Starting phenix.real_space_refine on Thu Aug 6 04:47:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sn0_40608/08_2026/8sn0_40608.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sn0_40608/08_2026/8sn0_40608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sn0_40608/08_2026/8sn0_40608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sn0_40608/08_2026/8sn0_40608.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8sn0_40608/08_2026/8sn0_40608.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sn0_40608/08_2026/8sn0_40608.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sn0_40608/08_2026/8sn0_40608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sn0_40608/08_2026/8sn0_40608.map" } resolution = 3.2 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= 0.120 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 Zn 2 6.06 5 P 294 5.49 5 S 32 5.16 5 C 7886 2.51 5 N 2605 2.21 5 O 3170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13989 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 682 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1188 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12296 SG CYS K 31 33.133 68.087 45.798 1.00 30.76 S ATOM 12446 SG CYS K 51 33.688 64.517 44.566 1.00 32.93 S ATOM 12470 SG CYS K 54 33.196 67.190 42.087 1.00 33.86 S ATOM 12187 SG CYS K 16 23.428 61.844 52.457 1.00 53.78 S ATOM 12205 SG CYS K 19 21.803 59.154 54.554 1.00 59.20 S ATOM 12335 SG CYS K 36 24.773 60.893 56.009 1.00 41.49 S ATOM 12357 SG CYS K 39 25.149 58.405 53.280 1.00 41.62 S Time building chain proxies: 2.97, per 1000 atoms: 0.21 Number of scatterers: 13989 At special positions: 0 Unit cell: (108.896, 128.816, 124.832, 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) Zn 2 29.99 S 32 16.00 P 294 15.00 O 3170 8.00 N 2605 7.00 C 7886 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 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 455.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " Number of angles added : 9 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1886 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 12 sheets defined 64.5% alpha, 4.7% beta 136 base pairs and 250 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.548A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.590A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.021A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.873A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.724A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.701A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.765A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.588A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.996A pdb=" N SER D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 105 through 123 removed outlier: 3.688A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.618A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.537A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.553A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.221A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.630A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.524A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.684A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 47 Processing helix chain 'K' and resid 58 through 68 removed outlier: 3.818A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 removed outlier: 3.862A pdb=" N LYS K 82 " --> pdb=" O THR K 78 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS K 83 " --> pdb=" O ILE K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 91 removed outlier: 3.535A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG K 91 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 Processing helix chain 'L' and resid 86 through 91 Processing helix chain 'L' and resid 98 through 112 removed outlier: 3.582A pdb=" N ALA L 107 " --> pdb=" O LEU L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.516A pdb=" N ALA L 124 " --> pdb=" O VAL L 120 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 145 removed outlier: 3.672A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG L 136 " --> pdb=" O ASP L 132 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE L 137 " --> pdb=" O LYS L 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.995A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.205A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.635A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.261A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.739A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28 Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 25 457 hydrogen bonds defined for protein. 