Starting phenix.real_space_refine on Tue Mar 11 19:49:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kfz_22857/03_2025/7kfz_22857.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kfz_22857/03_2025/7kfz_22857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kfz_22857/03_2025/7kfz_22857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kfz_22857/03_2025/7kfz_22857.map" model { file = "/net/cci-nas-00/data/ceres_data/7kfz_22857/03_2025/7kfz_22857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kfz_22857/03_2025/7kfz_22857.cif" } resolution = 3.47 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 27 5.16 5 C 4176 2.51 5 N 1134 2.21 5 O 1251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6592 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1345 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 4, 'TRANS': 163} Chain: "B" Number of atoms: 3877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3877 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 434} Chain breaks: 2 Chain: "C" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1337 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 163} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.25, per 1000 atoms: 0.64 Number of scatterers: 6592 At special positions: 0 Unit cell: (73.485, 100.11, 124.605, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 27 16.00 P 3 15.00 Mg 1 11.99 O 1251 8.00 N 1134 7.00 C 4176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 887.2 milliseconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1538 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 4 sheets defined 59.2% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 15 through 25 removed outlier: 3.715A pdb=" N LEU A 19 " --> pdb=" O GLY A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 39 Processing helix chain 'A' and resid 60 through 66 removed outlier: 4.461A pdb=" N GLU A 63 " --> pdb=" O GLY A 60 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER A 65 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ALA A 66 " --> pdb=" O GLU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 75 removed outlier: 3.864A pdb=" N THR A 74 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY A 75 " --> pdb=" O TYR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.708A pdb=" N GLU A 91 " --> pdb=" O THR A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 151 through 168 Processing helix chain 'B' and resid 575 through 579 removed outlier: 3.556A pdb=" N ALA B 578 " --> pdb=" O TYR B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 614 Processing helix chain 'B' and resid 620 through 631 removed outlier: 3.740A pdb=" N VAL B 624 " --> pdb=" O ASP B 620 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG B 625 " --> pdb=" O PRO B 621 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 649 Processing helix chain 'B' and resid 656 through 666 Processing helix chain 'B' and resid 671 through 681 removed outlier: 3.700A pdb=" N ARG B 676 " --> pdb=" O ALA B 672 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 679 " --> pdb=" O LYS B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 699 removed outlier: 3.550A pdb=" N LEU B 690 " --> pdb=" O GLN B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 Processing helix chain 'B' and resid 707 through 721 removed outlier: 3.558A pdb=" N LEU B 711 " --> pdb=" O ASP B 707 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 712 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 743 removed outlier: 3.810A pdb=" N ILE B 742 " --> pdb=" O GLN B 738 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 743 " --> pdb=" O ARG B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 774 removed outlier: 3.522A pdb=" N PHE B 774 " --> pdb=" O ILE B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 798 Processing helix chain 'B' and resid 800 through 804 Processing helix chain 'B' and resid 807 through 811 Processing helix chain 'B' and resid 813 through 818 Processing helix chain 'B' and resid 818 through 842 removed outlier: 3.625A pdb=" N THR B 842 " --> pdb=" O CYS B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 865 Processing helix chain 'B' and resid 867 through 879 removed outlier: 3.735A pdb=" N SER B 876 " --> pdb=" O LEU B 872 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA B 877 " --> pdb=" O GLU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 885 removed outlier: 3.917A pdb=" N ARG B 885 " --> pdb=" O SER B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 892 removed outlier: 3.502A pdb=" N PHE B 890 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 891 " --> pdb=" O ASP B 887 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN B 892 " --> pdb=" O HIS B 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 892' Processing helix chain 'B' and resid 894 through 906 Processing helix chain 'B' and resid 908 through 920 removed outlier: 