Starting phenix.real_space_refine on Thu Jul 2 04:15:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kfz_22857/07_2026/7kfz_22857.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kfz_22857/07_2026/7kfz_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7kfz_22857/07_2026/7kfz_22857.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kfz_22857/07_2026/7kfz_22857.cif" model { file = "/net/cci-nas-00/data/ceres_data/7kfz_22857/07_2026/7kfz_22857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kfz_22857/07_2026/7kfz_22857.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kfz_22857/07_2026/7kfz_22857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kfz_22857/07_2026/7kfz_22857.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 1.12, per 1000 atoms: 0.17 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: 0.51 Conformation dependent library (CDL) restraints added in 324.5 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: 0.10 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: 0.67 Time building geometry restraints manager: 0.66 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 - 14.17: 3581 14.17 - 28.35: 390 28.35 - 42.52: 107 42.52 - 56.69: 23 56.69 - 70.86: 10 Dihedral angle restraints: 4111 sinusoidal: 1742 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 4108 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: 0.390 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.830 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:0.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 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= 0.490 Angle : 0.805 10.759 9101 Z= 0.430 Chirality : 0.053 0.193 1004 Planarity : 0.005 0.092 1176 Dihedral : 13.418 70.862 2573 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.009 0.001 ARG C 135 TYR 0.014 0.002 TYR B 615 PHE 0.034 0.002 PHE B 930 TRP 0.014 0.002 TRP B 729 HIS 0.005 0.001 HIS B 888 Details of bonding type rmsd/Z covalent geometry : bond 0.01177 / 0.49 ( 6728) covalent geometry : angle 0.80473 / 0.43 ( 9101) hydrogen bonds : bond 0.26240 / 17.77 ( 314) hydrogen bonds : angle 8.78090 / 6.04 ( 903) *********************** 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 : 0.178 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: 0.0644 time to fit residues: 4.6421 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 : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.0020 chunk 61 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.2740 r_free = 0.2740 target = 0.034492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.026208 restraints weight = 37464.670| |-----------------------------------------------------------------------------| r_work (start): 0.2425 rms_B_bonded: 4.60 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6728 Z= 0.115 Angle : 0.537 7.691 9101 Z= 0.282 Chirality : 0.041 0.169 1004 Planarity : 0.004 0.076 1176 Dihedral : 4.601 58.030 887 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.68 % Allowed : 5.60 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.29), residues: 793 helix: 0.47 (0.25), residues: 401 sheet: -0.69 (0.50), residues: 88 loop : 0.35 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 97 TYR 0.025 0.001 TYR A 157 PHE 0.014 0.001 PHE B 588 TRP 0.007 0.001 TRP B 729 HIS 0.002 0.001 HIS B 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 6728) covalent geometry : angle 0.53689 / 0.28 ( 9101) hydrogen bonds : bond 0.04444 / 2.92 ( 314) hydrogen bonds : angle 4.71391 / 3.21 ( 903) *********************** 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 : 0.174 Fit side-chains revert: symmetry clash REVERT: A 111 MET cc_start: 0.9133 (ttm) cc_final: 0.8799 (ttp) REVERT: B 836 GLU cc_start: 0.9341 (mt-10) cc_final: 0.8574 (mm-30) REVERT: B 997 MET cc_start: 0.9486 (mtp) cc_final: 0.9146 (mtp) REVERT: C 41 ARG cc_start: 0.8748 (ttm-80) cc_final: 0.8533 (ttm-80) REVERT: C 72 MET cc_start: 0.9196 (mtt) cc_final: 0.8940 (mtt) REVERT: C 93 ILE cc_start: 0.9818 (mm) cc_final: 0.9617 (mm) outliers start: 5 outliers final: 1 residues processed: 38 average time/residue: 0.0538 time to fit residues: 3.0538 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 : 0.197 ------------------------------------------------------------------------------- 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 8 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 0.0020 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2742 r_free = 0.2742 target = 0.034498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.025825 restraints weight = 38507.117| |-----------------------------------------------------------------------------| r_work (start): 0.2411 rms_B_bonded: 4.61 r_work (final): 0.2411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6728 Z= 0.110 Angle : 0.467 6.675 9101 Z= 0.241 Chirality : 0.039 0.138 1004 Planarity : 0.004 0.075 1176 Dihedral : 4.199 58.975 887 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.55 % Allowed : 6.28 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.30), residues: 793 helix: 1.24 (0.26), residues: 406 sheet: -0.45 (0.50), residues: 91 loop : 0.65 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 