1354 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 349 hydrogen bonds 694 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 250 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.51 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: 2898 1.33 - 1.45: 4518 1.45 - 1.57: 6805 1.57 - 1.69: 586 1.69 - 1.81: 47 Bond restraints: 14854 Sorted by residual: bond pdb=" C3' DA J -73 " pdb=" C2' DA J -73 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.41e+01 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DC I 21 " pdb=" C2' DC I 21 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.72e+00 bond pdb=" C3' DT I 62 " pdb=" C2' DT I 62 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.71e+00 bond pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.30e+00 ... (remaining 14849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 20430 1.76 - 3.52: 878 3.52 - 5.27: 25 5.27 - 7.03: 3 7.03 - 8.79: 2 Bond angle restraints: 21338 Sorted by residual: angle pdb=" N3 DT J -17 " pdb=" C4 DT J -17 " pdb=" O4 DT J -17 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT J -24 " pdb=" C4 DT J -24 " pdb=" O4 DT J -24 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT I 1 " pdb=" C4 DT I 1 " pdb=" O4 DT I 1 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT I -17 " pdb=" C4 DT I -17 " pdb=" O4 DT I -17 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 21333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 6813 35.27 - 70.54: 1379 70.54 - 105.81: 27 105.81 - 141.08: 0 141.08 - 176.35: 2 Dihedral angle restraints: 8221 sinusoidal: 5301 harmonic: 2920 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 43.65 176.35 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 66.81 153.19 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" CA LYS K 46 " pdb=" C LYS K 46 " pdb=" N ALA K 47 " pdb=" CA ALA K 47 " ideal model delta harmonic sigma weight residual -180.00 -161.69 -18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 8218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1325 0.031 - 0.063: 723 0.063 - 0.094: 268 0.094 - 0.126: 95 0.126 - 0.157: 6 Chirality restraints: 2417 Sorted by residual: chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA ARG L 139 " pdb=" N ARG L 139 " pdb=" C ARG L 139 " pdb=" CB ARG L 139 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 2414 not shown) Planarity restraints: 1688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.85e+00 pdb=" N PRO D 103 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR K 84 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO K 85 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO K 85 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO K 85 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.025 2.00e-02 2.50e+03 1.04e-02 3.24e+00 pdb=" N9 DG I 47 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.002 2.00e-02 2.50e+03 ... (remaining 1685 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 688 2.72 - 3.26: 12175 3.26 - 3.81: 24802 3.81 - 4.35: 31855 4.35 - 4.90: 46731 Nonbonded interactions: 116251 Sorted by model distance: nonbonded pdb=" O ARG L 139 " pdb=" OG1 THR L 142 " model vdw 2.173 3.040 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.215 2.496 nonbonded pdb=" OE2 GLU C 61 " pdb=" OG SER K 60 " model vdw 2.225 3.040 nonbonded pdb=" NH2 ARG K 55 " pdb=" O GLN L 92 " model vdw 2.248 3.120 nonbonded pdb=" N4 DC I 21 " pdb=" O6 DG J -21 " model vdw 2.263 3.120 ... (remaining 116246 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' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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=0.50 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.630 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14864 Z= 0.484 Angle : 0.722 8.792 21353 Z= 0.621 Chirality : 0.044 0.157 2417 Planarity : 0.005 0.055 1686 Dihedral : 26.424 176.347 6329 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.04 (0.27), residues: 982 helix: 1.58 (0.21), residues: 630 sheet: 0.45 (0.99), residues: 24 loop : -1.05 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 139 TYR 0.021 0.001 TYR L 134 PHE 0.008 0.001 PHE B 61 TRP 0.010 0.001 TRP L 141 HIS 0.006 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.48 (14854) covalent geometry : angle 0.71717 / 0.62 (21338) hydrogen bonds : bond 0.11482 / 7.89 ( 806) hydrogen bonds : angle 4.01937 / 2.79 ( 2048) metal coordination : bond 0.01153 / 0.57 ( 8) metal coordination : angle 4.09211 / 2.16 ( 9) link_TRANS : bond 0.00219 / 0.11 ( 2) link_TRANS : angle 0.53196 / 0.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.9480 (p) cc_final: 0.9273 (p) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1386 time to fit residues: 19.1745 Evaluate side-chains 92 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS H 47 GLN L 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.149920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.114046 restraints weight = 23010.368| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.99 r_work: 0.2711 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.0590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14864 Z= 0.191 Angle : 0.652 9.709 21353 Z= 0.370 Chirality : 0.048 0.285 2417 Planarity : 0.005 0.053 1686 Dihedral : 29.616 177.878 4329 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.59 % Allowed : 6.80 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.12 (0.26), residues: 982 helix: 1.65 (0.21), residues: 635 sheet: 0.56 (1.01), residues: 24 loop : -1.10 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 139 TYR 0.025 0.002 TYR L 134 PHE 0.011 0.002 PHE B 61 TRP 0.008 0.002 TRP K 61 HIS 0.007 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (14854) covalent geometry : angle 0.64757 / 0.37 (21338) hydrogen bonds : bond 0.06478 / 4.38 ( 806) hydrogen bonds : angle 3.35328 / 2.41 ( 2048) metal coordination : bond 0.00901 / 0.43 ( 8) metal coordination : angle 3.80247 / 1.95 ( 9) link_TRANS : bond 0.00061 / 0.03 ( 2) link_TRANS : angle 0.46735 / 0.