Starting phenix.real_space_refine on Fri Jul 3 10:19:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sn2_40610/07_2026/8sn2_40610.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sn2_40610/07_2026/8sn2_40610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sn2_40610/07_2026/8sn2_40610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sn2_40610/07_2026/8sn2_40610.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8sn2_40610/07_2026/8sn2_40610.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sn2_40610/07_2026/8sn2_40610.cif" model { file = "/net/cci-nas-00/data/ceres_data/8sn2_40610/07_2026/8sn2_40610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sn2_40610/07_2026/8sn2_40610.cif" } resolution = 3.6 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= 0.071 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 2607 2.21 5 O 3171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s 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: 13992 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: 821 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Conformer: "B" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} bond proxies already assigned to first conformer: 820 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: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} 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: 691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Conformer: "B" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} bond proxies already assigned to first conformer: 698 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 12290 SG CYS K 31 75.714 52.537 66.546 1.00 43.01 S ATOM 12440 SG CYS K 51 76.545 50.797 63.302 1.00 44.84 S ATOM 12464 SG CYS K 54 74.977 48.802 66.187 1.00 44.65 S ATOM 12181 SG CYS K 16 84.103 56.800 57.767 1.00 44.32 S ATOM 12199 SG CYS K 19 86.199 57.014 54.674 1.00 41.66 S ATOM 12329 SG CYS K 36 83.580 59.855 55.726 1.00 45.57 S ATOM 12351 SG CYS K 39 82.441 56.789 54.183 1.00 43.08 S Time building chain proxies: 3.27, per 1000 atoms: 0.23 Number of scatterers: 13992 At special positions: 0 Unit cell: (108.896, 132.8, 126.16, 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 3171 8.00 N 2607 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: 1.22 Conformation dependent library (CDL) restraints added in 530.4 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 31 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " 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 11 sheets defined 65.5% alpha, 4.1% beta 135 base pairs and 234 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.922A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 removed outlier: 3.554A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.563A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.866A 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: 3.989A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.513A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.783A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.527A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.526A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (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: 3.763A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.504A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.600A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.978A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.778A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.888A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.532A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.526A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 removed outlier: 3.774A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 47 Processing helix chain 'K' and resid 58 through 69 removed outlier: 4.434A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 removed outlier: 4.157A pdb=" N ILE K 79 " --> pdb=" O GLU K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 91 removed outlier: 3.621A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (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 Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.930A pdb=" N ALA L 124 " --> pdb=" O VAL L 120 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 146 removed outlier: 3.735A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.946A 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 removed outlier: 3.519A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.924A 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 101 through 102 removed outlier: 6.879A 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: 7.402A 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 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 26 through 28 removed outlier: 3.667A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 25 469 hydrogen bonds defined for protein. 