694 TYR 0.016 0.001 TYR A 157 PHE 0.008 0.001 PHE A 156 TRP 0.007 0.001 TRP B 729 HIS 0.002 0.000 HIS B 911 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 6728) covalent geometry : angle 0.46705 / 0.24 ( 9101) hydrogen bonds : bond 0.03508 / 2.33 ( 314) hydrogen bonds : angle 4.12429 / 2.80 ( 903) *********************** 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: 4 poor density : 27 time to evaluate : 0.165 Fit side-chains REVERT: A 111 MET cc_start: 0.9185 (ttm) cc_final: 0.8846 (ttp) REVERT: C 67 MET cc_start: 0.8433 (mtm) cc_final: 0.7988 (mpp) REVERT: C 131 GLN cc_start: 0.9482 (mt0) cc_final: 0.9239 (mt0) outliers start: 4 outliers final: 1 residues processed: 30 average time/residue: 0.0593 time to fit residues: 2.5894 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 : 0.166 ------------------------------------------------------------------------------- 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 33 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 4 optimal weight: 0.2980 chunk 19 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2726 r_free = 0.2726 target = 0.033656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.025646 restraints weight = 38408.107| |-----------------------------------------------------------------------------| r_work (start): 0.2420 rms_B_bonded: 4.59 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 6728 Z= 0.091 Angle : 0.447 7.748 9101 Z= 0.228 Chirality : 0.039 0.137 1004 Planarity : 0.004 0.074 1176 Dihedral : 3.994 56.385 887 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.09 % Allowed : 6.01 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.30), residues: 793 helix: 1.64 (0.25), residues: 406 sheet: -0.13 (0.51), residues: 88 loop : 0.62 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 41 TYR 0.010 0.001 TYR A 157 PHE 0.008 0.001 PHE A 156 TRP 0.006 0.001 TRP B 809 HIS 0.001 0.000 HIS B 911 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 ( 6728) covalent geometry : angle 0.44665 / 0.23 ( 9101) hydrogen bonds : bond 0.02965 / 1.96 ( 314) hydrogen bonds : angle 3.87370 / 2.63 ( 903) *********************** 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 32 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.256 Fit side-chains REVERT: A 111 MET cc_start: 0.9183 (ttm) cc_final: 0.8943 (ttp) REVERT: C 67 MET cc_start: 0.8494 (mtm) cc_final: 0.8141 (mpp) REVERT: C 131 GLN cc_start: 0.9475 (mt0) cc_final: 0.9056 (mp10) outliers start: 8 outliers final: 2 residues processed: 32 average time/residue: 0.0561 time to fit residues: 2.7679 Evaluate side-chains 25 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 TYR 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 69 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2746 r_free = 0.2746 target = 0.033964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.025583 restraints weight = 39032.416| |-----------------------------------------------------------------------------| r_work (start): 0.2421 rms_B_bonded: 4.75 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3138 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= 0.088 Angle : 0.441 8.158 9101 Z= 0.222 Chirality : 0.039 0.134 1004 Planarity : 0.003 0.071 1176 Dihedral : 3.857 55.887 887 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.55 % Allowed : 6.97 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.30), residues: 793 helix: 1.94 (0.25), residues: 408 sheet: -0.03 (0.51), residues: 88 loop : 0.69 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 41 TYR 0.009 0.001 TYR C 157 PHE 0.008 0.001 PHE A 156 TRP 0.006 0.001 TRP B 809 HIS 0.002 0.000 HIS B 616 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 ( 6728) covalent geometry : angle 0.44114 / 0.22 ( 9101) hydrogen bonds : bond 0.02759 / 1.83 ( 314) hydrogen bonds : angle 3.71271 / 2.51 ( 903) *********************** 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 28 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.236 Fit side-chains REVERT: B 836 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8794 (mm-30) REVERT: B 997 MET cc_start: 0.9428 (mtp) cc_final: 0.8926 (mmm) REVERT: C 67 MET cc_start: 0.8607 (mtm) cc_final: 0.8284 (mpp) REVERT: C 131 GLN cc_start: 0.9472 (mt0) cc_final: 0.9079 (mp10) REVERT: C 135 ARG cc_start: 0.9392 (ttm110) cc_final: 0.9030 (ttp80) outliers start: 4 outliers final: 3 residues processed: 28 average time/residue: 0.0740 time to fit residues: 2.9032 Evaluate side-chains 24 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 606 VAL 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 45 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 60 optimal weight: 0.3980 chunk 37 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 755 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 = 0.2702 r_free = 0.2702 target = 0.032698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2385 r_free = 0.2385 target = 0.024617 restraints weight = 39258.086| |-----------------------------------------------------------------------------| r_work (start): 0.2395 rms_B_bonded: 4.66 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6728 