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.9493 (p) cc_final: 0.9290 (p) REVERT: A 120 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7990 (mtt) REVERT: G 74 LYS cc_start: 0.8272 (mptt) cc_final: 0.7983 (mmmm) outliers start: 5 outliers final: 4 residues processed: 92 average time/residue: 0.1389 time to fit residues: 17.5892 Evaluate side-chains 92 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 70 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.152993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.117862 restraints weight = 30053.825| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.10 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.0621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14864 Z= 0.145 Angle : 0.616 9.297 21353 Z= 0.353 Chirality : 0.046 0.263 2417 Planarity : 0.004 0.049 1686 Dihedral : 29.604 177.670 4329 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.70 % Allowed : 9.50 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.37 (0.27), residues: 982 helix: 1.88 (0.21), residues: 635 sheet: 0.20 (1.03), residues: 24 loop : -1.04 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 55 TYR 0.026 0.001 TYR L 134 PHE 0.008 0.001 PHE B 61 TRP 0.008 0.001 TRP K 61 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (14854) covalent geometry : angle 0.61140 / 0.35 (21338) hydrogen bonds : bond 0.05740 / 3.87 ( 806) hydrogen bonds : angle 3.19508 / 2.31 ( 2048) metal coordination : bond 0.01127 / 0.56 ( 8) metal coordination : angle 3.64176 / 1.83 ( 9) link_TRANS : bond 0.00152 / 0.07 ( 2) link_TRANS : angle 0.36318 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7981 (mtt) REVERT: D 76 GLU cc_start: 0.8743 (tp30) cc_final: 0.8396 (tp30) outliers start: 6 outliers final: 5 residues processed: 95 average time/residue: 0.1370 time to fit residues: 17.8684 Evaluate side-chains 97 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 70 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 101 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.148923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.111927 restraints weight = 22003.430| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.82 r_work: 0.2593 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14864 Z= 0.186 Angle : 0.641 9.627 21353 Z= 0.358 Chirality : 0.048 0.298 2417 Planarity : 0.005 0.050 1686 Dihedral : 29.889 176.865 4329 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.17 % Allowed : 10.79 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.30 (0.27), residues: 982 helix: 1.85 (0.21), residues: 635 sheet: 0.21 (1.03), residues: 24 loop : -1.13 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 139 TYR 0.025 0.002 TYR L 134 PHE 0.011 0.002 PHE B 61 TRP 0.010 0.002 TRP K 61 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (14854) covalent geometry : angle 0.63711 / 0.36 (21338) hydrogen bonds : bond 0.06240 / 4.26 ( 806) hydrogen bonds : angle 3.18098 / 2.29 ( 2048) metal coordination : bond 0.00813 / 0.39 ( 8) metal coordination : angle 3.70458 / 1.84 ( 9) link_TRANS : bond 0.00038 / 0.02 ( 2) link_TRANS : angle 0.60599 / 0.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8126 (mtt) REVERT: D 76 GLU cc_start: 0.9201 (tp30) cc_final: 0.8981 (tp30) REVERT: H 101 LEU cc_start: 0.9047 (mm) cc_final: 0.8740 (mm) outliers start: 10 outliers final: 7 residues processed: 97 average time/residue: 0.1362 time to fit residues: 18.2877 Evaluate side-chains 100 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 73 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 22 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 47 GLN K 83 HIS L 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.150160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.114743 restraints weight = 23334.185| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.14 r_work: 0.2721 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14864 Z= 0.145 Angle : 0.621 9.336 21353 Z= 0.349 Chirality : 0.046 0.273 2417 Planarity : 0.005 0.048 1686 Dihedral : 29.876 176.980 4329 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.17 % Allowed : 11.72 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.45 (0.27), residues: 982 helix: 1.97 (0.21), residues: 636 sheet: 0.22 (1.01), residues: 24 loop : -1.07 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 129 TYR 0.026 0.001 TYR L 134 PHE 0.009 0.001 PHE B 61 TRP 0.009 0.001 TRP K 61 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (14854) covalent geometry : angle 0.61683 / 0.35 (21338) hydrogen bonds : bond 0.05717 / 3.88 ( 806) hydrogen bonds : angle 3.10075 / 2.24 ( 2048) metal coordination : bond 0.00915 / 0.45 ( 8) metal coordination : angle 3.63619 / 1.78 ( 9) link_TRANS : bond 0.00092 / 0.04 ( 2) link_TRANS : angle 0.50473 / 0.