3.806A pdb=" N TYR B 912 " --> pdb=" O SER B 908 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS B 913 " --> pdb=" O GLU B 909 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS B 914 " --> pdb=" O ASP B 910 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR B 915 " --> pdb=" O HIS B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 944 removed outlier: 4.112A pdb=" N TYR B 933 " --> pdb=" O PHE B 929 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS B 939 " --> pdb=" O THR B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 976 removed outlier: 3.811A pdb=" N GLN B 972 " --> pdb=" O THR B 968 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN B 973 " --> pdb=" O GLY B 969 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN B 976 " --> pdb=" O GLN B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 993 Processing helix chain 'B' and resid 1001 through 1017 Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 67 through 75 removed outlier: 3.742A pdb=" N TYR C 71 " --> pdb=" O MET C 67 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR C 74 " --> pdb=" O GLN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 105 removed outlier: 3.763A pdb=" N PHE C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU C 91 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C 93 " --> pdb=" O SER C 89 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N HIS C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N HIS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 138 Processing helix chain 'C' and resid 151 through 168 removed outlier: 3.581A pdb=" N PHE C 156 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 46 removed outlier: 6.662A pdb=" N TYR A 4 " --> pdb=" O ASP A 54 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU A 56 " --> pdb=" O TYR A 4 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU A 6 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE A 78 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL A 114 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N CYS A 80 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN A 116 " --> pdb=" O CYS A 80 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE A 82 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 586 through 589 removed outlier: 6.443A pdb=" N ILE B 587 " --> pdb=" O LYS B 602 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE B 600 " --> pdb=" O GLU B 589 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 4 removed outlier: 6.649A pdb=" N THR C 2 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ASP C 54 " --> pdb=" O THR C 2 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TYR C 4 " --> pdb=" O ASP C 54 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU C 56 " --> pdb=" O TYR C 4 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 2 through 4 removed outlier: 6.649A pdb=" N THR C 2 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ASP C 54 " --> pdb=" O THR C 2 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TYR C 4 " --> pdb=" O ASP C 54 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU C 56 " --> pdb=" O TYR C 4 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU C 6 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N PHE C 78 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL C 114 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N CYS C 80 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASN C 116 " --> pdb=" O CYS C 80 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE C 82 " --> pdb=" O ASN C 116 " (cutoff:3.500A) 314 hydrogen bonds defined for protein. 903 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: 1.81 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1862 1.33 - 1.45: 1020 1.45 - 1.57: 3799 1.57 - 1.68: 3 1.68 - 1.80: 44 Bond restraints: 6728 Sorted by residual: bond pdb=" N3B GNP C 201 " pdb=" PG GNP C 201 " ideal model delta sigma weight residual 1.801 1.689 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" O5' GNP C 201 " pdb=" PA GNP C 201 " ideal model delta sigma weight residual 1.660 1.548 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" N3B GNP C 201 " pdb=" PB GNP C 201 " ideal model delta sigma weight residual 1.681 1.621 0.060 2.00e-02 2.50e+03 9.10e+00 bond pdb=" O3A GNP C 201 " pdb=" PB GNP C 201 " ideal model delta sigma weight residual 1.687 1.631 0.056 2.00e-02 2.50e+03 7.72e+00 bond pdb=" N ILE C 163 " pdb=" CA ILE C 163 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.65e+00 ... (remaining 6723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 8869 2.15 - 4.30: 202 4.30 - 6.46: 22 6.46 - 8.61: 3 8.61 - 10.76: 5 Bond angle restraints: 9101 Sorted by residual: angle pdb=" N3B GNP C 201 " pdb=" PB GNP C 201 " pdb=" O3A GNP C 201 " ideal model delta sigma weight residual 100.48 111.12 -10.64 3.00e+00 1.11e-01 1.26e+01 angle pdb=" PB GNP C 201 " pdb=" N3B GNP C 201 " pdb=" PG GNP C 