1391 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 2.68 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3379 1.34 - 1.46: 4208 1.46 - 1.58: 6637 1.58 - 1.70: 586 1.70 - 1.82: 47 Bond restraints: 14857 Sorted by residual: bond pdb=" C3' DT J -67 " pdb=" C2' DT J -67 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DA J -73 " pdb=" C2' DA J -73 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DG J 63 " pdb=" C2' DG J 63 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 ... (remaining 14852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 19799 1.29 - 2.59: 1387 2.59 - 3.88: 135 3.88 - 5.17: 18 5.17 - 6.47: 4 Bond angle restraints: 21343 Sorted by residual: angle pdb=" O4' DT I -26 " pdb=" C4' DT I -26 " pdb=" C3' DT I -26 " ideal model delta sigma weight residual 106.00 103.31 2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT J 22 " pdb=" C4 DT J 22 " pdb=" O4 DT J 22 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT I -28 " pdb=" C4 DT I -28 " pdb=" O4 DT I -28 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT J -24 " pdb=" C4 DT J -24 " pdb=" O4 DT J -24 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 ... (remaining 21338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 6883 35.27 - 70.55: 1322 70.55 - 105.82: 15 105.82 - 141.09: 0 141.09 - 176.36: 2 Dihedral angle restraints: 8222 sinusoidal: 5302 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 43.64 176.36 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 75.49 144.51 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" CA PHE L 62 " pdb=" C PHE L 62 " pdb=" N LYS L 63 " pdb=" CA LYS L 63 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 8219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1388 0.031 - 0.062: 678 0.062 - 0.093: 235 0.093 - 0.123: 108 0.123 - 0.154: 9 Chirality restraints: 2418 Sorted by residual: chirality pdb=" CB ILE D 94 " pdb=" CA ILE D 94 " pdb=" CG1 ILE D 94 " pdb=" CG2 ILE D 94 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CB ILE H 54 " pdb=" CA ILE H 54 " pdb=" CG1 ILE H 54 " pdb=" CG2 ILE H 54 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.66e-01 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 -2.58 -0.15 2.00e-01 2.50e+01 5.66e-01 ... (remaining 2415 not shown) Planarity restraints: 1689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO E 43 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 83 " -0.009 2.00e-02 2.50e+03 1.27e-02 3.23e+00 pdb=" CG TYR D 83 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR D 83 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR D 83 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR D 83 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 83 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 83 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 83 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR L 60 " 0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO L 61 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO L 61 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 61 " 0.022 5.00e-02 4.00e+02 ... (remaining 1686 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 153 2.63 - 3.19: 11417 3.19 - 3.76: 24353 3.76 - 4.33: 31481 4.33 - 4.90: 47139 Nonbonded interactions: 114543 Sorted by model distance: nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 59 " model vdw 2.058 3.040 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.175 2.496 nonbonded pdb=" O PRO L 61 " pdb=" NE1 TRP L 93 " model vdw 2.193 3.120 nonbonded pdb=" OH TYR L 45 " pdb=" O TYR L 74 " model vdw 2.224 3.040 nonbonded pdb=" OE2 GLU C 61 " pdb=" OG SER K 59 " model vdw 2.253 3.040 ... (remaining 114538 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 37 through 55 or resid 57 through 135)) selection = (chain 'E' and (resid 37 through 55 or resid 57 through 135)) } 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 123) selection = chain 'H' } 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=0.17 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.010 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.340 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 0.037 14867 Z= 0.476 Angle : 0.693 8.777 21358 Z= 0.604 Chirality : 0.043 0.154 2418 Planarity : 0.004 0.048 1687 Dihedral : 25.924 176.363 6330 