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.8036 (mtt) REVERT: G 78 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8308 (mp) REVERT: H 101 LEU cc_start: 0.8995 (mm) cc_final: 0.8693 (mm) REVERT: L 143 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7558 (mp10) outliers start: 10 outliers final: 6 residues processed: 95 average time/residue: 0.1378 time to fit residues: 18.1020 Evaluate side-chains 98 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 47 GLN L 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.151797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.116153 restraints weight = 21817.558| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.85 r_work: 0.2739 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14864 Z= 0.158 Angle : 0.617 9.094 21353 Z= 0.346 Chirality : 0.046 0.288 2417 Planarity : 0.004 0.047 1686 Dihedral : 29.903 177.103 4329 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.41 % Allowed : 11.84 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.47 (0.27), residues: 982 helix: 1.98 (0.21), residues: 635 sheet: 0.28 (1.01), residues: 24 loop : -1.05 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 63 TYR 0.026 0.001 TYR L 134 PHE 0.010 0.001 PHE B 61 TRP 0.009 0.001 TRP K 61 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (14854) covalent geometry : angle 0.61268 / 0.35 (21338) hydrogen bonds : bond 0.05725 / 3.89 ( 806) hydrogen bonds : angle 3.06670 / 2.21 ( 2048) metal coordination : bond 0.00827 / 0.40 ( 8) metal coordination : angle 3.67002 / 1.78 ( 9) link_TRANS : bond 0.00044 / 0.02 ( 2) link_TRANS : angle 0.49776 / 0.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7960 (mtt) REVERT: E 131 ARG cc_start: 0.9081 (mtm180) cc_final: 0.8872 (mtm180) REVERT: G 78 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8331 (mp) REVERT: H 101 LEU cc_start: 0.8986 (mm) cc_final: 0.8679 (mm) REVERT: L 143 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7566 (mp10) outliers start: 12 outliers final: 9 residues processed: 98 average time/residue: 0.1347 time to fit residues: 18.0311 Evaluate side-chains 103 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 119 optimal weight: 0.0570 chunk 95 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 37 optimal weight: 0.1980 chunk 116 optimal weight: 2.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.155216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.116138 restraints weight = 17533.322| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 0.99 r_work: 0.2816 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14864 Z= 0.126 Angle : 0.586 8.051 21353 Z= 0.334 Chirality : 0.043 0.265 2417 Planarity : 0.004 0.045 1686 Dihedral : 29.819 177.121 4329 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.06 % Allowed : 12.78 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.74 (0.27), residues: 982 helix: 2.20 (0.21), residues: 634 sheet: 0.37 (1.02), residues: 24 loop : -0.96 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 63 TYR 0.025 0.001 TYR L 134 PHE 0.008 0.001 PHE B 61 TRP 0.008 0.001 TRP K 61 HIS 0.006 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.13 (14854) covalent geometry : angle 0.58133 / 0.33 (21338) hydrogen bonds : bond 0.04991 / 3.37 ( 806) hydrogen bonds : angle 2.92854 / 2.11 ( 2048) metal coordination : bond 0.01121 / 0.56 ( 8) metal coordination : angle 3.73626 / 1.78 ( 9) link_TRANS : bond 0.00119 / 0.06 ( 2) link_TRANS : angle 0.36068 / 0.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: E 131 ARG cc_start: 0.9102 (mtm180) cc_final: 0.8880 (mtm180) REVERT: H 101 LEU cc_start: 0.9001 (mm) cc_final: 0.8665 (mm) REVERT: L 1 MET cc_start: 0.5453 (tpt) cc_final: 0.4645 (ppp) REVERT: L 143 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7530 (mp10) outliers start: 9 outliers final: 5 residues processed: 101 average time/residue: 0.1390 time to fit residues: 19.5085 Evaluate side-chains 98 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 7 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.150574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.115065 restraints weight = 27106.844| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.47 r_work: 0.2706 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14864 Z= 0.163 Angle : 0.610 8.366 21353 Z= 0.342 Chirality : 0.045 0.290 2417 Planarity : 0.005 0.047 1686 Dihedral : 29.907 177.154 4329 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.29 % Allowed : 13.01 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.62 (0.27), residues: 982 helix: 2.11 (0.21), residues: 634 sheet: 0.42 (1.01), residues: 24 loop : -1.02 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 63 TYR 0.025 0.002 TYR L 134 PHE 0.009 0.001 PHE B 61 TRP 0.009 0.001 TRP K 61 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (14854) covalent geometry : angle 0.60516 / 0.34 (21338) hydrogen bonds : bond 0.05568 / 3.78 ( 806) hydrogen bonds : angle 2.98839 / 2.15 ( 2048) metal coordination : bond 0.00776 / 0.38 ( 8) metal coordination : angle 3.71731 / 1.78 ( 9) link_TRANS : bond 0.00054 / 0.03 ( 2) link_TRANS : angle 0.47731 / 0.