201 " ideal model delta sigma weight residual 123.35 113.90 9.45 3.00e+00 1.11e-01 9.92e+00 angle pdb=" O1B GNP C 201 " pdb=" PB GNP C 201 " pdb=" O2B GNP C 201 " ideal model delta sigma weight residual 119.66 110.34 9.32 3.00e+00 1.11e-01 9.66e+00 angle pdb=" CA LEU A 23 " pdb=" CB LEU A 23 " pdb=" CG LEU A 23 " ideal model delta sigma weight residual 116.30 105.54 10.76 3.50e+00 8.16e-02 9.45e+00 angle pdb=" N PRO B 925 " pdb=" CA PRO B 925 " pdb=" C PRO B 925 " ideal model delta sigma weight residual 112.47 106.25 6.22 2.06e+00 2.36e-01 9.12e+00 ... (remaining 9096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 3674 15.90 - 31.80: 362 31.80 - 47.69: 76 47.69 - 63.59: 18 63.59 - 79.49: 9 Dihedral angle restraints: 4139 sinusoidal: 1770 harmonic: 2369 Sorted by residual: dihedral pdb=" CA PRO B 924 " pdb=" C PRO B 924 " pdb=" N PRO B 925 " pdb=" CA PRO B 925 " ideal model delta harmonic sigma weight residual 180.00 113.20 66.80 0 5.00e+00 4.00e-02 1.78e+02 dihedral pdb=" CA CYS B 926 " pdb=" C CYS B 926 " pdb=" N VAL B 927 " pdb=" CA VAL B 927 " ideal model delta harmonic sigma weight residual 180.00 161.92 18.08 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASN B 923 " pdb=" C ASN B 923 " pdb=" N PRO B 924 " pdb=" CA PRO B 924 " ideal model delta harmonic sigma weight residual -180.00 -162.04 -17.96 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 4136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 490 0.039 - 0.077: 376 0.077 - 0.116: 116 0.116 - 0.154: 18 0.154 - 0.193: 4 Chirality restraints: 1004 Sorted by residual: chirality pdb=" C2' GNP C 201 " pdb=" C1' GNP C 201 " pdb=" C3' GNP C 201 " pdb=" O2' GNP C 201 " both_signs ideal model delta sigma weight residual False -2.55 -2.74 0.19 2.00e-01 2.50e+01 9.31e-01 chirality pdb=" CA ILE C 163 " pdb=" N ILE C 163 " pdb=" C ILE C 163 " pdb=" CB ILE C 163 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CB VAL B 840 " pdb=" CA VAL B 840 " pdb=" CG1 VAL B 840 " pdb=" CG2 VAL B 840 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.96e-01 ... (remaining 1001 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 924 " -0.062 5.00e-02 4.00e+02 9.23e-02 1.36e+01 pdb=" N PRO B 925 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO B 925 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 925 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 930 " -0.019 2.00e-02 2.50e+03 1.50e-02 3.95e+00 pdb=" CG PHE B 930 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 930 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 930 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 930 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 930 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 930 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 923 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.88e+00 pdb=" N PRO B 924 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 924 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 924 " -0.023 5.00e-02 4.00e+02 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 27 2.50 - 3.10: 4830 3.10 - 3.70: 9801 3.70 - 4.30: 14713 4.30 - 4.90: 24663 Nonbonded interactions: 54034 Sorted by model distance: nonbonded pdb=" OG SER C 17 " pdb="MG MG C 202 " model vdw 1.897 2.170 nonbonded pdb=" OG1 THR C 35 " pdb="MG MG C 202 " model vdw 1.994 2.170 nonbonded pdb=" O1G GNP C 201 " pdb="MG MG C 202 " model vdw 2.123 2.170 nonbonded pdb=" OE2 GLU B 783 " pdb=" NE2 GLN B 787 " model vdw 2.188 3.120 nonbonded pdb=" O VAL C 8 " pdb=" OG1 THR C 58 " model vdw 2.223 3.040 ... (remaining 54029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 through 167 or (resid 168 and (name N or na \ me CA or name C or name O or name CB )))) selection = (chain 'C' and resid 1 through 168) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.290 Find NCS groups from input model: 0.130 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.012 0.112 6728 Z= 0.764 Angle : 0.805 10.759 9101 Z= 0.430 Chirality : 0.053 0.193 1004 Planarity : 0.005 0.092 1176 Dihedral : 13.579 79.491 2601 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.10 (0.28), residues: 793 helix: -1.10 (0.25), residues: 390 sheet: -0.69 (0.52), residues: 85 loop : 0.10 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 729 HIS 0.005 0.001 HIS B 888 PHE 0.034 0.002 PHE B 930 TYR 0.014 0.002 TYR B 615 ARG 0.009 0.001 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.6418 (ttm) cc_final: 0.5883 (ttm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1936 time to fit residues: 13.9998 Evaluate side-chains 24 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 566 GLN ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.034219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.025957 restraints weight = 37099.109| |-----------------------------------------------------------------------------| r_work (start): 0.2416 rms_B_bonded: 4.58 