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 2.22 (0.27), residues: 982 helix: 2.71 (0.22), residues: 612 sheet: 0.72 (0.87), residues: 29 loop : -0.86 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 71 TYR 0.031 0.001 TYR D 83 PHE 0.009 0.001 PHE L 62 TRP 0.007 0.001 TRP K 77 HIS 0.005 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.48 (14857) covalent geometry : angle 0.68611 / 0.60 (21343) hydrogen bonds : bond 0.10894 / 7.58 ( 816) hydrogen bonds : angle 3.82731 / 2.83 ( 2081) metal coordination : bond 0.00363 / 0.17 ( 8) metal coordination : angle 4.82378 / 2.49 ( 9) link_TRANS : bond 0.00158 / 0.08 ( 2) link_TRANS : angle 0.52871 / 0.24 ( 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 185 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 LYS cc_start: 0.8738 (mtpp) cc_final: 0.8388 (mttp) REVERT: C 41 GLU cc_start: 0.7306 (tt0) cc_final: 0.7102 (tt0) REVERT: D 71 GLU cc_start: 0.8317 (tp30) cc_final: 0.8086 (tp30) REVERT: F 25 ASN cc_start: 0.7791 (m110) cc_final: 0.7430 (m-40) REVERT: H 59 MET cc_start: 0.8622 (tpp) cc_final: 0.8399 (tpp) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1332 time to fit residues: 35.0973 Evaluate side-chains 141 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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: 0.0980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.0270 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.159597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.126474 restraints weight = 28598.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.125319 restraints weight = 48228.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126121 restraints weight = 43321.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129627 restraints weight = 26347.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.129597 restraints weight = 16566.244| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (11 function evaluations) r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14867 Z= 0.147 Angle : 0.599 11.262 21358 Z= 0.355 Chirality : 0.041 0.251 2418 Planarity : 0.005 0.044 1687 Dihedral : 29.296 178.622 4330 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.64 % Allowed : 9.12 % Favored : 89.24 % 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: 2.08 (0.27), residues: 982 helix: 2.64 (0.21), residues: 628 sheet: 0.47 (0.93), residues: 30 loop : -1.20 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 99 TYR 0.016 0.001 TYR H 83 PHE 0.009 0.001 PHE E 67 TRP 0.007 0.001 TRP K 77 HIS 0.004 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.15 (14857) covalent geometry : angle 0.58683 / 0.35 (21343) hydrogen bonds : bond 0.05304 / 3.62 ( 816) hydrogen bonds : angle 3.33086 / 2.48 ( 2081) metal coordination : bond 0.00520 / 0.20 ( 8) metal coordination : angle 5.81868 / 3.06 ( 9) link_TRANS : bond 0.00079 / 0.04 ( 2) link_TRANS : angle 0.46537 / 0.21 ( 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 159 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8485 (mttp) REVERT: D 71 GLU cc_start: 0.8525 (tp30) cc_final: 0.8227 (tp30) REVERT: E 59 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: F 25 ASN cc_start: 0.8021 (m110) cc_final: 0.7561 (m-40) REVERT: K 63 ARG cc_start: 0.9094 (ttp80) cc_final: 0.8635 (ttp80) outliers start: 14 outliers final: 9 residues processed: 148 average time/residue: 0.1352 time to fit residues: 28.5857 Evaluate side-chains 149 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 100 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 72 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 29 optimal weight: 0.0570 chunk 51 optimal weight: 3.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.156307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120167 restraints weight = 29722.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.121249 restraints weight = 58212.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.122273 restraints weight = 41497.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123727 restraints weight = 26334.