 152 average time/residue: 0.1710 time to fit residues: 34.4998 Evaluate side-chains 160 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 125 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 668 ASN Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 834 TYR Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 891 HIS Chi-restraints excluded: chain A residue 907 HIS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 769 TYR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 886 PHE Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 944 GLU Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1005 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 0.0170 chunk 11 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.138411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.117526 restraints weight = 19448.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.120550 restraints weight = 11967.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.122587 restraints weight = 8593.144| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.6348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6335 Z= 0.222 Angle : 0.798 13.873 8547 Z= 0.381 Chirality : 0.049 0.205 942 Planarity : 0.004 0.042 1098 Dihedral : 5.439 23.297 850 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 24.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.53 % Favored : 91.34 % Rotamer: Outliers : 6.19 % Allowed : 28.02 % Favored : 65.78 % 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 (0.31), residues: 762 helix: 0.18 (0.32), residues: 301 sheet: -1.89 (0.51), residues: 96 loop : -2.15 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 699 HIS 0.004 0.001 HIS B 750 PHE 0.021 0.002 PHE B 661 TYR 0.024 0.002 TYR B 627 ARG 0.009 0.000 ARG A 642 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1716.03 seconds wall clock time: 31 minutes 41.44 seconds (1901.44 seconds total)