Z= 0.143 Angle : 0.464 9.529 9101 Z= 0.234 Chirality : 0.039 0.129 1004 Planarity : 0.004 0.075 1176 Dihedral : 3.868 57.585 887 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.68 % Allowed : 7.65 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.30), residues: 793 helix: 2.12 (0.25), residues: 407 sheet: 0.07 (0.50), residues: 88 loop : 0.81 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 41 TYR 0.008 0.001 TYR C 157 PHE 0.009 0.001 PHE A 156 TRP 0.007 0.001 TRP B 729 HIS 0.002 0.001 HIS B 699 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 6728) covalent geometry : angle 0.46375 / 0.23 ( 9101) hydrogen bonds : bond 0.02970 / 1.98 ( 314) hydrogen bonds : angle 3.77734 / 2.55 ( 903) *********************** 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 27 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.204 Fit side-chains REVERT: B 997 MET cc_start: 0.9474 (mtp) cc_final: 0.8916 (mmm) REVERT: B 1001 MET cc_start: 0.9203 (mmm) cc_final: 0.8964 (mmp) REVERT: C 67 MET cc_start: 0.8883 (mtm) cc_final: 0.8543 (mpp) REVERT: C 131 GLN cc_start: 0.9460 (mt0) cc_final: 0.9077 (mp10) outliers start: 5 outliers final: 3 residues processed: 26 average time/residue: 0.0639 time to fit residues: 2.5504 Evaluate side-chains 23 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 606 VAL 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 20 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2687 r_free = 0.2687 target = 0.032083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2353 r_free = 0.2353 target = 0.023778 restraints weight = 39390.053| |-----------------------------------------------------------------------------| r_work (start): 0.2361 rms_B_bonded: 4.70 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6728 Z= 0.188 Angle : 0.507 9.407 9101 Z= 0.254 Chirality : 0.039 0.127 1004 Planarity : 0.004 0.075 1176 Dihedral : 3.992 59.207 887 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.68 % Allowed : 7.92 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.30), residues: 793 helix: 2.21 (0.25), residues: 409 sheet: 0.07 (0.50), residues: 90 loop : 0.95 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 41 TYR 0.009 0.001 TYR C 157 PHE 0.009 0.001 PHE A 156 TRP 0.009 0.001 TRP B 729 HIS 0.003 0.001 HIS B 699 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 ( 6728) covalent geometry : angle 0.50733 / 0.25 ( 9101) hydrogen bonds : bond 0.03177 / 2.11 ( 314) hydrogen bonds : angle 3.90706 / 2.65 ( 903) *********************** 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 25 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.187 Fit side-chains REVERT: B 997 MET cc_start: 0.9443 (mtp) cc_final: 0.8994 (mmm) REVERT: C 67 MET cc_start: 0.8834 (mtm) cc_final: 0.8509 (mpp) REVERT: C 131 GLN cc_start: 0.9466 (mt0) cc_final: 0.9085 (mp10) outliers start: 5 outliers final: 5 residues processed: 25 average time/residue: 0.0417 time to fit residues: 1.7867 Evaluate side-chains 24 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 1035 LEU 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 29 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 0.0020 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2708 r_free = 0.2708 target = 0.032654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.024272 restraints weight = 39430.281| |-----------------------------------------------------------------------------| r_work (start): 0.2387 rms_B_bonded: 4.80 r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3370 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= 0.120 Angle : 0.475 11.452 9101 Z= 0.234 Chirality : 0.039 0.129 1004 Planarity : 0.004 0.074 1176 Dihedral : 3.982 57.641 887 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.55 % Allowed : 8.20 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.30), residues: 793 helix: 2.33 (0.25), residues: 408 sheet: 0.25 (0.50), residues: 87 loop : 0.92 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 41 TYR 0.007 0.001 TYR C 157 PHE 0.009 0.001 PHE A 156 TRP 0.006 0.001 TRP B 729 HIS 0.003 0.001 HIS B 616 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 6728) covalent geometry : angle 0.47486 / 0.23 ( 9101) hydrogen bonds : bond 0.02890 / 1.92 ( 314) hydrogen bonds : angle 3.75912 / 2.55 ( 903) *********************** 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 24 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.192 Fit side-chains REVERT: B 824 MET cc_start: 0.9277 (tmm) cc_final: 0.8621 (tmm) REVERT: B 997 MET cc_start: 0.9496 (mtp) cc_final: 0.9157 (mmm) REVERT: C 67 MET cc_start: 0.8774 (mtm) cc_final: 0.8563 (mpp) REVERT: C 131 GLN cc_start: 0.9452 (mt0) cc_final: 0.9091 (mp10) outliers start: 4 outliers final: 4 residues processed: 24 average time/residue: 0.0553 time to fit residues: 2.2139 Evaluate side-chains 23 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 48 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 50 optimal weight: 0.0870 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 56 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 overall best weight: 1.6364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2691 