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.124008 restraints weight = 23236.602| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14867 Z= 0.154 Angle : 0.602 13.561 21358 Z= 0.346 Chirality : 0.041 0.267 2418 Planarity : 0.004 0.038 1687 Dihedral : 29.610 177.888 4330 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.40 % Allowed : 9.94 % Favored : 88.65 % 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: 2.08 (0.27), residues: 982 helix: 2.70 (0.21), residues: 622 sheet: 0.33 (0.90), residues: 30 loop : -1.25 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 71 TYR 0.026 0.001 TYR H 83 PHE 0.011 0.001 PHE L 51 TRP 0.037 0.003 TRP L 93 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (14857) covalent geometry : angle 0.58771 / 0.35 (21343) hydrogen bonds : bond 0.05235 / 3.56 ( 816) hydrogen bonds : angle 3.18981 / 2.36 ( 2081) metal coordination : bond 0.00670 / 0.30 ( 8) metal coordination : angle 6.47267 / 3.31 ( 9) link_TRANS : bond 0.00038 / 0.02 ( 2) link_TRANS : angle 0.16360 / 0.08 ( 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 152 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 TYR cc_start: 0.8801 (m-10) cc_final: 0.8462 (m-10) REVERT: C 36 LYS cc_start: 0.8760 (mtpp) cc_final: 0.8453 (mttp) REVERT: D 71 GLU cc_start: 0.8445 (tp30) cc_final: 0.8197 (tp30) REVERT: E 59 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7156 (pm20) REVERT: F 25 ASN cc_start: 0.7916 (m110) cc_final: 0.7513 (m-40) outliers start: 12 outliers final: 10 residues processed: 144 average time/residue: 0.1245 time to fit residues: 25.8741 Evaluate side-chains 150 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN D 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.157471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121894 restraints weight = 31580.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.124246 restraints weight = 60155.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.125160 restraints weight = 33703.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.126430 restraints weight = 23057.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126736 restraints weight = 20048.924| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14867 Z= 0.135 Angle : 0.572 11.655 21358 Z= 0.332 Chirality : 0.040 0.262 2418 Planarity : 0.004 0.042 1687 Dihedral : 29.678 178.184 4330 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.64 % Allowed : 11.46 % Favored : 86.90 % 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: 2.17 (0.27), residues: 982 helix: 2.76 (0.21), residues: 622 sheet: 0.50 (0.93), residues: 30 loop : -1.20 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.026 0.001 TYR H 83 PHE 0.012 0.001 PHE L 51 TRP 0.018 0.002 TRP L 93 HIS 0.003 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (14857) covalent geometry : angle 0.55831 / 0.33 (21343) hydrogen bonds : bond 0.04848 / 3.31 ( 816) hydrogen bonds : angle 3.06979 / 2.28 ( 2081) metal coordination : bond 0.00519 / 0.23 ( 8) metal coordination : angle 5.99939 / 3.10 ( 9) link_TRANS : bond 0.00041 / 0.02 ( 2) link_TRANS : angle 0.20165 / 0.10 ( 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 156 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 TYR cc_start: 0.8822 (m-10) cc_final: 0.8479 (m-10) REVERT: C 36 LYS cc_start: 0.8794 (mtpp) cc_final: 0.8546 (mttp) REVERT: D 71 GLU cc_start: 0.8511 (tp30) cc_final: 0.8205 (tp30) REVERT: E 59 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7655 (pm20) REVERT: F 25 ASN cc_start: 0.7994 (m110) cc_final: 0.7571 (m-40) REVERT: L 1 MET cc_start: 0.6714 (pmm) cc_final: 0.6471 (pmm) outliers start: 14 outliers final: 10 residues processed: 148 average time/residue: 0.1233 time to fit residues: 26.5850 Evaluate side-chains 147 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 100 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 96 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN G 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.156126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120037 restraints weight = 30382.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.121518 restraints weight = 60359.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.122659 restraints weight = 39888.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.124680 restraints weight = 25025.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.124967 restraints weight = 19727.175| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14867 Z= 0.154 Angle : 0.594 12.180 21358 Z= 0.339 Chirality : 0.041 0.275 2418 Planarity : 0.004 0.045 1687 Dihedral : 29.794 177.866 4330 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.34 % Allowed : 11.70 % Favored : 85.96 % 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: 2.16 (0.27), residues: 982 helix: 2.74 (0.21), residues: 623 sheet: 0.40 (0.94), residues: 30 loop : -1.18 (0.30), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.031 0.001 TYR H 83 PHE 0.009 0.001 PHE E 67 TRP 0.020 0.002 TRP L 93 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (14857) covalent geometry : angle 0.58038 / 0.34 (21343) hydrogen bonds : bond 0.05128 / 3.48 ( 816) hydrogen bonds : angle 3.11187 / 2.30 ( 2081) metal coordination : bond 0.00589 / 0.27 ( 8) metal coordination : angle 6.21918 / 3.19 ( 9) link_TRANS : bond 0.00026 / 0.01 ( 2) link_TRANS : angle 0.19152 / 0.08 ( 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 158 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 TYR cc_start: 0.8825 (m-10) cc_final: 0.8537 (m-10) REVERT: C 36 LYS cc_start: 0.8843 (mtpp) cc_final: 0.8466 (mttp) REVERT: D 71 GLU cc_start: 0.8499 (tp30) cc_final: 0.8235 (tp30) REVERT: E 59 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7642 (pm20) REVERT: F 25 ASN cc_start: 0.8039 (m110) cc_final: 0.7605 (m-40) REVERT: L 1 MET cc_start: 0.6900 (pmm) cc_final: 0.6499 (pmm) outliers start: 20 outliers final: 15 residues processed: 148 average time/residue: 0.1186 time to fit residues: 25.3126 Evaluate side-chains 146 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 64 optimal weight: 0.5980 chunk 85 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 23 optimal weight: 0.0060 chunk 57 optimal weight: 0.7980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.157619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.124214 restraints weight = 26633.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.122896 restraints weight = 41233.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.123798 restraints weight = 33063.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.124081 restraints weight = 23688.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124449 restraints weight = 23494.797| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14867 Z= 0.128 Angle : 0.570 11.305 21358 Z= 0.328 Chirality : 0.040 0.257 2418 Planarity : 0.004 0.049 1687 Dihedral : 29.736 178.215 4330 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.52 % Allowed : 12.87 % Favored : 85.61 % 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: 2.28 (0.27), residues: 982 helix: 2.83 (0.21), residues: 623 sheet: 0.36 (0.96), residues: 30 loop : -1.11 (0.30), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 71 TYR 0.028 0.001 TYR H 83 PHE 0.010 0.001 PHE K 53 TRP 0.021 0.002 TRP L 93 HIS 0.003 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.13 (14857) covalent geometry : angle 0.55560 / 0.33 (21343) hydrogen bonds : bond 0.04683 / 3.19 ( 816) hydrogen bonds : angle 3.00483 / 2.23 ( 2081) metal coordination : bond 0.00426 / 0.18 ( 8) metal coordination : angle 6.19263 / 3.18 ( 9) link_TRANS : bond 0.00050 / 0.02 ( 2) link_TRANS : angle 0.22616 / 0.10 ( 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 154 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 TYR cc_start: 0.8722 (m-10) cc_final: 0.8463 (m-10) REVERT: D 71 GLU cc_start: 0.8454 (tp30) cc_final: 0.8185 (tp30) REVERT: E 59 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7499 (pm20) REVERT: F 25 ASN cc_start: 0.7887 (m110) cc_final: 0.7491 (m-40) REVERT: H 59 MET cc_start: 0.8592 (tpp) cc_final: 0.8198 (mmm) outliers start: 13 outliers final: 12 residues processed: 148 average time/residue: 0.1127 time to fit residues: 24.2874 Evaluate side-chains 150 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 82 optimal weight: 9.9990 chunk 12 optimal weight: 0.2980 chunk 97 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.155163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118836 restraints weight = 29093.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120298 restraints weight = 57868.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.121149 restraints weight = 40747.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.122771 restraints weight = 25755.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122960 restraints weight = 22103.201| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14867 Z= 0.169 Angle : 0.612 12.038 21358 Z= 0.343 Chirality : 0.041 0.283 2418 Planarity : 0.005 0.050 1687 Dihedral : 29.882 177.342 4330 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.11 % Allowed : 13.10 % Favored : 84.80 % 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: 2.15 (0.27), residues: 982 helix: 2.76 (0.21), residues: 617 sheet: 0.26 (0.93), residues: 30 loop : -1.14 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.036 0.002 TYR H 83 PHE 0.009 0.001 PHE D 65 TRP 0.022 0.002 TRP L 93 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (14857) covalent geometry : angle 0.59754 / 0.34 (21343) hydrogen bonds : bond 0.05282 / 3.58 ( 816) hydrogen bonds : angle 3.09501 / 2.28 ( 2081) metal coordination : bond 0.00609 / 0.28 ( 8) metal coordination : angle 6.44294 / 3.30 ( 9) link_TRANS : bond 0.00053 / 0.03 ( 2) link_TRANS : angle 0.22864 / 0.09 ( 