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6728 Z= 0.170 Angle : 0.541 7.763 9101 Z= 0.285 Chirality : 0.041 0.165 1004 Planarity : 0.004 0.077 1176 Dihedral : 5.405 58.622 915 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.68 % Allowed : 5.46 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 0.30 (0.29), residues: 793 helix: 0.49 (0.25), residues: 401 sheet: -0.70 (0.50), residues: 88 loop : 0.35 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 729 HIS 0.003 0.001 HIS B 700 PHE 0.012 0.001 PHE B 588 TYR 0.026 0.001 TYR A 157 ARG 0.006 0.000 ARG C 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 111 MET cc_start: 0.9162 (ttm) cc_final: 0.8789 (ttp) REVERT: B 836 GLU cc_start: 0.9348 (mt-10) cc_final: 0.8557 (mm-30) REVERT: C 41 ARG cc_start: 0.8747 (ttm-80) cc_final: 0.8530 (ttm-80) REVERT: C 72 MET cc_start: 0.9197 (mtt) cc_final: 0.8935 (mtt) REVERT: C 93 ILE cc_start: 0.9820 (mm) cc_final: 0.9618 (mm) outliers start: 5 outliers final: 1 residues processed: 38 average time/residue: 0.1715 time to fit residues: 9.8235 Evaluate side-chains 26 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS C 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.034734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.026076 restraints weight = 38833.724| |-----------------------------------------------------------------------------| r_work (start): 0.2415 rms_B_bonded: 4.60 r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6728 Z= 0.145 Angle : 0.462 6.661 9101 Z= 0.239 Chirality : 0.039 0.142 1004 Planarity : 0.004 0.074 1176 Dihedral : 4.885 58.238 915 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.55 % Allowed : 6.15 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 1.10 (0.30), residues: 793 helix: 1.25 (0.26), residues: 403 sheet: -0.32 (0.50), residues: 88 loop : 0.56 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 809 HIS 0.001 0.000 HIS B 911 PHE 0.008 0.001 PHE A 156 TYR 0.014 0.001 TYR A 157 ARG 0.003 0.000 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.740 Fit side-chains REVERT: A 111 MET cc_start: 0.9183 (ttm) cc_final: 0.8843 (ttp) REVERT: B 997 MET cc_start: 0.9398 (mtp) cc_final: 0.9016 (mmm) REVERT: C 67 MET cc_start: 0.8448 (mtm) cc_final: 0.8025 (mpp) outliers start: 4 outliers final: 1 residues processed: 31 average time/residue: 0.1820 time to fit residues: 8.4550 Evaluate side-chains 23 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.032070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2355 r_free = 0.2355 target = 0.023975 restraints weight = 39297.361| |-----------------------------------------------------------------------------| r_work (start): 0.2358 rms_B_bonded: 4.61 r_work (final): 0.2358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6728 Z= 0.264 Angle : 0.511 7.744 9101 Z= 0.261 Chirality : 0.040 0.134 1004 Planarity : 0.004 0.078 1176 Dihedral : 4.789 59.584 915 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.23 % Allowed : 6.56 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 1.52 (0.29), residues: 793 helix: 1.62 (0.25), residues: 406 sheet: -0.14 (0.50), residues: 88 loop : 0.70 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 729 HIS 0.004 0.001 HIS B 616 PHE 0.009 0.001 PHE A 156 TYR 0.011 0.001 TYR A 157 ARG 0.008 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.815 Fit side-chains REVERT: A 111 MET cc_start: 0.9254 (ttm) cc_final: 0.8840 (ttp) REVERT: B 930 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8618 (m-80) REVERT: C 67 MET cc_start: 0.8812 (mtm) cc_final: 0.8367 (mpp) outliers start: 9 outliers final: 3 residues processed: 31 average time/residue: 0.1419 time to fit residues: 7.3420 Evaluate side-chains 25 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 930 PHE Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.0870 chunk 25 optimal weight: 8.9990 chunk 5 optimal weight: 0.0170 chunk 26 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.032812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2357 r_free = 0.2357 target = 0.024353 restraints weight = 39110.127| |-----------------------------------------------------------------------------| r_work (start): 0.2365 rms_B_bonded: 4.82 r_work (final): 0.2365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6728 Z= 0.150 Angle : 0.455 8.148 9101 Z= 0.229 Chirality : 0.039 0.134 1004 Planarity : 0.004 0.074 1176 Dihedral : 4.626 57.453 915 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.55 % Allowed : 7.38 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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 (0.30), residues: 793 helix: 1.91 (0.25), residues: 407 sheet: -0.05 (0.51), residues: 88 loop : 0.75 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 809 HIS 0.001 0.000 HIS C 27 PHE 0.008 0.001 PHE A 156 TYR 0.007 0.001 TYR A 157 ARG 0.005 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.745 Fit