Starting phenix.real_space_refine on Tue Feb 11 20:19:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kfz_22857/02_2025/7kfz_22857.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kfz_22857/02_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_22857/02_2025/7kfz_22857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kfz_22857/02_2025/7kfz_22857.map" model { file = "/net/cci-nas-00/data/ceres_data/7kfz_22857/02_2025/7kfz_22857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kfz_22857/02_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-5592/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: 4.08, per 1000 atoms: 0.62 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: 1.59 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.67 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: 1.85 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.090 Find NCS groups from input model: 0.150 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.290 ------------------------------------------------------------------------------- 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 : 0.834 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: 0.2077 time to fit residues: 15.0033 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 : 0.967 ------------------------------------------------------------------------------- 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: 0.3980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.2735 r_free = 0.2735 target = 0.034327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.026050 restraints weight = 37110.762| |-----------------------------------------------------------------------------| r_work (start): 0.2420 rms_B_bonded: 4.57 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6728 Z= 0.164 Angle : 0.538 7.638 9101 Z= 0.283 Chirality : 0.041 0.189 1004 Planarity : 0.004 0.076 1176 Dihedral : 5.373 58.298 915 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: 0.33 (0.29), residues: 793 helix: 0.52 (0.26), residues: 401 sheet: -0.69 (0.50), residues: 88 loop : 0.36 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 729 HIS 0.002 0.001 HIS B 700 PHE 0.012 0.001 PHE B 588 TYR 0.028 0.001 TYR A 157 ARG 0.006 0.001 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 41 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 111 MET cc_start: 0.9145 (ttm) cc_final: 0.8786 (ttp) REVERT: B 836 GLU cc_start: 0.9347 (mt-10) cc_final: 0.8558 (mm-30) REVERT: C 41 ARG cc_start: 0.8748 (ttm-80) cc_final: 0.8532 (ttm-80) REVERT: C 72 MET cc_start: 0.9192 (mtt) cc_final: 0.8931 (mtt) REVERT: C 93 ILE cc_start: 0.9818 (mm) cc_final: 0.9615 (mm) outliers start: 5 outliers final: 1 residues processed: 39 average time/residue: 0.1692 time to fit residues: 9.8530 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 : 0.769 ------------------------------------------------------------------------------- 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: 0.4980 chunk 49 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.2715 r_free = 0.2715 target = 0.033436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.025312 restraints weight = 38168.150| |-----------------------------------------------------------------------------| r_work (start): 0.2404 rms_B_bonded: 4.60 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6728 Z= 0.159 Angle : 0.465 6.703 9101 Z= 0.242 Chirality : 0.039 0.139 1004 Planarity : 0.004 0.075 1176 Dihedral : 4.883 59.038 915 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.41 % Allowed : 6.28 % 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: 1.16 (0.30), residues: 793 helix: 1.30 (0.26), residues: 403 sheet: -0.32 (0.50), residues: 88 loop : 0.59 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 729 HIS 0.002 0.000 HIS B 911 PHE 0.009 0.001 PHE A 156 TYR 0.015 0.001 TYR C 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 31 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.820 Fit side-chains REVERT: A 111 MET cc_start: 0.9221 (ttm) cc_final: 0.8842 (ttp) REVERT: C 67 MET cc_start: 0.8450 (mtm) cc_final: 0.8020 (mpp) outliers start: 3 outliers final: 1 residues processed: 31 average time/residue: 0.2056 time to fit residues: 9.4874 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 : 0.762 ------------------------------------------------------------------------------- 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: 2.9990 chunk 42 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.2710 r_free = 0.2710 target = 0.033034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2385 r_free = 0.2385 target = 0.024783 restraints weight = 39101.587| |-----------------------------------------------------------------------------| r_work (start): 0.2385 rms_B_bonded: 4.70 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6728 Z= 0.182 Angle : 0.464 7.787 9101 Z= 0.237 Chirality : 0.039 0.136 1004 Planarity : 0.004 0.075 1176 Dihedral : 4.662 57.765 915 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.23 % Allowed : 6.42 % Favored : 92.35 % 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: 1.56 (0.30), residues: 793 helix: 1.67 (0.25), residues: 406 sheet: -0.09 (0.50), residues: 88 loop : 0.67 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 729 HIS 0.002 0.001 HIS B 911 PHE 0.009 0.001 PHE A 156 TYR 0.009 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 : 0.839 Fit side-chains REVERT: A 111 MET cc_start: 0.9250 (ttm) cc_final: 0.8958 (ttp) REVERT: B 930 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8637 (m-80) REVERT: C 67 MET cc_start: 0.8610 (mtm) cc_final: 