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 155 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8181 (mtm) cc_final: 0.7966 (mtm) REVERT: B 98 TYR cc_start: 0.8776 (m-10) cc_final: 0.8488 (m-10) REVERT: D 71 GLU cc_start: 0.8468 (tp30) cc_final: 0.8212 (tp30) REVERT: E 59 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7829 (pm20) REVERT: F 25 ASN cc_start: 0.8014 (m110) cc_final: 0.7624 (m-40) REVERT: L 147 MET cc_start: 0.1904 (pmm) cc_final: 0.1408 (pmm) outliers start: 18 outliers final: 16 residues processed: 145 average time/residue: 0.1255 time to fit residues: 26.4377 Evaluate side-chains 152 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 83 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 47 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 114 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.153545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.116205 restraints weight = 23412.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.115215 restraints weight = 36358.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.116099 restraints weight = 34662.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.116018 restraints weight = 25904.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.116193 restraints weight = 28488.999| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14867 Z= 0.174 Angle : 0.629 12.330 21358 Z= 0.349 Chirality : 0.042 0.284 2418 Planarity : 0.005 0.053 1687 Dihedral : 30.011 176.469 4330 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.57 % Allowed : 13.80 % Favored : 83.63 % 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: 2.02 (0.27), residues: 982 helix: 2.64 (0.21), residues: 623 sheet: 0.16 (0.92), residues: 30 loop : -1.23 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 71 TYR 0.033 0.002 TYR H 83 PHE 0.010 0.002 PHE D 65 TRP 0.026 0.002 TRP L 93 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (14857) covalent geometry : angle 0.61387 / 0.35 (21343) hydrogen bonds : bond 0.05575 / 3.78 ( 816) hydrogen bonds : angle 3.15902 / 2.34 ( 2081) metal coordination : bond 0.00669 / 0.31 ( 8) metal coordination : angle 6.62886 / 3.41 ( 9) link_TRANS : bond 0.00058 / 0.03 ( 2) link_TRANS : angle 0.21298 / 0.09 ( 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 158 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 TYR cc_start: 0.8770 (m-10) cc_final: 0.8475 (m-10) REVERT: D 71 GLU cc_start: 0.8539 (tp30) cc_final: 0.8278 (tp30) REVERT: F 25 ASN cc_start: 0.8110 (m110) cc_final: 0.7712 (m-40) REVERT: H 59 MET cc_start: 0.8733 (tpp) cc_final: 0.8241 (tpp) REVERT: K 63 ARG cc_start: 0.9070 (ttp80) cc_final: 0.8710 (ttp-170) REVERT: L 147 MET cc_start: 0.1970 (pmm) cc_final: 0.1523 (pmm) outliers start: 22 outliers final: 17 residues processed: 146 average time/residue: 0.1212 time to fit residues: 25.4131 Evaluate side-chains 152 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 83 SER Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 12 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 chunk 87 optimal weight: 30.0000 chunk 65 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.150551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.114448 restraints weight = 24817.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.112819 restraints weight = 40596.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.113850 restraints weight = 35470.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.114098 restraints weight = 25191.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.114549 restraints weight = 25079.264| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14867 Z= 0.227 Angle : 0.701 13.448 21358 Z= 0.380 Chirality : 0.046 0.305 2418 Planarity : 0.005 0.052 1687 Dihedral : 30.249 174.245 4330 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.69 % Allowed : 14.27 % Favored : 83.04 % 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: 1.65 (0.27), residues: 982 helix: 2.38 (0.21), residues: 622 sheet: -0.03 (0.95), residues: 30 loop : -1.42 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 71 TYR 0.022 0.002 TYR H 83 PHE 0.012 0.002 PHE D 65 TRP 0.026 0.002 TRP L 93 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (14857) covalent geometry : angle 0.68559 / 0.38 (21343) hydrogen bonds : bond 0.06515 / 4.41 ( 816) hydrogen bonds : angle 3.32850 / 2.44 ( 2081) metal coordination : bond 0.00948 / 0.45 ( 8) metal coordination : angle 7.12267 / 3.64 ( 9) link_TRANS : bond 0.00110 / 0.06 ( 2) link_TRANS : angle 0.18639 / 0.09 ( 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 153 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 