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: E 131 ARG cc_start: 0.9108 (mtm180) cc_final: 0.8896 (mtm180) REVERT: G 78 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8310 (mp) REVERT: H 101 LEU cc_start: 0.8990 (mm) cc_final: 0.8657 (mm) REVERT: L 1 MET cc_start: 0.5477 (tpt) cc_final: 0.4489 (ppp) REVERT: L 143 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7443 (mp10) outliers start: 11 outliers final: 8 residues processed: 99 average time/residue: 0.1245 time to fit residues: 17.2515 Evaluate side-chains 102 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 97 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.152820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.112230 restraints weight = 20775.708| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.32 r_work: 0.2904 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14864 Z= 0.169 Angle : 0.617 8.435 21353 Z= 0.345 Chirality : 0.045 0.295 2417 Planarity : 0.005 0.050 1686 Dihedral : 29.937 177.576 4329 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.29 % Allowed : 13.01 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.55 (0.27), residues: 982 helix: 2.05 (0.21), residues: 635 sheet: 0.26 (1.01), residues: 24 loop : -1.02 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 63 TYR 0.024 0.002 TYR L 134 PHE 0.010 0.001 PHE B 61 TRP 0.009 0.001 TRP K 61 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (14854) covalent geometry : angle 0.61284 / 0.34 (21338) hydrogen bonds : bond 0.05640 / 3.82 ( 806) hydrogen bonds : angle 2.99451 / 2.16 ( 2048) metal coordination : bond 0.00769 / 0.37 ( 8) metal coordination : angle 3.69012 / 1.78 ( 9) link_TRANS : bond 0.00046 / 0.02 ( 2) link_TRANS : angle 0.51606 / 0.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: E 131 ARG cc_start: 0.9117 (mtm180) cc_final: 0.8910 (mtm180) REVERT: G 78 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8280 (mp) REVERT: H 101 LEU cc_start: 0.8990 (mm) cc_final: 0.8669 (mm) REVERT: L 1 MET cc_start: 0.5368 (tpt) cc_final: 0.4488 (ppp) REVERT: L 143 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7524 (mp10) outliers start: 11 outliers final: 9 residues processed: 101 average time/residue: 0.1445 time to fit residues: 20.2801 Evaluate side-chains 112 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 14 optimal weight: 0.5980 chunk 94 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 18 optimal weight: 0.0060 chunk 15 optimal weight: 0.7980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.153277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.112408 restraints weight = 23182.876| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.63 r_work: 0.2644 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14864 Z= 0.143 Angle : 0.608 8.343 21353 Z= 0.342 Chirality : 0.045 0.288 2417 Planarity : 0.005 0.052 1686 Dihedral : 29.923 177.037 4329 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.41 % Allowed : 12.90 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.62 (0.27), residues: 982 helix: 2.11 (0.21), residues: 635 sheet: 0.23 (1.00), residues: 24 loop : -1.01 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 63 TYR 0.024 0.001 TYR L 134 PHE 0.009 0.001 PHE B 61 TRP 0.009 0.001 TRP K 61 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (14854) covalent geometry : angle 0.60367 / 0.34 (21338) hydrogen bonds : bond 0.05451 / 3.69 ( 806) hydrogen bonds : angle 2.97982 / 2.15 ( 2048) metal coordination : bond 0.00760 / 0.37 ( 8) metal coordination : angle 3.71113 / 1.78 ( 9) link_TRANS : bond 0.00049 / 0.02 ( 2) link_TRANS : angle 0.54302 / 0.25 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: E 131 ARG cc_start: 0.9128 (mtm180) cc_final: 0.8915 (mtm180) REVERT: G 78 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8315 (mp) REVERT: H 101 LEU cc_start: 0.9011 (mm) cc_final: 0.8683 (mm) REVERT: L 1 MET cc_start: 0.5467 (tpt) cc_final: 0.4492 (ppp) REVERT: L 59 ASP cc_start: 0.6530 (p0) cc_final: 0.6015 (p0) REVERT: L 143 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7455 (mp10) outliers start: 12 outliers final: 9 residues processed: 109 average time/residue: 0.1395 time to fit residues: 21.4842 Evaluate side-chains 105 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 31 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.153691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.111373 restraints weight = 17876.837| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.08 r_work: 0.2952 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14864 Z= 0.136 Angle : 0.606 8.206 21353 Z= 0.342 Chirality : 0.045 0.275 2417 Planarity : 0.005 0.058 1686 Dihedral : 29.905 177.061 4329 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.29 % Allowed : 13.13 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.67 (0.27), residues: 982 helix: 2.15 (0.21), residues: 635 sheet: 0.19 (1.00), residues: 24 loop : -1.00 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 63 TYR 0.025 0.001 TYR L 134 PHE 0.008 0.001 PHE B 61 TRP 0.008 0.001 TRP K 61 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (14854) covalent geometry : angle 0.60173 / 0.34 (21338) hydrogen bonds : bond 0.05315 / 3.60 ( 806) hydrogen bonds : angle 2.95243 / 2.13 ( 2048) metal coordination : bond 0.00875 / 0.43 ( 8) metal coordination : angle 3.69938 / 1.77 ( 9) link_TRANS : bond 0.00044 / 0.02 ( 2) link_TRANS : angle 0.48531 / 0.22 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2851.36 seconds wall clock time: 49 minutes 26.87 seconds (2966.87 seconds total)