0.8250 (mpp) outliers start: 9 outliers final: 4 residues processed: 31 average time/residue: 0.1466 time to fit residues: 7.5170 Evaluate side-chains 26 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 606 VAL 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: 6.9990 chunk 50 optimal weight: 0.9980 chunk 12 optimal weight: 0.0040 chunk 69 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 = 0.2718 r_free = 0.2718 target = 0.033409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.025005 restraints weight = 38799.887| |-----------------------------------------------------------------------------| r_work (start): 0.2385 rms_B_bonded: 4.81 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3180 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= 0.126 Angle : 0.444 8.075 9101 Z= 0.223 Chirality : 0.039 0.136 1004 Planarity : 0.003 0.072 1176 Dihedral : 4.502 55.878 915 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.82 % Allowed : 7.38 % Favored : 91.80 % 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: 1.86 (0.30), residues: 793 helix: 1.99 (0.25), residues: 407 sheet: 0.05 (0.51), residues: 88 loop : 0.71 (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 0.004 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 30 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.789 Fit side-chains REVERT: B 824 MET cc_start: 0.9118 (tmm) cc_final: 0.8535 (tmm) REVERT: B 836 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8791 (mm-30) REVERT: C 67 MET cc_start: 0.8609 (mtm) cc_final: 0.8321 (mpp) REVERT: C 131 GLN cc_start: 0.9457 (mt0) cc_final: 0.9141 (mt0) REVERT: C 135 ARG cc_start: 0.9407 (ttp-110) cc_final: 0.9193 (ttm110) outliers start: 6 outliers final: 3 residues processed: 29 average time/residue: 0.2124 time to fit residues: 8.8685 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 : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 606 VAL 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: 9.9990 chunk 31 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 12 optimal weight: 0.0870 chunk 67 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.033423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.025058 restraints weight = 38731.417| |-----------------------------------------------------------------------------| r_work (start): 0.2391 rms_B_bonded: 4.77 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6728 Z= 0.129 Angle : 0.443 9.592 9101 Z= 0.220 Chirality : 0.039 0.133 1004 Planarity : 0.003 0.071 1176 Dihedral : 4.424 55.320 915 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.82 % Allowed : 8.06 % 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: 2.06 (0.30), residues: 793 helix: 2.19 (0.25), residues: 408 sheet: 0.08 (0.51), residues: 88 loop : 0.76 (0.38), residues: 297 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 0.006 0.001 TYR C 64 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 29 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.818 Fit side-chains REVERT: B 930 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: C 67 MET cc_start: 0.8803 (mtm) cc_final: 0.8514 (mpp) REVERT: C 131 GLN cc_start: 0.9440 (mt0) cc_final: 0.9078 (mt0) REVERT: C 135 ARG cc_start: 0.9435 (ttp-110) cc_final: 0.9209 (ttm110) outliers start: 6 outliers final: 4 residues processed: 28 average time/residue: 0.2246 time to fit residues: 9.0998 Evaluate side-chains 26 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 836 GLU 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: 4.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 0.0570 chunk 72 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.033225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2385 r_free = 0.2385 target = 0.024845 restraints weight = 39041.595| |-----------------------------------------------------------------------------| r_work (start): 0.2385 rms_B_bonded: 4.81 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6728 Z= 0.148 Angle : 0.451 9.006 9101 Z= 0.222 Chirality : 0.038 0.131 1004 Planarity : 0.003 0.068 1176 Dihedral : 4.398 55.470 915 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.82 % Allowed : 8.47 % Favored : 90.71 % 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: 2.20 (0.30), residues: 793 helix: 2.27 (0.25), residues: 409 sheet: 0.21 (0.51), residues: 87 loop : 0.85 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 729 HIS 0.004 0.000 HIS B 616 PHE 0.009 0.001 PHE A 156 TYR 0.005 0.001 TYR A 137 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 28 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.836 Fit side-chains REVERT: B 606 VAL cc_start: 0.9545 (OUTLIER) cc_final: 0.9339 (p) REVERT: B 997 MET cc_start: 0.9441 (mtp) cc_final: 0.8953 (mmm) REVERT: C 67 MET cc_start: 0.8663 (mtm) cc_final: 0.8421 (mpp) REVERT: C 131 GLN cc_start: 0.9447 (mt0) cc_final: 0.9039 (mt0) REVERT: C 135 ARG cc_start: 0.9442 (ttp-110) cc_final: 0.9211 (ttm110) outliers start: 6 outliers final: 4 residues processed: 27 average time/residue: 0.1887 time to fit residues: 7.8645 Evaluate side-chains 27 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 831 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 0.0970 chunk 47 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.2734 r_free = 0.2734 target = 0.033309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.025178 restraints weight = 38865.595| |-----------------------------------------------------------------------------| r_work (start): 0.2394 rms_B_bonded: 4.71 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.3493 