TYR cc_start: 0.8803 (m-10) cc_final: 0.8540 (m-10) REVERT: C 35 ARG cc_start: 0.8000 (mtt180) cc_final: 0.7718 (mtt180) REVERT: F 25 ASN cc_start: 0.8014 (m110) cc_final: 0.7681 (m-40) REVERT: H 59 MET cc_start: 0.8921 (tpp) cc_final: 0.8622 (tpp) REVERT: K 63 ARG cc_start: 0.9038 (ttp80) cc_final: 0.8701 (ttp-170) REVERT: L 147 MET cc_start: 0.1784 (pmm) cc_final: 0.1471 (pmm) outliers start: 23 outliers final: 18 residues processed: 140 average time/residue: 0.1186 time to fit residues: 24.2035 Evaluate side-chains 146 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 83 SER Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 84 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 102 optimal weight: 30.0000 chunk 15 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 65 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN D 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.154059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117394 restraints weight = 23758.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.116181 restraints weight = 39139.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.117217 restraints weight = 34433.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.117282 restraints weight = 25322.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.117611 restraints weight = 25795.781| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14867 Z= 0.138 Angle : 0.615 11.460 21358 Z= 0.346 Chirality : 0.041 0.260 2418 Planarity : 0.004 0.053 1687 Dihedral : 30.003 175.040 4330 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.75 % Allowed : 15.67 % Favored : 82.57 % 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: 2.03 (0.27), residues: 982 helix: 2.68 (0.21), residues: 623 sheet: -0.16 (0.95), residues: 30 loop : -1.28 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 71 TYR 0.019 0.001 TYR H 83 PHE 0.009 0.001 PHE L 62 TRP 0.029 0.002 TRP L 93 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (14857) covalent geometry : angle 0.60138 / 0.35 (21343) hydrogen bonds : bond 0.05078 / 3.45 ( 816) hydrogen bonds : angle 3.09123 / 2.29 ( 2081) metal coordination : bond 0.00552 / 0.25 ( 8) metal coordination : angle 6.38671 / 3.28 ( 9) link_TRANS : bond 0.00032 / 0.02 ( 2) link_TRANS : angle 0.16944 / 0.08 ( 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 144 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 TYR cc_start: 0.8801 (m-10) cc_final: 0.8578 (m-10) REVERT: D 79 ARG cc_start: 0.8609 (ttm-80) cc_final: 0.8204 (ttm-80) REVERT: F 25 ASN cc_start: 0.8121 (m110) cc_final: 0.7724 (m-40) REVERT: H 59 MET cc_start: 0.8648 (tpp) cc_final: 0.8093 (tpp) REVERT: K 63 ARG cc_start: 0.9134 (ttp80) cc_final: 0.8794 (ttp-170) REVERT: L 147 MET cc_start: 0.1900 (pmm) cc_final: 0.1593 (pmm) outliers start: 15 outliers final: 14 residues processed: 136 average time/residue: 0.1226 time to fit residues: 23.7237 Evaluate side-chains 138 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 43 optimal weight: 0.1980 chunk 85 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.151907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.111983 restraints weight = 21417.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.111401 restraints weight = 33025.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.111601 restraints weight = 31101.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.111861 restraints weight = 24786.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.111836 restraints weight = 24791.372| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14867 Z= 0.189 Angle : 0.658 12.733 21358 Z= 0.362 Chirality : 0.044 0.293 2418 Planarity : 0.005 0.052 1687 Dihedral : 30.138 174.437 4330 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.99 % Allowed : 15.67 % Favored : 82.34 % 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: 1.81 (0.27), residues: 982 helix: 2.51 (0.21), residues: 623 sheet: -0.19 (0.95), residues: 30 loop : -1.36 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.045 0.002 TYR H 83 PHE 0.010 0.001 PHE D 65 TRP 0.027 0.002 TRP L 93 HIS 0.007 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (14857) covalent geometry : angle 0.64381 / 0.36 (21343) hydrogen bonds : bond 0.05797 / 3.94 ( 816) hydrogen bonds : angle 3.22607 / 2.37 ( 2081) metal coordination : bond 0.00723 / 0.34 ( 8) metal coordination : angle 6.77600 / 3.44 ( 9) link_TRANS : bond 0.00079 / 0.04 ( 2) link_TRANS : angle 0.20352 / 0.08 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2036.47 seconds wall clock time: 35 minutes 54.16 seconds (2154.16 seconds total)