side-chains REVERT: A 111 MET cc_start: 0.9224 (ttm) cc_final: 0.8849 (ttp) REVERT: B 824 MET cc_start: 0.9145 (tmm) cc_final: 0.8563 (tmm) REVERT: B 836 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8809 (mm-30) REVERT: B 997 MET cc_start: 0.9472 (mtp) cc_final: 0.9087 (mmm) REVERT: C 67 MET cc_start: 0.8730 (mtm) cc_final: 0.8414 (mpp) REVERT: C 131 GLN cc_start: 0.9457 (mt0) cc_final: 0.9142 (mt0) REVERT: C 135 ARG cc_start: 0.9408 (ttp-110) cc_final: 0.9206 (ttm110) outliers start: 4 outliers final: 2 residues processed: 25 average time/residue: 0.1832 time to fit residues: 7.0702 Evaluate side-chains 25 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 12 optimal weight: 0.0670 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN B 755 GLN ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.032898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2366 r_free = 0.2366 target = 0.024460 restraints weight = 38952.474| |-----------------------------------------------------------------------------| r_work (start): 0.2370 rms_B_bonded: 4.82 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6728 Z= 0.149 Angle : 0.442 9.362 9101 Z= 0.222 Chirality : 0.039 0.132 1004 Planarity : 0.004 0.073 1176 Dihedral : 4.506 56.622 915 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.68 % Allowed : 8.20 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 2.04 (0.30), residues: 793 helix: 2.15 (0.25), residues: 408 sheet: 0.02 (0.51), residues: 88 loop : 0.80 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 809 HIS 0.002 0.000 HIS B 616 PHE 0.009 0.001 PHE A 156 TYR 0.005 0.001 TYR A 157 ARG 0.004 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.808 Fit side-chains REVERT: B 930 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8627 (m-80) REVERT: B 997 MET cc_start: 0.9459 (mtp) cc_final: 0.9068 (mmm) REVERT: C 67 MET cc_start: 0.8686 (mtm) cc_final: 0.8444 (mpp) REVERT: C 131 GLN cc_start: 0.9454 (mt0) cc_final: 0.9094 (mt0) REVERT: C 135 ARG cc_start: 0.9443 (ttp-110) cc_final: 0.9226 (ttm110) outliers start: 5 outliers final: 3 residues processed: 27 average time/residue: 0.2193 time to fit residues: 8.6409 Evaluate side-chains 26 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 930 PHE Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** 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 = 0.2678 r_free = 0.2678 target = 0.032159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2338 r_free = 0.2338 target = 0.023744 restraints weight = 39407.184| |-----------------------------------------------------------------------------| r_work (start): 0.2345 rms_B_bonded: 4.83 r_work (final): 0.2345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6728 Z= 0.229 Angle : 0.495 10.289 9101 Z= 0.244 Chirality : 0.039 0.127 1004 Planarity : 0.004 0.075 1176 Dihedral : 4.585 58.154 915 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.96 % Allowed : 8.20 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 2.16 (0.30), residues: 793 helix: 2.23 (0.25), residues: 409 sheet: -0.04 (0.50), residues: 90 loop : 0.94 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 729 HIS 0.002 0.001 HIS B 699 PHE 0.009 0.001 PHE A 156 TYR 0.005 0.001 TYR B 681 ARG 0.004 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.812 Fit side-chains REVERT: A 111 MET cc_start: 0.9079 (ttp) cc_final: 0.8757 (ttp) REVERT: B 930 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8642 (m-80) REVERT: B 997 MET cc_start: 0.9483 (mtp) cc_final: 0.9116 (mmm) REVERT: C 67 MET cc_start: 0.8771 (mtm) cc_final: 0.8523 (mpp) REVERT: C 131 GLN cc_start: 0.9451 (mt0) cc_final: 0.9171 (mt0) outliers start: 7 outliers final: 4 residues processed: 29 average time/residue: 0.1833 time to fit residues: 8.2063 Evaluate side-chains 25 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 930 PHE Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 0.0010 chunk 19 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 9.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** 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 = 0.2709 r_free = 0.2709 target = 0.032944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2380 r_free = 0.2380 target = 0.024616 restraints weight = 38713.367| |-----------------------------------------------------------------------------| r_work (start): 0.2383 rms_B_bonded: 4.80 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6728 Z= 0.131 Angle : 0.452 11.265 9101 Z= 0.223 Chirality : 0.039 0.131 1004 Planarity : 0.003 0.072 1176 Dihedral : 4.497 56.032 915 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.55 % Allowed : 8.88 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 2.25 (0.30), residues: 793 helix: 2.28 (0.25), residues: 408 sheet: 0.25 (0.51), residues: 87 loop : 0.92 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 809 HIS 0.004 0.001 HIS B 616 PHE 0.009 0.001 PHE A 156 TYR 