r_free = 0.2691 target = 0.032467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2351 r_free = 0.2351 target = 0.024000 restraints weight = 40159.612| |-----------------------------------------------------------------------------| r_work (start): 0.2354 rms_B_bonded: 4.90 r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.3460 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= 0.122 Angle : 0.487 12.033 9101 Z= 0.236 Chirality : 0.039 0.128 1004 Planarity : 0.003 0.073 1176 Dihedral : 3.951 57.379 887 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.96 % Allowed : 8.06 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.30), residues: 793 helix: 2.44 (0.25), residues: 410 sheet: 0.32 (0.51), residues: 87 loop : 0.92 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 41 TYR 0.007 0.001 TYR C 157 PHE 0.009 0.001 PHE A 156 TRP 0.006 0.001 TRP B 729 HIS 0.005 0.001 HIS B 616 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 6728) covalent geometry : angle 0.48716 / 0.24 ( 9101) hydrogen bonds : bond 0.02825 / 1.88 ( 314) hydrogen bonds : angle 3.72592 / 2.52 ( 903) *********************** 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 27 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.237 Fit side-chains REVERT: B 824 MET cc_start: 0.9298 (tmm) cc_final: 0.8645 (tmm) REVERT: B 930 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8539 (m-80) REVERT: B 997 MET cc_start: 0.9500 (mtp) cc_final: 0.9199 (mmm) REVERT: C 67 MET cc_start: 0.8815 (mtm) cc_final: 0.8607 (mpp) REVERT: C 131 GLN cc_start: 0.9435 (mt0) cc_final: 0.9071 (mp10) outliers start: 7 outliers final: 4 residues processed: 27 average time/residue: 0.0398 time to fit residues: 1.7981 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 : 0.184 ------------------------------------------------------------------------------- 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 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 27 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 73 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2710 r_free = 0.2710 target = 0.032940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2373 r_free = 0.2373 target = 0.024515 restraints weight = 39697.108| |-----------------------------------------------------------------------------| r_work (start): 0.2371 rms_B_bonded: 4.89 r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3583 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= 0.094 Angle : 0.468 11.856 9101 Z= 0.227 Chirality : 0.039 0.128 1004 Planarity : 0.003 0.073 1176 Dihedral : 3.927 55.949 887 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.55 % Allowed : 8.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.30), residues: 793 helix: 2.45 (0.25), residues: 410 sheet: 0.42 (0.51), residues: 87 loop : 0.94 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 41 TYR 0.006 0.001 TYR C 64 PHE 0.009 0.001 PHE A 156 TRP 0.005 0.001 TRP B 809 HIS 0.007 0.001 HIS B 616 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.09 ( 6728) covalent geometry : angle 0.46832 / 0.23 ( 9101) hydrogen bonds : bond 0.02648 / 1.77 ( 314) hydrogen bonds : angle 3.62724 / 2.45 ( 903) ********************** 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 25 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.192 Fit side-chains REVERT: B 617 MET cc_start: 0.9476 (mmm) cc_final: 0.9188 (mpp) REVERT: B 824 MET cc_start: 0.9249 (tmm) cc_final: 0.8695 (tmm) REVERT: B 997 MET cc_start: 0.9481 (mtp) cc_final: 0.9217 (mmm) REVERT: C 131 GLN cc_start: 0.9415 (mt0) cc_final: 0.9005 (mp10) outliers start: 4 outliers final: 3 residues processed: 25 average time/residue: 0.0744 time to fit residues: 2.8322 Evaluate side-chains 23 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 606 VAL 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 49 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2718 r_free = 0.2718 target = 0.032911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.024624 restraints weight = 39427.210| |-----------------------------------------------------------------------------| r_work (start): 0.2372 rms_B_bonded: 4.82 r_work (final): 0.2372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3597 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= 0.112 Angle : 0.479 11.468 9101 Z= 0.233 Chirality : 0.039 0.128 1004 Planarity : 0.003 0.070 1176 Dihedral : 3.889 56.186 887 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.55 % Allowed : 9.02 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.30), residues: 793 helix: 2.47 (0.25), residues: 411 sheet: 0.44 (0.51), residues: 87 loop : 0.98 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 135 TYR 0.007 0.001 TYR C 64 PHE 0.009 0.001 PHE A 156 TRP 0.005 0.001 TRP B 729 HIS 0.005 0.001 HIS B 616 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 6728) covalent geometry : angle 0.47949 / 0.23 ( 9101) hydrogen bonds : bond 0.02695 / 1.80 ( 314) hydrogen bonds : angle 3.64999 / 2.47 ( 903) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 821.82 seconds wall clock time: 14 minutes 57.99 seconds (897.99 seconds total)