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= 0.149 Angle : 0.446 10.728 9101 Z= 0.221 Chirality : 0.039 0.130 1004 Planarity : 0.003 0.069 1176 Dihedral : 4.396 55.561 915 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.82 % Allowed : 9.02 % Favored : 90.16 % 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: 2.27 (0.30), residues: 793 helix: 2.32 (0.25), residues: 409 sheet: 0.26 (0.51), residues: 87 loop : 0.88 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 729 HIS 0.005 0.001 HIS B 616 PHE 0.008 0.001 PHE A 156 TYR 0.006 0.001 TYR C 64 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 28 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.770 Fit side-chains REVERT: B 606 VAL cc_start: 0.9554 (OUTLIER) cc_final: 0.9346 (p) REVERT: B 997 MET cc_start: 0.9447 (mtp) cc_final: 0.8987 (mmm) REVERT: C 72 MET cc_start: 0.8707 (mtt) cc_final: 0.8402 (mmm) REVERT: C 131 GLN cc_start: 0.9439 (mt0) cc_final: 0.8984 (mt0) REVERT: C 135 ARG cc_start: 0.9437 (ttp-110) cc_final: 0.9200 (ttm110) outliers start: 6 outliers final: 3 residues processed: 27 average time/residue: 0.1848 time to fit residues: 7.7186 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 : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 831 LEU 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: 10.0000 chunk 35 optimal weight: 0.0070 chunk 74 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.1604 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.033343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2419 r_free = 0.2419 target = 0.025215 restraints weight = 39280.488| |-----------------------------------------------------------------------------| r_work (start): 0.2405 rms_B_bonded: 4.74 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3580 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= 0.144 Angle : 0.447 11.051 9101 Z= 0.220 Chirality : 0.039 0.130 1004 Planarity : 0.003 0.068 1176 Dihedral : 4.389 55.258 915 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.68 % Allowed : 9.15 % Favored : 90.16 % 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: 2.37 (0.30), residues: 793 helix: 2.41 (0.25), residues: 409 sheet: 0.38 (0.52), residues: 87 loop : 0.90 (0.38), residues: 297 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 0.006 0.001 TYR C 64 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 26 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.881 Fit side-chains REVERT: B 617 MET cc_start: 0.9371 (mmm) cc_final: 0.9135 (mpp) REVERT: B 997 MET cc_start: 0.9431 (mtp) cc_final: 0.8980 (mmm) REVERT: C 131 GLN cc_start: 0.9442 (mt0) cc_final: 0.8977 (mt0) REVERT: C 135 ARG cc_start: 0.9438 (ttp-110) cc_final: 0.9194 (ttm110) outliers start: 5 outliers final: 4 residues processed: 25 average time/residue: 0.1899 time to fit residues: 7.4529 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 : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 831 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 20 optimal weight: 4.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.033446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.025260 restraints weight = 39491.075| |-----------------------------------------------------------------------------| r_work (start): 0.2400 rms_B_bonded: 4.77 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3657 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= 0.137 Angle : 0.463 11.051 9101 Z= 0.225 Chirality : 0.038 0.130 1004 Planarity : 0.003 0.068 1176 Dihedral : 4.384 54.829 915 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.82 % Allowed : 9.02 % Favored : 90.16 % 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: 2.41 (0.30), residues: 793 helix: 2.44 (0.25), residues: 407 sheet: 0.44 (0.52), residues: 87 loop : 0.92 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 809 HIS 0.004 0.000 HIS B 616 PHE 0.009 0.001 PHE A 156 TYR 0.008 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 27 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.825 Fit side-chains REVERT: B 997 MET cc_start: 0.9438 (mtp) cc_final: 0.8989 (mmm) REVERT: C 131 GLN cc_start: 0.9436 (mt0) cc_final: 0.8972 (mt0) REVERT: C 135 ARG cc_start: 0.9430 (ttp-110) cc_final: 0.9184 (ttm110) outliers start: 6 outliers final: 5 residues processed: 25 average time/residue: 0.2117 time to fit residues: 8.4946 Evaluate side-chains 26 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain C residue 67 MET 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: 7.9990 chunk 57 optimal weight: 0.0170 chunk 37 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 0.0000 chunk 17 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.6024 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.033909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.025451 restraints weight = 39357.767| |-----------------------------------------------------------------------------| r_work (start): 0.2419 rms_B_bonded: 4.93 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6728 Z= 0.118 Angle : 0.465 10.958 9101 Z= 0.223 Chirality : 0.038 0.131 1004 Planarity : 0.003 0.067 1176 Dihedral : 4.318 53.277 915 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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: 2.47 (0.30), residues: 793 helix: 2.54 (0.25), residues: 401 sheet: 0.53 (0.52), residues: 87 loop : 0.87 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 809 HIS 0.006 0.000 HIS B 616 PHE 0.009 0.001 PHE A 156 TYR 0.008 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: 2057.52 seconds wall clock time: 38 minutes 2.63 seconds (2282.63 seconds total)