0.005 0.001 TYR B 796 ARG 0.003 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.777 Fit side-chains REVERT: A 111 MET cc_start: 0.9100 (ttp) cc_final: 0.8763 (ttp) REVERT: B 930 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8502 (m-80) REVERT: B 997 MET cc_start: 0.9496 (mtp) cc_final: 0.9215 (mmm) REVERT: C 131 GLN cc_start: 0.9435 (mt0) cc_final: 0.8993 (mt0) REVERT: C 135 ARG cc_start: 0.9444 (ttp-110) cc_final: 0.9200 (ttm110) outliers start: 4 outliers final: 3 residues processed: 25 average time/residue: 0.1851 time to fit residues: 7.2125 Evaluate side-chains 25 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 930 PHE Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 74 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** 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 = 0.2738 r_free = 0.2738 target = 0.033372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2419 r_free = 0.2419 target = 0.025191 restraints weight = 39129.578| |-----------------------------------------------------------------------------| r_work (start): 0.2403 rms_B_bonded: 4.77 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6728 Z= 0.128 Angle : 0.467 12.066 9101 Z= 0.224 Chirality : 0.039 0.131 1004 Planarity : 0.003 0.068 1176 Dihedral : 4.406 54.614 915 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.82 % Allowed : 9.15 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 2.39 (0.30), residues: 793 helix: 2.39 (0.25), residues: 410 sheet: 0.43 (0.51), residues: 87 loop : 0.96 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 809 HIS 0.006 0.000 HIS B 616 PHE 0.009 0.001 PHE A 156 TYR 0.006 0.001 TYR C 71 ARG 0.003 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.864 Fit side-chains REVERT: A 111 MET cc_start: 0.9033 (ttp) cc_final: 0.8696 (ttp) REVERT: B 930 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8488 (m-80) REVERT: B 997 MET cc_start: 0.9463 (mtp) cc_final: 0.9241 (mmm) REVERT: C 131 GLN cc_start: 0.9430 (mt0) cc_final: 0.8971 (mt0) REVERT: C 135 ARG cc_start: 0.9448 (ttp-110) cc_final: 0.9209 (ttm110) outliers start: 6 outliers final: 3 residues processed: 28 average time/residue: 0.1900 time to fit residues: 8.2556 Evaluate side-chains 25 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 930 PHE Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** 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 = 0.2705 r_free = 0.2705 target = 0.032807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.024327 restraints weight = 39983.530| |-----------------------------------------------------------------------------| r_work (start): 0.2375 rms_B_bonded: 4.89 r_work (final): 0.2375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6728 Z= 0.175 Angle : 0.469 11.464 9101 Z= 0.231 Chirality : 0.039 0.139 1004 Planarity : 0.003 0.069 1176 Dihedral : 4.430 55.883 915 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.55 % Allowed : 9.43 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 2.44 (0.30), residues: 793 helix: 2.40 (0.25), residues: 411 sheet: 0.45 (0.50), residues: 87 loop : 1.01 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 809 HIS 0.008 0.001 HIS B 616 PHE 0.009 0.001 PHE A 156 TYR 0.005 0.001 TYR C 64 ARG 0.003 0.000 ARG C 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.796 Fit side-chains REVERT: A 111 MET cc_start: 0.9046 (ttp) cc_final: 0.8705 (ttp) REVERT: B 930 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8525 (m-80) REVERT: B 997 MET cc_start: 0.9481 (mtp) cc_final: 0.9229 (mmm) REVERT: C 131 GLN cc_start: 0.9436 (mt0) cc_final: 0.9086 (mt0) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.1481 time to fit residues: 6.0903 Evaluate side-chains 24 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 930 PHE Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** 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 = 0.2697 r_free = 0.2697 target = 0.032606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2358 r_free = 0.2358 target = 0.024102 restraints weight = 39864.282| |-----------------------------------------------------------------------------| r_work (start): 0.2365 rms_B_bonded: 4.89 r_work (final): 0.2365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6728 Z= 0.181 Angle : 0.469 11.401 9101 Z= 0.231 Chirality : 0.039 0.127 1004 Planarity : 0.003 0.070 1176 Dihedral : 4.474 56.457 915 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.68 % Allowed : 9.29 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 2.52 (0.30), residues: 793 helix: 2.50 (0.25), residues: 405 sheet: 0.47 (0.50), residues: 87 loop : 1.04 (0.38), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 729 HIS 0.007 0.001 HIS B 616 PHE 0.009 0.001 PHE A 156 TYR 0.005 0.001 TYR C 64 ARG 0.003 0.000 ARG C 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2110.24 seconds wall clock time: 37 minutes 37.02 seconds (2257.02 seconds total)